Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/r/relion/relion_3.1.3-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/relion-3.1.3-1zrw_xra3/relion_3.1.3-1_amd64.buildinfo Get source package info: relion=3.1.3-1 Source URL: http://snapshot.notset.fr/mr/package/relion/3.1.3-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 autoconf=2.71-2 automake=1:1.16.4-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-3+b2 binutils=2.37-7 binutils-common=2.37-7 binutils-x86-64-linux-gnu=2.37-7 bsdextrautils=2.37.2-3 bsdutils=1:2.37.2-3 build-essential=12.9 bzip2=1.0.8-4 cmake=3.21.3-4 cmake-data=3.21.3-4 coreutils=8.32-4+b1 cpp=4:11.2.0-2 cpp-10=10.3.0-11 cpp-11=11.2.0-9 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.77 debhelper=13.5.2 debianutils=5.5-1 dh-autoreconf=20 dh-elpa-helper=2.0.9 dh-strip-nondeterminism=1.12.0-1 diffutils=1:3.7-5 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 emacsen-common=3.0.4 file=1:5.39-3 findutils=4.8.0-1 fluid=1.3.5-3 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 g++=4:11.2.0-2 g++-11=11.2.0-9 gcc=4:11.2.0-2 gcc-10=10.3.0-11 gcc-10-base=10.3.0-11 gcc-11=11.2.0-9 gcc-11-base=11.2.0-9 gettext=0.21-4 gettext-base=0.21-4 gfortran-10=10.3.0-11 grep=3.7-1 groff-base=1.22.4-7 gzip=1.10-4 hostname=3.23 ibverbs-providers=36.0-1 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libarchive13=3.4.3-2+b1 libasan6=11.2.0-9 libatomic1=11.2.0-9 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1 libbinutils=2.37-7 libblkid1=2.37.2-3 libbrotli1=1.0.9-2+b2 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-4 libc-bin=2.32-4 libc-dev-bin=2.32-4 libc6=2.32-4 libc6-dev=2.32-4 libcairo2=1.16.0-5 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcbor0.8=0.8.0-1 libcc1-0=11.2.0-9 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.25-2 libcrypt1=1:4.4.25-2 libctf-nobfd0=2.37-7 libctf0=2.37-7 libcurl4=7.74.0-1.3+b1 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.260 libdebhelper-perl=13.5.2 libdeflate-dev=1.8-1 libdeflate0=1.8-1 libdpkg-perl=1.20.9 libdrm-amdgpu1=2.4.107-8 libdrm-common=2.4.107-8 libdrm-intel1=2.4.107-8 libdrm-nouveau2=2.4.107-8 libdrm-radeon1=2.4.107-8 libdrm2=2.4.107-8 libedit2=3.1-20210910-1 libelf1=0.185-2 libevent-2.1-7=2.1.12-stable-1 libevent-core-2.1-7=2.1.12-stable-1 libevent-dev=2.1.12-stable-1 libevent-extra-2.1-7=2.1.12-stable-1 libevent-openssl-2.1-7=2.1.12-stable-1 libevent-pthreads-2.1-7=2.1.12-stable-1 libexpat1=2.4.1-2+b1 libfabric1=1.11.0-2 libffi8=3.4.2-3 libfftw3-bin=3.3.8-2 libfftw3-dev=3.3.8-2 libfftw3-double3=3.3.8-2 libfftw3-long3=3.3.8-2 libfftw3-quad3=3.3.8-2 libfftw3-single3=3.3.8-2 libfido2-1=1.8.0-1+b1 libfile-stripnondeterminism-perl=1.12.0-1 libfltk-cairo1.3=1.3.5-3 libfltk-forms1.3=1.3.5-3 libfltk-gl1.3=1.3.5-3 libfltk-images1.3=1.3.5-3 libfltk1.3=1.3.5-3 libfltk1.3-dev=1.3.5-3 libfontconfig1=2.13.1-4.2 libfreetype6=2.11.0+dfsg-1 libgcc-10-dev=10.3.0-11 libgcc-11-dev=11.2.0-9 libgcc-s1=11.2.0-9 libgcrypt20=1.9.4-3+b1 libgdbm-compat4=1.21-1 libgdbm6=1.21-1 libgfortran-10-dev=10.3.0-11 libgfortran5=11.2.0-9 libgl1=1.3.4-2+b1 libgl1-mesa-dri=21.2.4-1 libglapi-mesa=21.2.4-1 libglvnd0=1.3.4-2+b1 libglx-mesa0=21.2.4-1 libglx0=1.3.4-2+b1 libgmp10=2:6.2.1+dfsg-2 libgnutls30=3.7.2-2 libgomp1=11.2.0-9 libgpg-error0=1.42-3 libgssapi-krb5-2=1.18.3-7 libhogweed6=3.7.3-1 libhwloc-dev=2.5.0+dfsg-2 libhwloc-plugins=2.5.0+dfsg-2 libhwloc15=2.5.0+dfsg-2 libibverbs-dev=36.0-1 libibverbs1=36.0-1 libicu67=67.1-7 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=11.2.0-9 libjbig-dev=2.1-3.1+b2 libjbig0=2.1-3.1+b2 libjpeg-dev=1:2.0.6-4 libjpeg62-turbo=1:2.0.6-4 libjpeg62-turbo-dev=1:2.0.6-4 libjs-jquery=3.5.1+dfsg+~3.5.5-7 libjs-jquery-ui=1.12.1+dfsg-8 libjsoncpp24=1.9.4-5 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 libldap-2.4-2=2.4.59+dfsg-1 libllvm12=1:12.0.1-10 liblsan0=11.2.0-9 libltdl-dev=2.4.6-15 libltdl7=2.4.6-15 liblz4-1=1.9.3-2 liblzma-dev=5.2.5-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmd0=1.0.4-1 libmount1=2.37.2-3 libmpc3=1.2.1-1 libmpfr6=4.1.0-3 libncurses6=6.2+20210905-1 libncursesw6=6.2+20210905-1 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnl-3-200=3.4.0-1+b1 libnl-3-dev=3.4.0-1+b1 libnl-route-3-200=3.4.0-1+b1 libnl-route-3-dev=3.4.0-1+b1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnuma-dev=2.0.14-3 libnuma1=2.0.14-3 libopenmpi-dev=4.1.2~rc1-4 libopenmpi3=4.1.2~rc1-4 libp11-kit0=0.24.0-5 libpam-modules=1.4.0-10 libpam-modules-bin=1.4.0-10 libpam-runtime=1.4.0-10 libpam0g=1.4.0-10 libpciaccess0=0.16-1 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.3-1 libpixman-1-0=0.40.0-1 libpmix-dev=4.1.1~rc4-1 libpmix2=4.1.1~rc4-1 libpng16-16=1.6.37-3 libprocps8=2:3.3.17-5 libpsl5=0.21.0-1.2 libpsm-infinipath1=3.3+20.604758e7-6.1 libpsm2-2=11.2.185-1 libpthread-stubs0-dev=0.4-1 libquadmath0=11.2.0-9 librdmacm1=36.0-1 librhash0=1.4.2-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2.1 libsasl2-modules-db=2.1.27+dfsg-2.1 libseccomp2=2.5.2-2 libselinux1=3.1-3 libsemanage-common=3.1-1 libsemanage1=3.1-1+b2 libsensors-config=1:3.6.0-7 libsensors5=1:3.6.0-7 libsepol1=3.1-1 libsigsegv2=2.13-1 libsmartcols1=2.37.2-3 libssh2-1=1.10.0-2 libssl1.1=1.1.1l-1 libstdc++-11-dev=11.2.0-9 libstdc++6=11.2.0-9 libsub-override-perl=0.09-2 libsystemd0=249.5-1 libtasn1-6=4.17.0-2 libtiff-dev=4.3.0-2 libtiff5=4.3.0-2 libtiffxx5=4.3.0-2 libtinfo6=6.2+20210905-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-9 libubsan1=11.2.0-9 libuchardet0=0.0.7-1 libucx0=1.11.2-1 libudev1=249.5-1 libunistring2=0.9.10-6 libuuid1=2.37.2-3 libuv1=1.42.0-1 libvulkan1=1.2.189.0-2 libwebp6=0.6.1-2.1 libx11-6=2:1.7.2-2+b1 libx11-data=2:1.7.2-2 libx11-dev=2:1.7.2-2+b1 libx11-xcb1=2:1.7.2-2+b1 libxau-dev=1:1.0.9-1 libxau6=1:1.0.9-1 libxcb-dri2-0=1.14-3 libxcb-dri3-0=1.14-3 libxcb-glx0=1.14-3 libxcb-present0=1.14-3 libxcb-render0=1.14-3 libxcb-shm0=1.14-3 libxcb-sync1=1.14-3 libxcb-xfixes0=1.14-3 libxcb1=1.14-3 libxcb1-dev=1.14-3 libxcursor1=1:1.2.0-2 libxdmcp-dev=1:1.1.2-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.4-1 libxfixes3=1:5.0.3-2 libxft2=2.3.2-2 libxinerama1=2:1.1.4-2 libxml2=2.9.12+dfsg-5 libxnvctrl0=470.57.02-2 libxrender1=1:0.9.10-1 libxshmfence1=1.3-1 libxxf86vm1=1:1.1.4-1+b2 libz3-4=4.8.12-1+b1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.14.12-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20210905-1 ncurses-bin=6.2+20210905-1 ocl-icd-libopencl1=2.2.14-3 openmpi-bin=4.1.2~rc1-4 openmpi-common=4.1.2~rc1-4 openssh-client=1:8.4p1-6 passwd=1:4.8.1-1 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 po-debconf=1.0.21+nmu1 procps=2:3.3.17-5 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.00-1 tar=1.34+dfsg-1 ucf=3.0043 util-linux=2.37.2-3 x11proto-dev=2021.5-1 xorg-sgml-doctools=1:1.11-1.1 xtrans-dev=1.4.0-1 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211024T025444Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211024T025444Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211019T151710Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d relion=3.1.3-1 && mkdir -p /build/relion-x7zN9B && dpkg-source --no-check -x /*.dsc /build/relion-x7zN9B/relion-3.1.3 && chown -R builduser:builduser /build/relion-x7zN9B" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/relion-x7zN9B/relion-3.1.3 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1634627764" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/relion-x7zN9B /tmp/relion-3.1.3-1zrw_xra3 bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211019T151710Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.7Ra6eDGlM6 as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.7Ra6eDGlM6 Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-3). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20211019T151710Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211019T151710Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (891 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4668 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.32-4) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211024T025444Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211024T025444Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211019T151710Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.7Ra6eDGlM6 Get:1 http://snapshot.notset.fr/archive/debian/20211024T025444Z bookworm InRelease [128 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20211019T151710Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20211024T025444Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211024T025444Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211024T025444Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211024T025444Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211024T025444Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211024T025444Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20211024T025444Z bookworm/main Sources [11.7 MB] Get:4 http://snapshot.notset.fr/archive/debian/20211024T025444Z bookworm/main amd64 Packages [11.2 MB] Fetched 23.1 MB in 20s (1181 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.7Ra6eDGlM6 I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d relion=3.1.3-1 && mkdir -p /build/relion-x7zN9B && dpkg-source --no-check -x /*.dsc /build/relion-x7zN9B/relion-3.1.3 && chown -R builduser:builduser /build/relion-x7zN9B"' exec /tmp/mmdebstrap.7Ra6eDGlM6 Reading package lists... NOTICE: 'relion' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/relion.git Please use: git clone https://salsa.debian.org/med-team/relion.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2355 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211024T025444Z bookworm/main relion 3.1.3-1 (dsc) [2150 B] Get:2 http://snapshot.notset.fr/archive/debian/20211024T025444Z bookworm/main relion 3.1.3-1 (tar) [2345 kB] Get:3 http://snapshot.notset.fr/archive/debian/20211024T025444Z bookworm/main relion 3.1.3-1 (diff) [7092 B] Fetched 2355 kB in 2s (1232 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'relion_3.1.3-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting relion in /build/relion-x7zN9B/relion-3.1.3 dpkg-source: info: unpacking relion_3.1.3.orig.tar.gz dpkg-source: info: unpacking relion_3.1.3-1.debian.tar.xz I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/relion-x7zN9B/relion-3.1.3 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1634627764" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.7Ra6eDGlM6 dpkg-buildpackage: info: source package relion dpkg-buildpackage: info: source version 3.1.3-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/relion-x7zN9B/relion-3.1.3' dh_clean rm -rf build make[1]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_build make[1]: Entering directory '/build/relion-x7zN9B/relion-3.1.3' mkdir /build/relion-x7zN9B/relion-3.1.3/build cd /build/relion-x7zN9B/relion-3.1.3/build; \ CC=gcc CXX=g++ cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_SKIP_RPATH=TRUE -DDoublePrec_GPU=ON -DGUI=ON -DCUDA=OFF /build/relion-x7zN9B/relion-3.1.3;\ make -j10; DESTDIR=/build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli make install CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Warning (dev) at /usr/share/cmake-3.21/Modules/CMakeDetermineCompilerId.cmake:93 (if): Policy CMP0054 is not set: Only interpret if() arguments as variables or keywords when unquoted. Run "cmake --help-policy CMP0054" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Quoted variables like "CUDA" will no longer be dereferenced when the policy is set to NEW. Since the policy is not set the OLD behavior will be used. Call Stack (most recent call first): /usr/share/cmake-3.21/Modules/CMakeDetermineCCompiler.cmake:123 (CMAKE_DETERMINE_COMPILER_ID) CMakeLists.txt:6 (project) This warning is for project developers. Use -Wno-dev to suppress it. -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- BUILD TYPE set to the default type: 'Release' -- Setting fallback CUDA_ARCH=35 -- ALLOW_CTF_IN_SAGD enabled - This build of RELION allows modulation of particle images by a contrast transfer function inside stochastic average gradient descent, as specified in Claim 1 of patent US10,282,513B2 -- Setting cpu precision to double -- Setting accelerated code precision to single -- Using non-cuda compilation.... CMake Warning (dev) at /usr/share/cmake-3.21/Modules/FindPackageHandleStandardArgs.cmake:438 (message): The package name passed to `find_package_handle_standard_args` (PkgConfig) does not match the name of the calling package (MPI). This can lead to problems in calling code that expects `find_package` result variables (e.g., `_FOUND`) to follow a certain pattern. Call Stack (most recent call first): /usr/share/cmake-3.21/Modules/FindPkgConfig.cmake:70 (find_package_handle_standard_args) /usr/share/cmake-3.21/Modules/FindMPI.cmake:270 (include) CMakeLists.txt:215 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE) -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- MPI_INCLUDE_PATH : /usr/lib/x86_64-linux-gnu/openmpi/include;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -- MPI_LIBRARIES : /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -- MPI_CXX_INCLUDE_PATH : /usr/lib/x86_64-linux-gnu/openmpi/include;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -- MPI_CXX_LIBRARIES : /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -- CMAKE_C_COMPILER : /usr/bin/gcc -- CMAKE_CXX_COMPILER : /usr/bin/g++ -- MPI_C_COMPILER : /usr/bin/mpicc -- MPI_CXX_COMPILER : /usr/bin/mpicxx -- CMAKE_CXX_COMPILER_ID : GNU -- Found X11: /usr/include -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Found FLTK: fltk_images;fltk_forms;fltk -- X11 and FLTK were found -- FLTK_LIBRARIES: fltk_images;fltk_forms;fltk;/usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libm.so -- Found FFTW -- FFTW_PATH: /usr/include -- FFTW_INCLUDES: /usr/include -- FFTW_LIBRARIES: /usr/lib/x86_64-linux-gnu/libfftw3f.so;/usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for sincos -- Looking for sincos - found -- Looking for __sincos -- Looking for __sincos - not found -- Found TIFF: /usr/lib/x86_64-linux-gnu/libtiff.so (found version "4.3.0") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Could NOT find PNG (missing: PNG_LIBRARY PNG_PNG_INCLUDE_DIR) BUILD_SHARED_LIBS = OFF -- Building static libs (larger build size and binaries) Running apps/CMakeLists.txt... -- CMAKE_BINARY_DIR:/build/relion-x7zN9B/relion-3.1.3/build -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: DoublePrec_GPU -- Build files have been written to: /build/relion-x7zN9B/relion-3.1.3/build make[2]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' /usr/bin/cmake -S/build/relion-x7zN9B/relion-3.1.3 -B/build/relion-x7zN9B/relion-3.1.3/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/relion-x7zN9B/relion-3.1.3/build/CMakeFiles /build/relion-x7zN9B/relion-3.1.3/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/depend make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' /usr/bin/cmake -E copy /build/relion-x7zN9B/relion-3.1.3/scripts/star_printtable /build/relion-x7zN9B/relion-3.1.3/build/bin/relion_star_printtable make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' /usr/bin/cmake -E copy /build/relion-x7zN9B/relion-3.1.3/scripts/star_plottable /build/relion-x7zN9B/relion-3.1.3/build/bin/relion_star_plottable [ 0%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -MF CMakeFiles/relion_lib.dir/__/__/macros.cpp.o.d -o CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/build/macros.cpp [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o -MF CMakeFiles/relion_lib.dir/__/args.cpp.o.d -o CMakeFiles/relion_lib.dir/__/args.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/args.cpp [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -MF CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o.d -o CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/CPlot2D.cpp [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o -MF CMakeFiles/relion_lib.dir/__/assembly.cpp.o.d -o CMakeFiles/relion_lib.dir/__/assembly.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/assembly.cpp [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.cpp cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -MF CMakeFiles/relion_lib.dir/__/backprojector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/backprojector.cpp /usr/bin/cmake -E copy /build/relion-x7zN9B/relion-3.1.3/scripts/star_loopheader /build/relion-x7zN9B/relion-3.1.3/build/bin/relion_star_loopheader [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/autopicker.cpp cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o -MF CMakeFiles/relion_lib.dir/__/complex.cpp.o.d -o CMakeFiles/relion_lib.dir/__/complex.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/complex.cpp cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctf.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctf.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/ctf.cpp /usr/bin/cmake -E copy /build/relion-x7zN9B/relion-3.1.3/scripts/star_datablock_stack /build/relion-x7zN9B/relion-3.1.3/build/bin/relion_star_datablock_stack /usr/bin/cmake -E copy /build/relion-x7zN9B/relion-3.1.3/scripts/star_datablock_singlefiles /build/relion-x7zN9B/relion-3.1.3/build/bin/relion_star_datablock_singlefiles /usr/bin/cmake -E copy /build/relion-x7zN9B/relion-3.1.3/scripts/star_datablock_ctfdat /build/relion-x7zN9B/relion-3.1.3/build/bin/relion_star_datablock_ctfdat /usr/bin/cmake -E copy /build/relion-x7zN9B/relion-3.1.3/scripts/qsub.csh /build/relion-x7zN9B/relion-3.1.3/build/bin/relion_qsub.csh make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.cpp [ 4%] Built target copy_scripts [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.cpp [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o -MF CMakeFiles/relion_lib.dir/__/error.cpp.o.d -o CMakeFiles/relion_lib.dir/__/error.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/error.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.cpp:45: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.cpp:45: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.cpp:45: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.cpp:45: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.cpp:45: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.cpp:45: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.cpp:45: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.cpp:45: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.cpp:45: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.cpp:45: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.cpp:45: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.cpp:45: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.cpp:45: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.cpp:45: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.cpp:45: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.cpp:45: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.cpp:45: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.cpp:45: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.cpp:27: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.cpp:27: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.cpp:27: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.cpp:27: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.cpp:27: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.cpp:27: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.cpp:27: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.cpp:27: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.cpp:27: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.cpp:27: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.cpp:27: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.cpp:27: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.cpp:27: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.cpp:27: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.cpp:27: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.cpp:27: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.cpp:27: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.cpp:27: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o -MF CMakeFiles/relion_lib.dir/__/euler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/euler.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/euler.cpp [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/exp_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/exp_model.cpp [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o -MF CMakeFiles/relion_lib.dir/__/filename.cpp.o.d -o CMakeFiles/relion_lib.dir/__/filename.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/filename.cpp [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o -MF CMakeFiles/relion_lib.dir/__/fftw.cpp.o.d -o CMakeFiles/relion_lib.dir/__/fftw.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/fftw.cpp [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -MF CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o.d -o CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.cpp [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o -MF CMakeFiles/relion_lib.dir/__/funcs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/funcs.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/funcs.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/flex_analyser.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -MF CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o.d -o CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/healpix_sampling.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-x7zN9B/relion-3.1.3/src/CPlot2D.cpp: In member function ‘void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)’: /build/relion-x7zN9B/relion-3.1.3/src/CPlot2D.cpp:743:41: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 743 | sprintf(m_cYAxisLabelFormat,"%%.%df",nfrac); | ^~ /build/relion-x7zN9B/relion-3.1.3/src/CPlot2D.cpp:743:37: note: directive argument in the range [0, 2147483647] 743 | sprintf(m_cYAxisLabelFormat,"%%.%df",nfrac); | ^~~~~~~~ /build/relion-x7zN9B/relion-3.1.3/src/CPlot2D.cpp:743:16: note: ‘sprintf’ output between 5 and 14 bytes into a destination of size 10 743 | sprintf(m_cYAxisLabelFormat,"%%.%df",nfrac); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/relion-x7zN9B/relion-3.1.3/src/CPlot2D.cpp:733:41: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 733 | sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac); | ^~ /build/relion-x7zN9B/relion-3.1.3/src/CPlot2D.cpp:733:37: note: directive argument in the range [0, 2147483647] 733 | sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac); | ^~~~~~~~ /build/relion-x7zN9B/relion-3.1.3/src/CPlot2D.cpp:733:16: note: ‘sprintf’ output between 5 and 14 bytes into a destination of size 10 733 | sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o -MF CMakeFiles/relion_lib.dir/__/helix.cpp.o.d -o CMakeFiles/relion_lib.dir/__/helix.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/helix.cpp [ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -MF CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/helix.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/helix.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/helix.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/helix.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/helix.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/helix.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/helix.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/helix.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/helix.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/helix.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/helix.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/helix.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/helix.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/helix.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/helix.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/helix.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/helix.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/helix.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/helix_inimodel2d.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o -MF CMakeFiles/relion_lib.dir/__/image.cpp.o.d -o CMakeFiles/relion_lib.dir/__/image.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/image.cpp [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -MF CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o.d -o CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.cpp [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/image.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/image.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/image.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/image.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/image.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/image.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/image.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/image.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/image.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/image.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/image.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/image.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/image.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/image.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/image.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/image.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/image.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/image.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o -MF CMakeFiles/relion_lib.dir/__/mask.cpp.o.d -o CMakeFiles/relion_lib.dir/__/mask.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/mask.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -MF CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/matrix1d.cpp [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -MF CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/matrix2d.cpp [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o -MF CMakeFiles/relion_lib.dir/__/memory.cpp.o.d -o CMakeFiles/relion_lib.dir/__/memory.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/memory.cpp [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/metadata_container.cpp [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/metadata_label.cpp [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/metadata_table.cpp [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/micrograph_model.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/micrograph_model.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/micrograph_model.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/micrograph_model.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/micrograph_model.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/micrograph_model.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/micrograph_model.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/micrograph_model.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/micrograph_model.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/micrograph_model.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/micrograph_model.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/micrograph_model.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/micrograph_model.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/micrograph_model.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/micrograph_model.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/micrograph_model.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/micrograph_model.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/micrograph_model.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/micrograph_model.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_model.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_model.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/ml_model.cpp [ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.cpp:44: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.cpp:44: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.cpp:44: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.cpp:44: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.cpp:44: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.cpp:44: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.cpp:44: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.cpp:44: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.cpp:44: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.cpp:44: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.cpp:44: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.cpp:44: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.cpp:44: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.cpp:44: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.cpp:44: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.cpp:44: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.cpp:44: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.cpp:44: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -MF CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.cpp [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/mpi.cpp [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o -MF CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o.d -o CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/multidim_array.cpp [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o -MF CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o.d -o CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.h:48, from /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.cpp:49: In function ‘void free_Tvector(T*&, int, int) [with T = double]’, inlined from ‘double brent(double, double, double, double (*)(double*, void*), void*, double, double*, int, double*, double*)’ at /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.cpp:594:25: /build/relion-x7zN9B/relion-3.1.3/src/memory.h:74:13: warning: ‘void free(void*)’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.cpp: In function ‘double brent(double, double, double, double (*)(double*, void*), void*, double, double*, int, double*, double*)’: /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.cpp:579:13: note: declared here 579 | RFLOAT *xt=NULL; | ^~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.h:48, from /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.cpp:49: In function ‘void free_Tvector(T*&, int, int) [with T = double]’, inlined from ‘void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)’ at /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.cpp:767:25: /build/relion-x7zN9B/relion-3.1.3/src/memory.h:74:13: warning: ‘void free(void*)’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.cpp: In function ‘void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)’: /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.cpp:703:24: note: declared here 703 | RFLOAT *pt, *ptt, *xit; | ^~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.h:48, from /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.cpp:49: In function ‘void free_Tvector(T*&, int, int) [with T = double]’, inlined from ‘void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)’ at /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.cpp:768:25: /build/relion-x7zN9B/relion-3.1.3/src/memory.h:74:13: warning: ‘void free(void*)’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.cpp: In function ‘void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)’: /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.cpp:703:18: note: declared here 703 | RFLOAT *pt, *ptt, *xit; | ^~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.h:48, from /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.cpp:49: In function ‘void free_Tvector(T*&, int, int) [with T = double]’, inlined from ‘void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)’ at /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.cpp:769:25: /build/relion-x7zN9B/relion-3.1.3/src/memory.h:74:13: warning: ‘void free(void*)’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.cpp: In function ‘void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)’: /build/relion-x7zN9B/relion-3.1.3/src/numerical_recipes.cpp:703:13: note: declared here 703 | RFLOAT *pt, *ptt, *xit; | ^~ [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o -MF CMakeFiles/relion_lib.dir/__/parallel.cpp.o.d -o CMakeFiles/relion_lib.dir/__/parallel.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/parallel.cpp [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -MF CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/particle_subtractor.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/pipeline_control.cpp [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/pipeline_jobs.cpp [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/pipeliner.cpp [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.cpp [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o -MF CMakeFiles/relion_lib.dir/__/projector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/projector.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/projector.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/projector.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/projector.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/projector.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/projector.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/projector.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/projector.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/projector.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/projector.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/projector.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/projector.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/projector.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/projector.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/projector.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/projector.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/projector.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/projector.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/projector.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/projector.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.cpp [ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.cpp [ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -MF CMakeFiles/relion_lib.dir/__/renderEER.cpp.o.d -o CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/renderEER.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -MF CMakeFiles/relion_lib.dir/__/scheduler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/scheduler.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/renderEER.cpp:10: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/renderEER.cpp:10: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/renderEER.cpp:10: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/renderEER.cpp:10: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/renderEER.cpp:10: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/renderEER.cpp:10: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/renderEER.cpp:10: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/renderEER.cpp:10: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/renderEER.cpp:10: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/renderEER.cpp:10: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/renderEER.cpp:10: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/renderEER.cpp:10: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/renderEER.cpp:10: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/renderEER.cpp:10: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/renderEER.cpp:10: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/renderEER.cpp:10: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/renderEER.cpp:10: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/renderEER.cpp:10: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o -MF CMakeFiles/relion_lib.dir/__/strings.cpp.o.d -o CMakeFiles/relion_lib.dir/__/strings.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/strings.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -MF CMakeFiles/relion_lib.dir/__/symmetries.cpp.o.d -o CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/symmetries.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -MF CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/tabfuncs.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp: In member function ‘void TIFFConverter::estimate(FileName)’: /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp:141:101: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘long int’ [-Wformat=] 141 | printf(" %s Frame %03d #Changed %10d #Mismatch %10d, #Negative %10d, #Unreliable %10d / %10d\n", | ~~~^ | | | int | %10ld /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.cpp:141:108: warning: format ‘%d’ expects argument of type ‘int’, but argument 8 has type ‘long int’ [-Wformat=] 141 | printf(" %s Frame %03d #Changed %10d #Mismatch %10d, #Negative %10d, #Unreliable %10d / %10d\n", | ~~~^ | | | int | %10ld [ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o -MF CMakeFiles/relion_lib.dir/__/time.cpp.o.d -o CMakeFiles/relion_lib.dir/__/time.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/time.cpp [ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o -MF CMakeFiles/relion_lib.dir/__/transformations.cpp.o.d -o CMakeFiles/relion_lib.dir/__/transformations.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/transformations.cpp [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -MF CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o.d -o CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /build/relion-x7zN9B/relion-3.1.3/src/Healpix_2.15a/cxxutils.cc [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -MF CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o.d -o CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /build/relion-x7zN9B/relion-3.1.3/src/Healpix_2.15a/healpix_base.cc [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/Gaussian_pyramid.cpp [ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.cpp [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.cpp [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.cpp [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/damage_helper.cpp [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/convolution_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/complex_io.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/fftw_helper.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/damage_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/damage_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/damage_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/damage_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/damage_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/damage_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/damage_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/damage_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/damage_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/damage_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/damage_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/damage_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/damage_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/damage_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/damage_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/damage_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/damage_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/damage_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.cpp [ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.cpp [ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/jaz_config.cpp [ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/image_log.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/interpolation.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.cpp [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/new_ft.cpp [ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.cpp [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/parallel_ft.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/noise_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/reference_map.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/resampling_helper.cpp [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.cpp [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.cpp [ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/refinement_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/slice_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/structure_tensor.cpp [ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/svd_helper.cpp [ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/t_complex.cpp [ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_converter.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.cpp [ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.cpp [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/optimization/gradient_descent.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/volume_integration.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/optimization/lbfgs.cpp [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/optimization/nelder_mead.cpp [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/optimization/optimization.cpp [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/equation2x2.cpp [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp [ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.cpp [ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/math/Zernike.cpp [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp [ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/image_op.cpp [ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/imod_helper.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/projection_helper.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp [ 49%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.cpp [ 49%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/d3x3/dsyev2.c [ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/d3x3/dsyevc3.c [ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/d3x3/dsyevh3.c [ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/d3x3/dsyevd3.c [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/d3x3/dsyevj3.c In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/d3x3/dsyevq3.c [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/d3x3/dsyevv3.c [ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/d3x3/dsytrd3.c [ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -c /build/relion-x7zN9B/relion-3.1.3/src/jaz/d3x3/slvsec3.c In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 53%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat 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Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/image_handler.dir/build.make 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Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 54%] Building CXX object src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o [ 54%] Building CXX object src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o [ 54%] Building CXX object src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. 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CMakeFiles/image_handler.dir/image_handler.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/image_handler.cpp cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -MF CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o.d -o CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse.cpp cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o -MF CMakeFiles/mask_create.dir/mask_create.cpp.o.d -o CMakeFiles/mask_create.dir/mask_create.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/mask_create.cpp cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -MF CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o.d -o CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse_mpi.cpp [ 55%] Building CXX object src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -MF CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o.d -o CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_symmetry_expand.cpp [ 56%] Building CXX object src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -MF CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o.d -o CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/external_reconstruct.cpp [ 56%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/displayer.cpp [ 56%] Building CXX object src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o -MF CMakeFiles/pipeliner.dir/pipeliner.cpp.o.d -o CMakeFiles/pipeliner.dir/pipeliner.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/pipeliner.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/image_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/image_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/image_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/image_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/image_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/image_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/image_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/image_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/image_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/image_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/image_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/image_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/image_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/image_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/image_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/image_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/image_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/image_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/exp_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/flex_analyse.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 56%] Linking CXX executable ../../bin/relion_helix_inimodel2d cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_inimodel2d.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -o ../../bin/relion_helix_inimodel2d ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mask_create.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mask_create.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mask_create.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mask_create.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mask_create.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mask_create.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mask_create.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mask_create.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mask_create.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mask_create.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mask_create.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mask_create.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mask_create.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mask_create.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mask_create.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mask_create.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mask_create.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mask_create.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.h:40, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.h:40, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.h:40, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.h:40, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.h:40, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.h:40, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.h:40, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.h:40, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.h:40, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.h:40, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.h:40, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.h:40, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.h:40, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.h:40, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.h:40, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.h:40, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.h:40, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.h:40, from /build/relion-x7zN9B/relion-3.1.3/src/displayer.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 56%] Built target helix_inimodel2d make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 57%] Building CXX object src/apps/CMakeFiles/project.dir/project.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/project.dir/project.cpp.o -MF CMakeFiles/project.dir/project.cpp.o.d -o CMakeFiles/project.dir/project.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/project.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/project.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/project.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/project.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/project.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/project.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/project.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/project.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/project.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/project.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/project.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/project.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/project.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/project.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/project.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/project.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/project.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/project.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/project.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 57%] Linking CXX executable ../../bin/relion_particle_symmetry_expand cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_symmetry_expand.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -o ../../bin/relion_particle_symmetry_expand ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 57%] Built target particle_symmetry_expand make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 57%] Building CXX object src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o -MF CMakeFiles/convert_star.dir/convert_star.cpp.o.d -o CMakeFiles/convert_star.dir/convert_star.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_star.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_star.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_star.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_star.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_star.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_star.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_star.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_star.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_star.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_star.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_star.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_star.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_star.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_star.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_star.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_star.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_star.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_star.cpp:24: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_star.cpp:24: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 57%] Linking CXX executable ../../bin/relion_flex_analyse_mpi cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -o ../../bin/relion_flex_analyse_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 58%] Linking CXX executable ../../bin/relion_flex_analyse cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -o ../../bin/relion_flex_analyse ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 59%] Linking CXX executable ../../bin/relion_convert_star cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_star.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_star.dir/convert_star.cpp.o -o ../../bin/relion_convert_star ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 60%] Linking CXX executable ../../bin/relion_pipeliner cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/pipeliner.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pipeliner.dir/pipeliner.cpp.o -o ../../bin/relion_pipeliner ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 60%] Built target flex_analyse_mpi make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 60%] Building CXX object src/apps/CMakeFiles/refine.dir/refine.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/refine.dir/refine.cpp.o -MF CMakeFiles/refine.dir/refine.cpp.o.d -o CMakeFiles/refine.dir/refine.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/refine.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 60%] Built target convert_star make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 60%] Building CXX object src/apps/CMakeFiles/import.dir/import.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/import.dir/import.cpp.o -MF CMakeFiles/import.dir/import.cpp.o.d -o CMakeFiles/import.dir/import.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/import.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 60%] Built target flex_analyse make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/helix_toolbox.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 61%] Building CXX object src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -MF CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o.d -o CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_toolbox.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 61%] Built target pipeliner make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 62%] Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/autopick.dir/autopick.cpp.o -MF CMakeFiles/autopick.dir/autopick.cpp.o.d -o CMakeFiles/autopick.dir/autopick.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/import.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/import.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/import.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/import.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/import.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/import.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/import.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/import.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/import.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/import.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/import.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/import.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/import.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/import.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/import.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/import.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/import.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/import.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 63%] Linking CXX executable ../../bin/relion_find_tiltpairs cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/find_tiltpairs.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -o ../../bin/relion_find_tiltpairs ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 63%] Built target find_tiltpairs make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 63%] Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -MF CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o.d -o CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick_mpi.cpp [ 63%] Linking CXX executable ../../bin/relion_autopick cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/autopick.dir/autopick.cpp.o -o ../../bin/relion_autopick ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 63%] Linking CXX executable ../../bin/relion_import cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/import.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/import.dir/import.cpp.o -o ../../bin/relion_import ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 63%] Built target autopick make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 63%] Building CXX object src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker.h:10, from /build/relion-x7zN9B/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-x7zN9B/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -MF CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o.d -o CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff.cpp [ 63%] Linking CXX executable ../../bin/relion_refine cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine.dir/refine.cpp.o -o ../../bin/relion_refine ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 63%] Linking CXX executable ../../bin/relion_external_reconstruct cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/external_reconstruct.dir/link.txt --verbose=1 [ 63%] Linking CXX executable ../../bin/relion_mask_create cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mask_create.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -o ../../bin/relion_external_reconstruct ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mask_create.dir/mask_create.cpp.o -o ../../bin/relion_mask_create ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 63%] Built target import make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 63%] Building CXX object src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -MF CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o.d -o CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/mrc2vtk.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 63%] Built target external_reconstruct make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 64%] Building CXX object src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -MF CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o.d -o CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_toolbox.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 64%] Built target mask_create make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/depend make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake --color= [ 64%] Built target refine make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 64%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -MF CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o.d -o CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/align_symmetry.cpp [ 64%] Building CXX object src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o -MF CMakeFiles/postprocess.dir/postprocess.cpp.o.d -o CMakeFiles/postprocess.dir/postprocess.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess.cpp [ 64%] Linking CXX executable ../../bin/relion_convert_to_tiff cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -o ../../bin/relion_convert_to_tiff ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/align_symmetry.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/align_symmetry.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/align_symmetry.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/align_symmetry.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/align_symmetry.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/align_symmetry.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/align_symmetry.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/align_symmetry.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/align_symmetry.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/align_symmetry.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/align_symmetry.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/align_symmetry.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/align_symmetry.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/align_symmetry.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/align_symmetry.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/align_symmetry.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/align_symmetry.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/align_symmetry.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 65%] Linking CXX executable ../../bin/relion_autopick_mpi cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick_mpi.dir/link.txt --verbose=1 [ 65%] Built target convert_to_tiff make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake --color= /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -o ../../bin/relion_autopick_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 65%] Building CXX object src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -MF CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o.d -o CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_mask_test.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 65%] Built target autopick_mpi make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 66%] Building CXX object src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o -MF CMakeFiles/merge_particles.dir/merge_particles.cpp.o.d -o CMakeFiles/merge_particles.dir/merge_particles.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/merge_particles.cpp [ 67%] Linking CXX executable ../../bin/relion_image_handler cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/image_handler.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/image_handler.dir/image_handler.cpp.o -o ../../bin/relion_image_handler ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/merge_particles.cpp:2: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/merge_particles.cpp:2: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/merge_particles.cpp:2: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/merge_particles.cpp:2: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/merge_particles.cpp:2: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/merge_particles.cpp:2: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/merge_particles.cpp:2: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/merge_particles.cpp:2: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/merge_particles.cpp:2: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/merge_particles.cpp:2: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/merge_particles.cpp:2: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/merge_particles.cpp:2: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/merge_particles.cpp:2: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/merge_particles.cpp:2: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/merge_particles.cpp:2: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/merge_particles.cpp:2: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/merge_particles.cpp:2: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/merge_particles.cpp:2: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 67%] Linking CXX executable ../../bin/relion_mrc2vtk [ 67%] Built target image_handler cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mrc2vtk.dir/link.txt --verbose=1 make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -o ../../bin/relion_mrc2vtk ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 68%] Building CXX object src/apps/CMakeFiles/localsym.dir/localsym.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/localsym.dir/localsym.cpp.o -MF CMakeFiles/localsym.dir/localsym.cpp.o.d -o CMakeFiles/localsym.dir/localsym.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym.cpp [ 68%] Linking CXX executable ../../bin/relion_project cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/project.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/project.dir/project.cpp.o -o ../../bin/relion_project ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 68%] Linking CXX executable ../../bin/relion_postprocess cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/postprocess.dir/postprocess.cpp.o -o ../../bin/relion_postprocess ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 68%] Built target mrc2vtk make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 69%] Building CXX object src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -MF CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o.d -o CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind_mpi.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 69%] Built target project make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 70%] Building CXX object src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -MF CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o.d -o CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 70%] Built target postprocess make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 70%] Building CXX object src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -MF CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o.d -o CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess_mpi.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 70%] Linking CXX executable ../../bin/relion_merge_particles cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/merge_particles.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/merge_particles.dir/merge_particles.cpp.o -o ../../bin/relion_merge_particles ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 70%] Built target merge_particles make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 71%] Building CXX object src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -MF CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o.d -o CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_reposition.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 72%] Linking CXX executable ../../bin/relion_ctf_mask_test cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_mask_test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -o ../../bin/relion_ctf_mask_test ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 72%] Linking CXX executable ../../bin/relion_localsym cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym.dir/link.txt --verbose=1 [ 72%] Linking CXX executable ../../bin/relion_convert_to_tiff_mpi cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/localsym.dir/localsym.cpp.o -o ../../bin/relion_localsym ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -o ../../bin/relion_convert_to_tiff_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 72%] Built target ctf_mask_test make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 72%] Building CXX object src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -MF CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o.d -o CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine_mpi.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 72%] Built target localsym make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 73%] Building CXX object src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -MF CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o.d -o CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym_mpi.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_reposition.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_reposition.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_reposition.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_reposition.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_reposition.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_reposition.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_reposition.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_reposition.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_reposition.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_reposition.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_reposition.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_reposition.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_reposition.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_reposition.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_reposition.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_reposition.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_reposition.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_reposition.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 73%] Built target convert_to_tiff_mpi make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 73%] Building CXX object src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -MF CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o.d -o CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine.cpp [ 73%] Linking CXX executable ../../bin/relion_ctf_toolbox cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_toolbox.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -o ../../bin/relion_ctf_toolbox ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-x7zN9B/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/ctf_refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 73%] Linking CXX executable ../../bin/relion_run_ctffind_mpi cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -o ../../bin/relion_run_ctffind_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 73%] Built target ctf_toolbox make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 74%] Building CXX object src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o -MF CMakeFiles/motion_refine.dir/motion_refine.cpp.o.d -o CMakeFiles/motion_refine.dir/motion_refine.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine.cpp [ 74%] Linking CXX executable ../../bin/relion_align_symmetry cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/align_symmetry.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -o ../../bin/relion_align_symmetry ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 74%] Built target run_ctffind_mpi make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/postprocess_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 75%] Building CXX object src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -MF CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o.d -o CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess_mpi.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 75%] Built target align_symmetry make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 76%] Building CXX object src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -MF CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o.d -o CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_FCC.cpp [ 76%] Linking CXX executable ../../bin/relion_localsym_mpi cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -o ../../bin/relion_localsym_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 76%] Linking CXX executable ../../bin/relion_ctf_refine_mpi cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -o ../../bin/relion_ctf_refine_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 77%] Linking CXX executable ../../bin/relion_ctf_refine cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine.dir/link.txt --verbose=1 [ 77%] Linking CXX executable ../../bin/relion_preprocess_mpi cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -o ../../bin/relion_ctf_refine ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -o ../../bin/relion_preprocess_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 77%] Linking CXX executable ../../bin/relion_helix_toolbox cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_toolbox.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -o ../../bin/relion_helix_toolbox ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_FCC.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_FCC.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_FCC.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_FCC.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_FCC.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_FCC.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_FCC.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_FCC.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_FCC.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_FCC.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_FCC.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_FCC.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_FCC.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_FCC.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_FCC.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_FCC.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_FCC.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_FCC.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 77%] Built target preprocess_mpi make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 77%] Building CXX object src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o -MF CMakeFiles/tomo_test.dir/tomo_test.cpp.o.d -o CMakeFiles/tomo_test.dir/tomo_test.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/tomo_test.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/postprocessing.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 77%] Linking CXX executable ../../bin/relion_motion_refine cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine.dir/link.txt --verbose=1 [ 77%] Built target ctf_refine_mpi make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake --color= /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/motion_refine.dir/motion_refine.cpp.o -o ../../bin/relion_motion_refine ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 77%] Building CXX object src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o -MF CMakeFiles/demodulate.dir/demodulate.cpp.o.d -o CMakeFiles/demodulate.dir/demodulate.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/demodulate.cpp [ 78%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/gui_entries.cpp [ 78%] Built target localsym_mpi make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 78%] Building CXX object src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o -MF CMakeFiles/particle_select.dir/particle_select.cpp.o.d -o CMakeFiles/particle_select.dir/particle_select.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_select.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 78%] Built target helix_toolbox make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 78%] Building CXX object src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -MF CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o.d -o CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tomo_test.cpp:2: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tomo_test.cpp:2: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tomo_test.cpp:2: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tomo_test.cpp:2: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tomo_test.cpp:2: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tomo_test.cpp:2: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tomo_test.cpp:2: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tomo_test.cpp:2: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tomo_test.cpp:2: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tomo_test.cpp:2: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tomo_test.cpp:2: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tomo_test.cpp:2: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tomo_test.cpp:2: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tomo_test.cpp:2: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tomo_test.cpp:2: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tomo_test.cpp:2: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tomo_test.cpp:2: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tomo_test.cpp:2: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/demodulate.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/demodulate.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/demodulate.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/demodulate.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/demodulate.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/demodulate.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/demodulate.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/demodulate.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/demodulate.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/demodulate.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/demodulate.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/demodulate.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/demodulate.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/demodulate.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/demodulate.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/demodulate.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/demodulate.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/demodulate.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 78%] Built target ctf_refine make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 78%] Building CXX object src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -MF CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o.d -o CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract_mpi.cpp [ 78%] Linking CXX executable ../../bin/relion_particle_FCC cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_FCC.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -o ../../bin/relion_particle_FCC ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_select.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_select.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_select.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_select.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_select.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_select.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_select.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_select.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_select.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_select.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_select.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_select.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_select.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_select.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_select.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_select.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_select.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_select.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 78%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/gui_jobwindow.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 78%] Built target motion_refine make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 78%] Building CXX object src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o -MF CMakeFiles/reconstruct.dir/reconstruct.cpp.o.d -o CMakeFiles/reconstruct.dir/reconstruct.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 78%] Built target particle_FCC make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake --color= [ 78%] Linking CXX executable ../../bin/relion_postprocess_mpi cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess_mpi.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -o ../../bin/relion_postprocess_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 78%] Building CXX object src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -MF CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o.d -o CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine_mpi.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 78%] Built target postprocess_mpi make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/plot_delocalisation.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 78%] Building CXX object src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -MF CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o.d -o CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/plot_delocalisation.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/ctf.h:50, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-x7zN9B/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 79%] Linking CXX executable ../../bin/relion_tomo_test cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tomo_test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tomo_test.dir/tomo_test.cpp.o -o ../../bin/relion_tomo_test ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 80%] Linking CXX executable ../../bin/relion_particle_select cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_select.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_select.dir/particle_select.cpp.o -o ../../bin/relion_particle_select ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 80%] Built target tomo_test make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 80%] Building CXX object src/apps/CMakeFiles/reposition.dir/reposition.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reposition.dir/reposition.cpp.o -MF CMakeFiles/reposition.dir/reposition.cpp.o.d -o CMakeFiles/reposition.dir/reposition.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/reposition.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 80%] Built target particle_select make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 80%] Building CXX object src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -MF CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o.d -o CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/prepare_subtomo.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/helix.h:30, from /build/relion-x7zN9B/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reposition.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reposition.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reposition.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reposition.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reposition.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reposition.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reposition.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reposition.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reposition.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reposition.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reposition.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reposition.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reposition.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reposition.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reposition.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reposition.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reposition.cpp:1: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reposition.cpp:1: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 81%] Linking CXX executable ../../bin/relion_plot_delocalisation cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/plot_delocalisation.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -o ../../bin/relion_plot_delocalisation ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 82%] Linking CXX executable ../../bin/relion_demodulate cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/demodulate.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/demodulate.dir/demodulate.cpp.o -o ../../bin/relion_demodulate ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 83%] Linking CXX executable ../../bin/relion_reconstruct cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconstruct.dir/reconstruct.cpp.o -o ../../bin/relion_reconstruct ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 83%] Built target plot_delocalisation make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 83%] Building CXX object src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o -MF CMakeFiles/preprocess.dir/preprocess.cpp.o.d -o CMakeFiles/preprocess.dir/preprocess.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess.cpp [ 84%] Linking CXX executable ../../bin/relion_particle_subtract cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -o ../../bin/relion_particle_subtract ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 85%] Linking CXX executable ../../bin/relion_motion_refine_mpi cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -o ../../bin/relion_motion_refine_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 85%] Linking CXX executable ../../bin/relion_particle_subtract_mpi cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract_mpi.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -o ../../bin/relion_particle_subtract_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 85%] Built target demodulate make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 85%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -MF CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o.d -o CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct_mpi.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 85%] Built target reconstruct make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 86%] Building CXX object src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -MF CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o.d -o CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/refine_mpi.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/preprocessing.h:29, from /build/relion-x7zN9B/relion-3.1.3/src/apps/preprocess.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 86%] Built target motion_refine_mpi make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 86%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -MF CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o.d -o CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 86%] Built target particle_subtract make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 87%] Building CXX object src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -MF CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o.d -o CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/backprojector.h:33, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 87%] Built target particle_subtract_mpi make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 87%] Building CXX object src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -MF CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o.d -o CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/estimate_gain.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine_mpi.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/projector.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/ml_model.h:23, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-x7zN9B/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/apps/refine_mpi.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_ctffind.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 88%] Linking CXX executable ../../bin/relion_preprocess cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess.dir/preprocess.cpp.o -o ../../bin/relion_preprocess ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 88%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.cpp [ 88%] Linking CXX executable ../../bin/relion_run_ctffind cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -o ../../bin/relion_run_ctffind ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/estimate_gain.cpp:27: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/estimate_gain.cpp:27: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/estimate_gain.cpp:27: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/estimate_gain.cpp:27: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/estimate_gain.cpp:27: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/estimate_gain.cpp:27: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/estimate_gain.cpp:27: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/estimate_gain.cpp:27: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/estimate_gain.cpp:27: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/estimate_gain.cpp:27: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/estimate_gain.cpp:27: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/estimate_gain.cpp:27: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/estimate_gain.cpp:27: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/estimate_gain.cpp:27: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/estimate_gain.cpp:27: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/estimate_gain.cpp:27: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/estimate_gain.cpp:27: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/estimate_gain.cpp:27: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 88%] Built target run_ctffind make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 88%] Building CXX object src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -MF CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o.d -o CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 88%] Built target preprocess make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 89%] Building CXX object src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o -MF CMakeFiles/stack_create.dir/stack_create.cpp.o.d -o CMakeFiles/stack_create.dir/stack_create.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/stack_create.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.cpp:22: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.cpp:22: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 90%] Linking CXX executable ../../bin/relion_reposition cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reposition.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reposition.dir/reposition.cpp.o -o ../../bin/relion_reposition ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 90%] Linking CXX executable ../../bin/relion_particle_reposition cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_reposition.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -o ../../bin/relion_particle_reposition ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 91%] Linking CXX executable ../../bin/relion_reconstruct_mpi cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -o ../../bin/relion_reconstruct_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 91%] Linking CXX executable ../../bin/relion_run_motioncorr cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -o ../../bin/relion_run_motioncorr ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-x7zN9B/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-x7zN9B/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 91%] Built target reposition make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake --color= In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/stack_create.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/stack_create.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/stack_create.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/stack_create.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/stack_create.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/stack_create.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/stack_create.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/stack_create.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/stack_create.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/stack_create.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/stack_create.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/stack_create.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/stack_create.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/stack_create.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/stack_create.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/stack_create.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/stack_create.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/stack_create.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 91%] Building CXX object src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o -MF CMakeFiles/scheduler.dir/scheduler.cpp.o.d -o CMakeFiles/scheduler.dir/scheduler.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/scheduler.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 91%] Built target particle_reposition make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 91%] Built target run_motioncorr make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake --color= [ 92%] Building CXX object src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o -MF CMakeFiles/star_handler.dir/star_handler.cpp.o.d -o CMakeFiles/star_handler.dir/star_handler.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/star_handler.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 92%] Building CXX object src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -MF CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o.d -o CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/tiltpair_plot.cpp make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 92%] Built target reconstruct_mpi [ 93%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/scheduler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/scheduler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/scheduler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/scheduler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/scheduler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/scheduler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/scheduler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/scheduler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/scheduler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/scheduler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/scheduler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/scheduler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/scheduler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/scheduler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/scheduler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/scheduler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/scheduler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/apps/scheduler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/star_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/star_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/star_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/star_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/star_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/star_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/star_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/star_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/star_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/star_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/star_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/star_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/star_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/star_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/star_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/star_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/star_handler.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/star_handler.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.h:43, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.h:43, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.h:43, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.h:43, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.h:43, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.h:43, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.h:43, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.h:43, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.h:43, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.h:43, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.h:43, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.h:43, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.h:43, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.h:43, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.h:43, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.h:43, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.h:43, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.cpp:21: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.h:43, from /build/relion-x7zN9B/relion-3.1.3/src/manualpicker.cpp:21: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 93%] Linking CXX executable ../../bin/relion_refine_mpi cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -o ../../bin/relion_refine_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 94%] Linking CXX executable ../../bin/relion_run_motioncorr_mpi cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -o ../../bin/relion_run_motioncorr_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory 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'/build/relion-x7zN9B/relion-3.1.3/build' [ 94%] Built target refine_mpi [ 95%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -MF CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o.d -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /build/relion-x7zN9B/relion-3.1.3/src/Healpix_2.15a/healpix_base.cc [ 95%] Linking CXX executable 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tiltpair_plot make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 96%] Built target estimate_gain make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 96%] Built target scheduler [ 96%] Linking CXX executable ../../bin/relion_stack_create cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/stack_create.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/stack_create.dir/stack_create.cpp.o -o ../../bin/relion_stack_create ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 96%] Built target stack_create [ 97%] Linking CXX executable 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/build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/relion.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/build make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 97%] Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o [ 97%] Building CXX object src/apps/CMakeFiles/display.dir/display.cpp.o [ 97%] Building CXX object src/apps/CMakeFiles/relion.dir/maingui.cpp.o cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o -MF CMakeFiles/manualpick.dir/manualpick.cpp.o.d -o CMakeFiles/manualpick.dir/manualpick.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/manualpick.cpp cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/display.dir/display.cpp.o -MF CMakeFiles/display.dir/display.cpp.o.d -o CMakeFiles/display.dir/display.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/display.cpp cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-x7zN9B/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-x7zN9B/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-x7zN9B/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion.dir/maingui.cpp.o -MF CMakeFiles/relion.dir/maingui.cpp.o.d -o CMakeFiles/relion.dir/maingui.cpp.o -c /build/relion-x7zN9B/relion-3.1.3/src/apps/maingui.cpp In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/display.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/display.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/display.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/display.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/display.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/display.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/display.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/display.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/display.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/display.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/display.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/display.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/display.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/display.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/display.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/display.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/display.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/display.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/manualpick.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/manualpick.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/manualpick.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/manualpick.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/manualpick.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/manualpick.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/manualpick.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/manualpick.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/manualpick.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/manualpick.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/manualpick.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/manualpick.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/manualpick.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/manualpick.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/manualpick.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/manualpick.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/apps/manualpick.cpp:25: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/apps/manualpick.cpp:25: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/apps/maingui.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/apps/maingui.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/apps/maingui.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/apps/maingui.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/apps/maingui.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/apps/maingui.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/apps/maingui.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/apps/maingui.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/apps/maingui.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/apps/maingui.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/apps/maingui.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/apps/maingui.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/apps/maingui.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/apps/maingui.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/apps/maingui.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/apps/maingui.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-x7zN9B/relion-3.1.3/src/image.h:455, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/apps/maingui.cpp:23: /build/relion-x7zN9B/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/relion-x7zN9B/relion-3.1.3/src/image.h:57, from /build/relion-x7zN9B/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-x7zN9B/relion-3.1.3/src/scheduler.h:26, from /build/relion-x7zN9B/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-x7zN9B/relion-3.1.3/src/apps/maingui.cpp:23: /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 98%] Linking CXX executable ../../bin/relion_display cd /build/relion-x7zN9B/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/display.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 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/usr/bin/cmake -E copy /build/relion-x7zN9B/relion-3.1.3/scripts/star_loopheader /build/relion-x7zN9B/relion-3.1.3/build/bin/relion_star_loopheader /usr/bin/cmake -E copy /build/relion-x7zN9B/relion-3.1.3/scripts/star_datablock_stack /build/relion-x7zN9B/relion-3.1.3/build/bin/relion_star_datablock_stack /usr/bin/cmake -E copy /build/relion-x7zN9B/relion-3.1.3/scripts/star_datablock_singlefiles /build/relion-x7zN9B/relion-3.1.3/build/bin/relion_star_datablock_singlefiles /usr/bin/cmake -E copy /build/relion-x7zN9B/relion-3.1.3/scripts/star_datablock_ctfdat /build/relion-x7zN9B/relion-3.1.3/build/bin/relion_star_datablock_ctfdat /usr/bin/cmake -E copy /build/relion-x7zN9B/relion-3.1.3/scripts/qsub.csh /build/relion-x7zN9B/relion-3.1.3/build/bin/relion_qsub.csh make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 0%] Built target copy_scripts make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target relion_lib make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion_lib.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 53%] Built target relion_lib make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target image_handler make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/image_handler.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 54%] Built target image_handler make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/helix_inimodel2d.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target helix_inimodel2d make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/helix_inimodel2d.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 55%] Built target helix_inimodel2d make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/find_tiltpairs.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target find_tiltpairs make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/find_tiltpairs.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 56%] Built target find_tiltpairs make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/flex_analyse_mpi.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target flex_analyse_mpi make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/flex_analyse_mpi.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 56%] Built target flex_analyse_mpi make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/flex_analyse.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target flex_analyse make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/flex_analyse.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 57%] Built target flex_analyse make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/mask_create.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target mask_create make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/mask_create.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 57%] Built target mask_create make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target external_reconstruct make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/external_reconstruct.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 58%] Built target external_reconstruct make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target particle_symmetry_expand make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_symmetry_expand.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 59%] Built target particle_symmetry_expand make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target relion_gui_lib make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion_gui_lib.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 62%] Built target relion_gui_lib make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target display make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/display.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 63%] Built target display make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target pipeliner make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/pipeliner.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 64%] Built target pipeliner make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target project make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/project.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 65%] Built target project make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target convert_star make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_star.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 66%] Built target convert_star make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target refine make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/refine.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 66%] Built target refine make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target import make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/import.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 66%] Built target import make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/helix_toolbox.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target helix_toolbox make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/helix_toolbox.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 67%] Built target helix_toolbox make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target autopick make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/autopick.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 68%] Built target autopick make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target autopick_mpi make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/autopick_mpi.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 69%] Built target autopick_mpi make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target convert_to_tiff make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_to_tiff.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 69%] Built target convert_to_tiff make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target mrc2vtk make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/mrc2vtk.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 69%] Built target mrc2vtk make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target ctf_toolbox make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_toolbox.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 70%] Built target ctf_toolbox make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target align_symmetry make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/align_symmetry.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 70%] Built target align_symmetry make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target postprocess make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/postprocess.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 70%] Built target postprocess make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target ctf_mask_test make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_mask_test.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 71%] Built target ctf_mask_test make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target merge_particles make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/merge_particles.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 72%] Built target merge_particles make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target localsym make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/localsym.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 73%] Built target localsym make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target run_ctffind_mpi make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_ctffind_mpi.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 74%] Built target run_ctffind_mpi make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target convert_to_tiff_mpi make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 75%] Built target convert_to_tiff_mpi make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target preprocess_mpi make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/preprocess_mpi.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 75%] Built target preprocess_mpi make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/relion.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target relion make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 76%] Built target relion make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target particle_reposition make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_reposition.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 77%] Built target particle_reposition make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target ctf_refine_mpi make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_refine_mpi.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 77%] Built target ctf_refine_mpi make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target manualpick make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/manualpick.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 78%] Built target manualpick make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target localsym_mpi make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/localsym_mpi.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 79%] Built target localsym_mpi make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target ctf_refine make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_refine.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 80%] Built target ctf_refine make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target motion_refine make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/motion_refine.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 81%] Built target motion_refine make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/postprocess_mpi.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target postprocess_mpi make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/postprocess_mpi.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 82%] Built target postprocess_mpi make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target particle_FCC make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_FCC.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 83%] Built target particle_FCC make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target tomo_test make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/tomo_test.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 84%] Built target tomo_test make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target demodulate make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/demodulate.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 85%] Built target demodulate make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target particle_select make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_select.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 86%] Built target particle_select make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target particle_subtract make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_subtract.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 87%] Built target particle_subtract make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target particle_subtract_mpi make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_subtract_mpi.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 87%] Built target particle_subtract_mpi make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target reconstruct make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/reconstruct.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 88%] Built target reconstruct make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target motion_refine_mpi make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/motion_refine_mpi.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 89%] Built target motion_refine_mpi make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/plot_delocalisation.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target plot_delocalisation make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/plot_delocalisation.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 90%] Built target plot_delocalisation make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target reposition make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/reposition.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 91%] Built target reposition make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target prepare_subtomo make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/prepare_subtomo.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 92%] Built target prepare_subtomo make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target preprocess make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/preprocess.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 93%] Built target preprocess make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target reconstruct_mpi make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/reconstruct_mpi.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 94%] Built target reconstruct_mpi make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target refine_mpi make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/refine_mpi.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 95%] Built target refine_mpi make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target run_ctffind make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_ctffind.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 95%] Built target run_ctffind make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target run_motioncorr make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_motioncorr.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 96%] Built target run_motioncorr make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target estimate_gain make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/estimate_gain.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 96%] Built target estimate_gain make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target run_motioncorr_mpi make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_motioncorr_mpi.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 97%] Built target run_motioncorr_mpi make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target stack_create make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/stack_create.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 98%] Built target stack_create make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target scheduler make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/scheduler.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 98%] Built target scheduler make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target star_handler make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/star_handler.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [ 99%] Built target star_handler make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' cd /build/relion-x7zN9B/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-x7zN9B/relion-3.1.3 /build/relion-x7zN9B/relion-3.1.3/src/apps /build/relion-x7zN9B/relion-3.1.3/build /build/relion-x7zN9B/relion-3.1.3/build/src/apps /build/relion-x7zN9B/relion-3.1.3/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target tiltpair_plot make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/build make[4]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/tiltpair_plot.dir/build'. make[4]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' [100%] Built target tiltpair_plot make[3]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' /usr/bin/cmake -E cmake_progress_start /build/relion-x7zN9B/relion-3.1.3/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/relion-x7zN9B/relion-3.1.3/build' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_inimodel2d -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_star -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_pipeliner -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_find_tiltpairs -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_import -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_external_reconstruct -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mask_create -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_to_tiff -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick_mpi -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_image_handler -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mrc2vtk -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_project -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_merge_particles -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_mask_test -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_toolbox -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_align_symmetry -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym_mpi -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_refine -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_preprocess_mpi -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_FCC -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess_mpi -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_tomo_test -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_select -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_plot_delocalisation -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_demodulate -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine_mpi -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_preprocess -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reposition -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_reposition -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct_mpi -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine_mpi -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_estimate_gain -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_tiltpair_plot -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_scheduler -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_stack_create -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_prepare_subtomo -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_display -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_handler -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_manualpick -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_printtable -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_plottable -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_loopheader -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_datablock_stack -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_datablock_singlefiles -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_datablock_ctfdat -- Installing: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_qsub.csh -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_align_symmetry -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick_mpi -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_star -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_to_tiff -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_mask_test -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_refine -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_toolbox -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_demodulate -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_display -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_estimate_gain -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_external_reconstruct -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_find_tiltpairs -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_inimodel2d -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_image_handler -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_import -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym_mpi -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_manualpick -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mask_create -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_merge_particles -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine_mpi -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mrc2vtk -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_FCC -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_reposition -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_select -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_pipeliner -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_plot_delocalisation -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess_mpi -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_prepare_subtomo -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_preprocess -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_preprocess_mpi -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_project -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct_mpi -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine_mpi -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reposition -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_scheduler -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_stack_create -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_handler -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_tiltpair_plot -- Up-to-date: /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_tomo_test make[2]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3/build' mkdir -p /build/relion-x7zN9B/relion-3.1.3/debian/tmp/gui/usr/bin rm /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/*.csh # Useless ... for prog in relion relion_display relion_maingui relion_manualpick; do \ mv /build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/$prog \ /build/relion-x7zN9B/relion-3.1.3/debian/tmp/gui/usr/bin; done mv: cannot stat '/build/relion-x7zN9B/relion-3.1.3/debian/tmp/cli/usr/bin/relion_maingui': No such file or directory make[1]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3' create-stamp debian/debhelper-build-stamp debian/rules override_dh_prep make[1]: Entering directory '/build/relion-x7zN9B/relion-3.1.3' # We don't want debian/tmp to be removed again ... dh_prep -X debian/tmp make[1]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3' debian/rules override_dh_install-arch make[1]: Entering directory '/build/relion-x7zN9B/relion-3.1.3' dh_install -a make[1]: Leaving directory '/build/relion-x7zN9B/relion-3.1.3' dh_installdocs -a dh_installchangelogs -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'relion-dbgsym' in '../relion-dbgsym_3.1.3-1_amd64.deb'. dpkg-deb: building package 'relion' in '../relion_3.1.3-1_amd64.deb'. dpkg-deb: building package 'relion-gui-dbgsym' in '../relion-gui-dbgsym_3.1.3-1_amd64.deb'. dpkg-deb: building package 'relion-gui' in '../relion-gui_3.1.3-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../relion_3.1.3-1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/relion-x7zN9B /tmp/relion-3.1.3-1zrw_xra3 I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.7Ra6eDGlM6... I: success in 1188.0924 seconds md5: relion-dbgsym_3.1.3-1_amd64.deb: OK md5: relion-gui-dbgsym_3.1.3-1_amd64.deb: OK md5: relion-gui_3.1.3-1_amd64.deb: OK md5: relion_3.1.3-1_amd64.deb: OK sha1: relion-dbgsym_3.1.3-1_amd64.deb: OK sha1: relion-gui-dbgsym_3.1.3-1_amd64.deb: OK sha1: relion-gui_3.1.3-1_amd64.deb: OK sha1: relion_3.1.3-1_amd64.deb: OK sha256: relion-dbgsym_3.1.3-1_amd64.deb: OK sha256: relion-gui-dbgsym_3.1.3-1_amd64.deb: OK sha256: relion-gui_3.1.3-1_amd64.deb: OK sha256: relion_3.1.3-1_amd64.deb: OK Checksums: OK