Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/c/cctbx/cctbx_2021.12+ds1-4_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/cctbx-2021.12+ds1-46t9gz55i/cctbx_2021.12+ds1-4_amd64.buildinfo Get source package info: cctbx=2021.12+ds1-4 Source URL: http://snapshot.notset.fr/mr/package/cctbx/2021.12+ds1-4/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.121 autoconf=2.71-2 automake=1:1.16.5-1.3 autopoint=0.21-6 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6 binutils=2.38-3 binutils-common=2.38-3 binutils-x86-64-linux-gnu=2.38-3 blt=2.5.3+dfsg-4.1 bsdextrautils=2.37.3-1+b1 bsdutils=1:2.37.3-1+b1 build-essential=12.9 bzip2=1.0.8-5 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-10=10.3.0-15 cpp-11=11.2.0-19 dash=0.5.11+git20210903+057cd650a4ed-8 debconf=1.5.79 debhelper=13.6 debianutils=5.7-0.1 dh-autoreconf=20 dh-exec=0.23.4 dh-python=5.20220215 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dpkg=1.21.5 dpkg-dev=1.21.5 dwz=0.14-1 fftw-dev=2.1.5-6 fftw2=2.1.5-6 file=1:5.41-3 findutils=4.9.0-2 fontconfig-config=2.13.1-4.4 fonts-dejavu-core=2.37-2 fonts-lyx=2.3.6-1 fonts-urw-base35=20200910-1 g++=4:11.2.0-2 g++-11=11.2.0-19 gcc=4:11.2.0-2 gcc-10=10.3.0-15 gcc-10-base=10.3.0-15 gcc-11=11.2.0-19 gcc-11-base=11.2.0-19 gcc-12-base=12-20220319-1 gettext=0.21-6 gettext-base=0.21-6 grep=3.7-1 groff-base=1.22.4-8 gzip=1.10-4 hdf5-helpers=1.10.7+repack-4 hostname=3.23 ibverbs-providers=39.0-1+b1 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 jq=1.6-2.1 libacl1=2.3.1-1 libaec-dev=1.0.6-1 libaec0=1.0.6-1 libann-dev=1.1.2+doc-7 libann0=1.1.2+doc-7 libantlr3c-3.4-0=3.4+dfsg-4 libantlr3c-dev=3.4+dfsg-4 libarchive-zip-perl=1.68-1 libasan6=11.2.0-19 libatomic1=12-20220319-1 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libbinutils=2.38-3 libblas3=3.10.0-2 libblkid1=2.37.3-1+b1 libboost-atomic1.74-dev=1.74.0-14 libboost-atomic1.74.0=1.74.0-14 libboost-chrono1.74-dev=1.74.0-14 libboost-chrono1.74.0=1.74.0-14 libboost-date-time1.74-dev=1.74.0-14 libboost-date-time1.74.0=1.74.0-14 libboost-dev=1.74.0.3 libboost-numpy-dev=1.74.0.3 libboost-numpy1.74-dev=1.74.0-14 libboost-numpy1.74.0=1.74.0-14 libboost-python-dev=1.74.0.3 libboost-python1.74-dev=1.74.0-14 libboost-python1.74.0=1.74.0-14 libboost-serialization1.74-dev=1.74.0-14 libboost-serialization1.74.0=1.74.0-14 libboost-system1.74-dev=1.74.0-14 libboost-system1.74.0=1.74.0-14 libboost-thread-dev=1.74.0.3 libboost-thread1.74-dev=1.74.0-14 libboost-thread1.74.0=1.74.0-14 libboost1.74-dev=1.74.0-14 libbrotli1=1.0.9-2+b3 libbsd0=0.11.5-1+b1 libbz2-1.0=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcbf-dev=0.9.6+dfsg1-3+b1 libcbf1=0.9.6+dfsg1-3+b1 libcc1-0=12-20220319-1 libccp4-data=6.5.1-5 libccp4-dev=6.5.1-5 libccp4c0=6.5.1-5 libccp4f0=6.5.1-5 libclipper-dev=2.1.20201109-1 libclipper2=2.1.20201109-1 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-3 libctf0=2.38-3 libcurl3-gnutls=7.82.0-2 libcurl4=7.82.0-2 libcurl4-openssl-dev=7.82.0-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.6 libdeflate0=1.10-2 libdpkg-perl=1.21.5 libeigen3-dev=3.4.0-2 libelf1=0.186-1 libevent-core-2.1-7=2.1.12-stable-1 libevent-pthreads-2.1-7=2.1.12-stable-1 libexpat1=2.4.7-1 libexpat1-dev=2.4.7-1 libfabric1=1.11.0-3 libffi8=3.4.2-4 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 libfile-stripnondeterminism-perl=1.13.0-1 libfontconfig1=2.13.1-4.4 libfreetype6=2.11.1+dfsg-1 libfribidi0=1.0.8-2 libgcc-10-dev=10.3.0-15 libgcc-11-dev=11.2.0-19 libgcc-s1=12-20220319-1 libgcrypt20=1.9.4-5 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgfortran5=12-20220319-1 libglib2.0-0=2.72.0-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.3-4+b1 libgomp1=12-20220319-1 libgpg-error0=1.43-3 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.19.2-2+b1 libharfbuzz0b=2.7.4-1 libhdf5-103-1=1.10.7+repack-4 libhdf5-cpp-103-1=1.10.7+repack-4 libhdf5-dev=1.10.7+repack-4 libhdf5-fortran-102=1.10.7+repack-4 libhdf5-hl-100=1.10.7+repack-4 libhdf5-hl-cpp-100=1.10.7+repack-4 libhdf5-hl-fortran-100=1.10.7+repack-4 libhogweed6=3.7.3-1 libhwloc-plugins=2.7.1-1 libhwloc15=2.7.1-1 libibverbs1=39.0-1+b1 libicu67=67.1-7 libidn2-0=2.3.2-2 libimagequant0=2.17.0-1 libisl23=0.24-2 libitm1=12-20220319-1 libjbig0=2.1-3.1+b2 libjpeg-dev=1:2.1.2-1 libjpeg62-turbo=1:2.1.2-1 libjpeg62-turbo-dev=1:2.1.2-1 libjq1=1.6-2.1 libjs-jquery=3.6.0+dfsg+~3.5.13-1 libjs-jquery-ui=1.13.1+dfsg-1 libjs-sphinxdoc=4.3.2-1 libjs-underscore=1.13.2~dfsg-2 libk5crypto3=1.19.2-2+b1 libkeyutils1=1.6.1-3 libkrb5-3=1.19.2-2+b1 libkrb5support0=1.19.2-2+b1 liblapack3=3.10.0-2 liblbfgsb0=3.0+dfsg.3-10 liblcms2-2=2.12~rc1-2 libldap-2.5-0=2.5.11+dfsg-1 liblsan0=12-20220319-1 liblz4-1=1.9.3-2 liblz4-dev=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-3 libmagic1=1:5.41-3 libmd0=1.0.4-1 libmmdb2-0=2.0.22-1 libmmdb2-dev=2.0.22-1 libmount1=2.37.3-1+b1 libmpc3=1.2.1-2 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncursesw6=6.3-2 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnl-3-200=3.5.0-0.1 libnl-route-3-200=3.5.0-0.1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnuma1=2.0.14-3 libonig5=6.9.7.1-2 libopenjp2-7=2.4.0-6 libopenmpi3=4.1.2-2 libp11-kit0=0.24.0-6 libpam-modules=1.4.0-11 libpam-modules-bin=1.4.0-11 libpam-runtime=1.4.0-11 libpam0g=1.4.0-11 libpciaccess0=0.16-3 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libperl5.34=5.34.0-3 libpipeline1=1.5.5-1 libpmix2=4.1.2-2 libpng16-16=1.6.37-3 libpsl5=0.21.0-1.2 libpsm-infinipath1=3.3+20.604758e7-6.1 libpsm2-2=11.2.185-1 libpython3-all-dev=3.10.4-1 libpython3-dev=3.10.4-1 libpython3-stdlib=3.10.4-1 libpython3.10=3.10.4-1 libpython3.10-dev=3.10.4-1 libpython3.10-minimal=3.10.4-1 libpython3.10-stdlib=3.10.4-1 libpython3.9=3.9.12-1 libpython3.9-dev=3.9.12-1 libpython3.9-minimal=3.9.12-1 libpython3.9-stdlib=3.9.12-1 libqhull-r8.0=2020.2-4 libquadmath0=12-20220319-1 libraqm0=0.7.0-4 librdmacm1=39.0-1+b1 libreadline8=8.1.2-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.28+dfsg-2+b1 libsasl2-modules-db=2.1.28+dfsg-2+b1 libseccomp2=2.5.3-2 libselinux1=3.3-1+b2 libsemanage-common=3.3-1 libsemanage2=3.3-1+b2 libsepol2=3.3-1 libsigsegv2=2.14-1 libsmartcols1=2.37.3-1+b1 libsqlite3-0=3.38.2-1 libssh2-1=1.10.0-3 libssl-dev=1.1.1n-1 libssl1.1=1.1.1n-1 libstdc++-11-dev=11.2.0-19 libstdc++6=12-20220319-1 libsub-override-perl=0.09-2 libsystemd0=250.4-1 libsz2=1.0.6-1 libtasn1-6=4.18.0-4 libtcl8.6=8.6.12+dfsg-1 libtiff5=4.3.0-6 libtinfo6=6.3-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtk8.6=8.6.12-1 libtool=2.4.7-2 libtsan0=11.2.0-19 libubsan1=12-20220319-1 libuchardet0=0.0.7-1 libucx0=1.12.1-1 libudev1=250.4-1 libunistring2=1.0-1 libuuid1=2.37.3-1+b1 libwebp7=1.2.2-2+b1 libwebpdemux2=1.2.2-2+b1 libwebpmux3=1.2.2-2+b1 libx11-6=2:1.7.2-2+b1 libx11-data=2:1.7.2-2 libxau6=1:1.0.9-1 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.4-1 libxft2=2.3.2-2 libxml2=2.9.13+dfsg-1 libxnvctrl0=470.103.01-1 libxrender1=1:0.9.10-1 libxslt1.1=1.1.34-4 libxss1=1:1.2.3-1 libzstd1=1.4.9+dfsg-1 linux-libc-dev=5.16.14-1 login=1:4.11.1+dfsg1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.2-1 mawk=1.3.4.20200120-3+b1 media-types=7.0.0 ncurses-base=6.3-2 ncurses-bin=6.3-2 ocl-icd-libopencl1=2.2.14-3 passwd=1:4.11.1+dfsg1-2 patch=2.7.6-7 perl=5.34.0-3 perl-base=5.34.0-3 perl-modules-5.34=5.34.0-3 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 python-matplotlib-data=3.5.1-2 python3=3.10.4-1 python3-all=3.10.4-1 python3-all-dev=3.10.4-1 python3-appdirs=1.4.4-2 python3-attr=21.2.0-1 python3-biopython=1.79+dfsg-3 python3-brotli=1.0.9-2+b3 python3-cycler=0.11.0-1 python3-dateutil=2.8.1-6 python3-decorator=4.4.2-2 python3-dev=3.10.4-1 python3-distutils=3.9.12-1 python3-fonttools=4.29.1-2 python3-fs=2.4.12-1 python3-future=0.18.2-5 python3-kiwisolver=1.3.2-1+b1 python3-lib2to3=3.9.12-1 python3-lxml=4.8.0-1 python3-lz4=3.1.3+dfsg-1+b1 python3-matplotlib=3.5.1-2+b1 python3-minimal=3.10.4-1 python3-mpmath=1.2.1-2 python3-msgpack=1.0.3-1 python3-numpy=1:1.21.5-1 python3-packaging=21.3-1 python3-pil=9.0.1-1 python3-pil.imagetk=9.0.1-1 python3-pkg-resources=59.6.0-1.2 python3-psutil=5.9.0-1 python3-pyparsing=3.0.7-1 python3-renderpm=3.6.8-1 python3-reportlab=3.6.8-1 python3-reportlab-accel=3.6.8-1 python3-scipy=1.7.3-2 python3-setuptools=59.6.0-1.2 python3-six=1.16.0-3 python3-sympy=1.9-1 python3-tk=3.9.12-1 python3-tz=2022.1-1 python3-ufolib2=0.13.1+dfsg1-1 python3-unicodedata2=14.0.0+ds-8 python3.10=3.10.4-1 python3.10-dev=3.10.4-1 python3.10-minimal=3.10.4-1 python3.9=3.9.12-1 python3.9-dev=3.9.12-1 python3.9-minimal=3.9.12-1 readline-common=8.1.2-1 rpcsvc-proto=1.4.2-4 scons=4.0.1+dfsg-2 sed=4.8-1 sensible-utils=0.0.17 sfftw-dev=2.1.5-6 sfftw2=2.1.5-6 sgml-base=1.30 sysvinit-utils=3.01-1 tar=1.34+dfsg-1 tk8.6-blt2.5=2.5.3+dfsg-4.1 tzdata=2022a-1 ucf=3.0043 unicode-data=14.0.0-1.1 util-linux=2.37.3-1+b1 w3c-sgml-lib=1.3-2 x11-common=1:7.7+23 xml-core=0.18+nmu1 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-4 zlib1g-dev=1:1.2.11.dfsg-4 --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/20220403T030457Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220403T030457Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220329T085355Z/ 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 cctbx=2021.12+ds1-4 && mkdir -p /build/cctbx-TO2hyq && dpkg-source --no-check -x /*.dsc /build/cctbx-TO2hyq/cctbx-2021.12+ds1 && chown -R builduser:builduser /build/cctbx-TO2hyq" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/cctbx-TO2hyq/cctbx-2021.12+ds1 && env DEB_BUILD_OPTIONS="parallel=6" LANG="en_GB.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1648545375" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/cctbx-TO2hyq /tmp/cctbx-2021.12+ds1-46t9gz55i bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220329T085355Z 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.De5lYqQBmC 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.De5lYqQBmC Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.3-1+b1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 135 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220329T085355Z unstable/main amd64 libfakeroot amd64 1.28-1 [48.2 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220329T085355Z unstable/main amd64 fakeroot amd64 1.28-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 kB in 0s (680 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 ... 4702 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.28-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.28-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.28-1_amd64.deb ... Unpacking fakeroot (1.28-1) ... Setting up libfakeroot:amd64 (1.28-1) ... Setting up fakeroot (1.28-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-7) ... 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/20220403T030457Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220403T030457Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220329T085355Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.De5lYqQBmC Get:1 http://snapshot.notset.fr/archive/debian/20220403T030457Z bookworm InRelease [130 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20220329T085355Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20220403T030457Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220403T030457Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220403T030457Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220403T030457Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220403T030457Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220403T030457Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20220403T030457Z bookworm/main Sources [11.9 MB] Get:4 http://snapshot.notset.fr/archive/debian/20220403T030457Z bookworm/main amd64 Packages [11.3 MB] Fetched 23.4 MB in 20s (1164 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.De5lYqQBmC I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d cctbx=2021.12+ds1-4 && mkdir -p /build/cctbx-TO2hyq && dpkg-source --no-check -x /*.dsc /build/cctbx-TO2hyq/cctbx-2021.12+ds1 && chown -R builduser:builduser /build/cctbx-TO2hyq"' exec /tmp/mmdebstrap.De5lYqQBmC Reading package lists... NOTICE: 'cctbx' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/science-team/cctbx.git Please use: git clone https://salsa.debian.org/science-team/cctbx.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 22.2 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220403T030457Z bookworm/main cctbx 2021.12+ds1-4 (dsc) [2727 B] Get:2 http://snapshot.notset.fr/archive/debian/20220403T030457Z bookworm/main cctbx 2021.12+ds1-4 (tar) [22.2 MB] Get:3 http://snapshot.notset.fr/archive/debian/20220403T030457Z bookworm/main cctbx 2021.12+ds1-4 (diff) [23.3 kB] Fetched 22.2 MB in 17s (1285 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'cctbx_2021.12+ds1-4.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting cctbx in /build/cctbx-TO2hyq/cctbx-2021.12+ds1 dpkg-source: info: unpacking cctbx_2021.12+ds1.orig.tar.xz dpkg-source: info: unpacking cctbx_2021.12+ds1-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying scons_soname.patch dpkg-source: info: applying workaround_env_config.patch dpkg-source: info: applying adding-setup_py.patch dpkg-source: info: applying system_libs.patch dpkg-source: info: applying reproducible-timestamp.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/cctbx-TO2hyq/cctbx-2021.12+ds1 && env DEB_BUILD_OPTIONS="parallel=6" LANG="en_GB.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1648545375" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.De5lYqQBmC dpkg-buildpackage: info: source package cctbx dpkg-buildpackage: info: source version 2021.12+ds1-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Neil Williams dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/cctbx-TO2hyq/cctbx-2021.12+ds1' dh_auto_clean W: pybuild base:266: missing command (plugin=custom, method=clean, interpreter=python3.9, version=3.9) W: pybuild base:266: missing command (plugin=custom, method=clean, interpreter=python3.10, version=3.10) rm -f -r /build/cctbx-TO2hyq/cctbx-2021.12+ds1/build find . -name __pycache__ -type d -exec rm -rf {} \; make[1]: Leaving directory '/build/cctbx-TO2hyq/cctbx-2021.12+ds1' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild W: pybuild base:266: missing command (plugin=custom, method=configure, interpreter=python3.9, version=3.9) W: pybuild base:266: missing command (plugin=custom, method=configure, interpreter=python3.10, version=3.10) debian/rules override_dh_auto_build make[1]: Entering directory '/build/cctbx-TO2hyq/cctbx-2021.12+ds1' python3 setup.py build /build/cctbx-TO2hyq/cctbx-2021.12+ds1/setup.py:1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.core import setup, Extension running build running build_py file cctbx/stdlib.py (for module stdlib) not found creating build creating build/lib.linux-x86_64-3.10 creating build/lib.linux-x86_64-3.10/boost copying with modification boost_adaptbx/boost/__init__.py -> build/lib.linux-x86_64-3.10/boost/__init__.py copying with modification boost_adaptbx/boost/optional.py -> build/lib.linux-x86_64-3.10/boost/optional.py copying with modification boost_adaptbx/boost/python.py -> build/lib.linux-x86_64-3.10/boost/python.py copying with modification boost_adaptbx/boost/rational.py -> build/lib.linux-x86_64-3.10/boost/rational.py copying with modification boost_adaptbx/boost/std_pair.py -> build/lib.linux-x86_64-3.10/boost/std_pair.py copying with modification boost_adaptbx/boost/tuple.py -> build/lib.linux-x86_64-3.10/boost/tuple.py creating build/lib.linux-x86_64-3.10/clipper copying with modification clipper_adaptbx/clipper/__init__.py -> build/lib.linux-x86_64-3.10/clipper/__init__.py copying with modification clipper_adaptbx/clipper/tst_hendrickson_lattman.py -> build/lib.linux-x86_64-3.10/clipper/tst_hendrickson_lattman.py copying with modification clipper_adaptbx/clipper/tst_sigmaa.py -> build/lib.linux-x86_64-3.10/clipper/tst_sigmaa.py creating build/lib.linux-x86_64-3.10/adp_restraints copying with modification cctbx/adp_restraints/__init__.py -> build/lib.linux-x86_64-3.10/adp_restraints/__init__.py copying with modification cctbx/adp_restraints/energies.py -> build/lib.linux-x86_64-3.10/adp_restraints/energies.py copying with modification cctbx/adp_restraints/flags.py -> build/lib.linux-x86_64-3.10/adp_restraints/flags.py copying with modification cctbx/adp_restraints/tst_ext.py -> build/lib.linux-x86_64-3.10/adp_restraints/tst_ext.py creating build/lib.linux-x86_64-3.10/array_family copying cctbx/array_family/__init__.py -> build/lib.linux-x86_64-3.10/array_family copying with modification cctbx/array_family/flex.py -> build/lib.linux-x86_64-3.10/array_family/flex.py creating build/lib.linux-x86_64-3.10/command_line copying cctbx/command_line/__init__.py -> build/lib.linux-x86_64-3.10/command_line copying with modification cctbx/command_line/auto_sharpen.py -> build/lib.linux-x86_64-3.10/command_line/auto_sharpen.py copying with modification cctbx/command_line/brehm_diederichs.py -> build/lib.linux-x86_64-3.10/command_line/brehm_diederichs.py copying with modification cctbx/command_line/cctbx_test_nightly.py -> build/lib.linux-x86_64-3.10/command_line/cctbx_test_nightly.py copying with modification cctbx/command_line/cod_select_and_pickle.py -> build/lib.linux-x86_64-3.10/command_line/cod_select_and_pickle.py copying with modification cctbx/command_line/diffuse.py -> build/lib.linux-x86_64-3.10/command_line/diffuse.py copying with modification cctbx/command_line/eltbx.show_fp_fdp.py -> build/lib.linux-x86_64-3.10/command_line/eltbx.show_fp_fdp.py copying with modification cctbx/command_line/euclidean_model_matching.py -> build/lib.linux-x86_64-3.10/command_line/euclidean_model_matching.py copying with modification cctbx/command_line/find_reticular_twin_laws.py -> build/lib.linux-x86_64-3.10/command_line/find_reticular_twin_laws.py copying with modification cctbx/command_line/form_factor_query.py -> build/lib.linux-x86_64-3.10/command_line/form_factor_query.py copying with modification cctbx/command_line/precession_view.py -> build/lib.linux-x86_64-3.10/command_line/precession_view.py copying with modification cctbx/command_line/samosa_join.py -> build/lib.linux-x86_64-3.10/command_line/samosa_join.py copying with modification cctbx/command_line/samosa_scale.py -> build/lib.linux-x86_64-3.10/command_line/samosa_scale.py copying with modification cctbx/command_line/segment_and_split_map.py -> build/lib.linux-x86_64-3.10/command_line/segment_and_split_map.py copying with modification cctbx/command_line/space_group_info.py -> build/lib.linux-x86_64-3.10/command_line/space_group_info.py copying with modification cctbx/command_line/structure_factor_timings.py -> build/lib.linux-x86_64-3.10/command_line/structure_factor_timings.py copying with modification cctbx/command_line/subgroups.py -> build/lib.linux-x86_64-3.10/command_line/subgroups.py copying with modification cctbx/command_line/version.py -> build/lib.linux-x86_64-3.10/command_line/version.py copying with modification cctbx/command_line/wavelength_units.py -> build/lib.linux-x86_64-3.10/command_line/wavelength_units.py copying with modification cctbx/command_line/xray_structure.show.py -> build/lib.linux-x86_64-3.10/command_line/xray_structure.show.py creating build/lib.linux-x86_64-3.10/covariance copying with modification cctbx/covariance/__init__.py -> build/lib.linux-x86_64-3.10/covariance/__init__.py creating build/lib.linux-x86_64-3.10/crystal copying with modification cctbx/crystal/__init__.py -> build/lib.linux-x86_64-3.10/crystal/__init__.py copying with modification cctbx/crystal/burzlaff_zimmermann_dewolff.py -> build/lib.linux-x86_64-3.10/crystal/burzlaff_zimmermann_dewolff.py copying with modification cctbx/crystal/close_packing.py -> build/lib.linux-x86_64-3.10/crystal/close_packing.py copying with modification cctbx/crystal/coordination_sequences.py -> build/lib.linux-x86_64-3.10/crystal/coordination_sequences.py copying with modification cctbx/crystal/direct_space_asu.py -> build/lib.linux-x86_64-3.10/crystal/direct_space_asu.py copying with modification cctbx/crystal/distance_based_connectivity.py -> build/lib.linux-x86_64-3.10/crystal/distance_based_connectivity.py copying with modification cctbx/crystal/find_best_cell.py -> build/lib.linux-x86_64-3.10/crystal/find_best_cell.py copying with modification cctbx/crystal/reindex.py -> build/lib.linux-x86_64-3.10/crystal/reindex.py copying with modification cctbx/crystal/super_cell.py -> build/lib.linux-x86_64-3.10/crystal/super_cell.py copying with modification cctbx/crystal/tst_distance_based_connectivity.py -> build/lib.linux-x86_64-3.10/crystal/tst_distance_based_connectivity.py copying with modification cctbx/crystal/tst_ext.py -> build/lib.linux-x86_64-3.10/crystal/tst_ext.py copying with modification cctbx/crystal/tst_super_cell.py -> build/lib.linux-x86_64-3.10/crystal/tst_super_cell.py creating build/lib.linux-x86_64-3.10/development copying cctbx/development/__init__.py -> build/lib.linux-x86_64-3.10/development copying with modification cctbx/development/approx_amplitude_vs_resolution.py -> build/lib.linux-x86_64-3.10/development/approx_amplitude_vs_resolution.py copying with modification cctbx/development/cns_density_modification.py -> build/lib.linux-x86_64-3.10/development/cns_density_modification.py copying with modification cctbx/development/create_models_or_maps.py -> build/lib.linux-x86_64-3.10/development/create_models_or_maps.py copying with modification cctbx/development/debug_utils.py -> build/lib.linux-x86_64-3.10/development/debug_utils.py copying with modification cctbx/development/direct_or_fft.py -> build/lib.linux-x86_64-3.10/development/direct_or_fft.py copying with modification cctbx/development/electron_density_sampling.py -> build/lib.linux-x86_64-3.10/development/electron_density_sampling.py copying with modification cctbx/development/fmt_utils.py -> build/lib.linux-x86_64-3.10/development/fmt_utils.py copying with modification cctbx/development/github.py -> build/lib.linux-x86_64-3.10/development/github.py copying with modification cctbx/development/make_cns_input.py -> build/lib.linux-x86_64-3.10/development/make_cns_input.py copying with modification cctbx/development/make_settings.py -> build/lib.linux-x86_64-3.10/development/make_settings.py copying with modification cctbx/development/random_structure.py -> build/lib.linux-x86_64-3.10/development/random_structure.py copying with modification cctbx/development/run_shelx.py -> build/lib.linux-x86_64-3.10/development/run_shelx.py copying with modification cctbx/development/run_shelx76.py -> build/lib.linux-x86_64-3.10/development/run_shelx76.py copying with modification cctbx/development/space_group_option_parser.py -> build/lib.linux-x86_64-3.10/development/space_group_option_parser.py copying with modification cctbx/development/structure_factor_utils.py -> build/lib.linux-x86_64-3.10/development/structure_factor_utils.py copying with modification cctbx/development/tst_cns_epsilon.py -> build/lib.linux-x86_64-3.10/development/tst_cns_epsilon.py copying with modification cctbx/development/tst_cns_hl.py -> build/lib.linux-x86_64-3.10/development/tst_cns_hl.py creating build/lib.linux-x86_64-3.10/eltbx copying cctbx/eltbx/__init__.py -> build/lib.linux-x86_64-3.10/eltbx copying with modification cctbx/eltbx/attenuation_coefficient.py -> build/lib.linux-x86_64-3.10/eltbx/attenuation_coefficient.py copying with modification cctbx/eltbx/chemical_elements.py -> build/lib.linux-x86_64-3.10/eltbx/chemical_elements.py copying with modification cctbx/eltbx/covalent_radii.py -> build/lib.linux-x86_64-3.10/eltbx/covalent_radii.py copying with modification cctbx/eltbx/distance_based_connectivity.py -> build/lib.linux-x86_64-3.10/eltbx/distance_based_connectivity.py copying with modification cctbx/eltbx/e_scattering.py -> build/lib.linux-x86_64-3.10/eltbx/e_scattering.py copying with modification cctbx/eltbx/formula.py -> build/lib.linux-x86_64-3.10/eltbx/formula.py copying with modification cctbx/eltbx/fp_fdp.py -> build/lib.linux-x86_64-3.10/eltbx/fp_fdp.py copying with modification cctbx/eltbx/gaussian_fit.py -> build/lib.linux-x86_64-3.10/eltbx/gaussian_fit.py copying with modification cctbx/eltbx/henke.py -> build/lib.linux-x86_64-3.10/eltbx/henke.py copying with modification cctbx/eltbx/icsd_radii.py -> build/lib.linux-x86_64-3.10/eltbx/icsd_radii.py copying with modification cctbx/eltbx/neutron.py -> build/lib.linux-x86_64-3.10/eltbx/neutron.py copying with modification cctbx/eltbx/read_custom_scattering_dict.py -> build/lib.linux-x86_64-3.10/eltbx/read_custom_scattering_dict.py copying with modification cctbx/eltbx/sasaki.py -> build/lib.linux-x86_64-3.10/eltbx/sasaki.py copying with modification cctbx/eltbx/tiny_pse.py -> build/lib.linux-x86_64-3.10/eltbx/tiny_pse.py copying with modification cctbx/eltbx/van_der_waals_radii.py -> build/lib.linux-x86_64-3.10/eltbx/van_der_waals_radii.py copying with modification cctbx/eltbx/wavelengths.py -> build/lib.linux-x86_64-3.10/eltbx/wavelengths.py creating build/lib.linux-x86_64-3.10/examples copying cctbx/examples/__init__.py -> build/lib.linux-x86_64-3.10/examples copying with modification cctbx/examples/adp_symmetry_constraints.py -> build/lib.linux-x86_64-3.10/examples/adp_symmetry_constraints.py copying with modification cctbx/examples/all_axes.py -> build/lib.linux-x86_64-3.10/examples/all_axes.py copying with modification cctbx/examples/analyze_adp.py -> build/lib.linux-x86_64-3.10/examples/analyze_adp.py copying with modification cctbx/examples/ccp4_map.py -> build/lib.linux-x86_64-3.10/examples/ccp4_map.py copying with modification cctbx/examples/change_hand_p31.py -> build/lib.linux-x86_64-3.10/examples/change_hand_p31.py copying with modification cctbx/examples/convert_ccp4_symop_lib.py -> build/lib.linux-x86_64-3.10/examples/convert_ccp4_symop_lib.py copying with modification cctbx/examples/cr2o3_consistency_checks.py -> build/lib.linux-x86_64-3.10/examples/cr2o3_consistency_checks.py copying with modification cctbx/examples/cr2o3_primitive_cell.py -> build/lib.linux-x86_64-3.10/examples/cr2o3_primitive_cell.py copying with modification cctbx/examples/exp_i_alpha_derivatives.py -> build/lib.linux-x86_64-3.10/examples/exp_i_alpha_derivatives.py copying with modification cctbx/examples/f_model_example.py -> build/lib.linux-x86_64-3.10/examples/f_model_example.py copying with modification cctbx/examples/fft_map_electron_density_around_atom.py -> build/lib.linux-x86_64-3.10/examples/fft_map_electron_density_around_atom.py copying with modification cctbx/examples/find_distances_using_cpp_objects.py -> build/lib.linux-x86_64-3.10/examples/find_distances_using_cpp_objects.py copying with modification cctbx/examples/find_sys_abs_equiv_space_groups.py -> build/lib.linux-x86_64-3.10/examples/find_sys_abs_equiv_space_groups.py copying with modification cctbx/examples/g_exp_i_alpha_derivatives.py -> build/lib.linux-x86_64-3.10/examples/g_exp_i_alpha_derivatives.py copying with modification cctbx/examples/g_exp_i_partial_derivatives.py -> build/lib.linux-x86_64-3.10/examples/g_exp_i_partial_derivatives.py copying with modification cctbx/examples/getting_started.py -> build/lib.linux-x86_64-3.10/examples/getting_started.py copying with modification cctbx/examples/hirshfeld_test.py -> build/lib.linux-x86_64-3.10/examples/hirshfeld_test.py copying with modification cctbx/examples/le_page_1982_vs_lebedev_2005.py -> build/lib.linux-x86_64-3.10/examples/le_page_1982_vs_lebedev_2005.py copying with modification cctbx/examples/lebedev_2005_perturbation.py -> build/lib.linux-x86_64-3.10/examples/lebedev_2005_perturbation.py copying with modification cctbx/examples/list_non_principal_continuous_shifts.py -> build/lib.linux-x86_64-3.10/examples/list_non_principal_continuous_shifts.py copying with modification cctbx/examples/location_part.py -> build/lib.linux-x86_64-3.10/examples/location_part.py copying with modification cctbx/examples/map_skewness.py -> build/lib.linux-x86_64-3.10/examples/map_skewness.py copying with modification cctbx/examples/maximum_subgroups.py -> build/lib.linux-x86_64-3.10/examples/maximum_subgroups.py copying with modification cctbx/examples/miller_common_sets.py -> build/lib.linux-x86_64-3.10/examples/miller_common_sets.py copying with modification cctbx/examples/miller_transform.py -> build/lib.linux-x86_64-3.10/examples/miller_transform.py copying with modification cctbx/examples/neutron_structure_factors.py -> build/lib.linux-x86_64-3.10/examples/neutron_structure_factors.py copying with modification cctbx/examples/phase_o_phrenia.py -> build/lib.linux-x86_64-3.10/examples/phase_o_phrenia.py copying with modification cctbx/examples/quartz_structure.py -> build/lib.linux-x86_64-3.10/examples/quartz_structure.py copying with modification cctbx/examples/random_f_calc.py -> build/lib.linux-x86_64-3.10/examples/random_f_calc.py copying with modification cctbx/examples/random_puckers.py -> build/lib.linux-x86_64-3.10/examples/random_puckers.py copying with modification cctbx/examples/reduced_cell_two_folds.py -> build/lib.linux-x86_64-3.10/examples/reduced_cell_two_folds.py copying with modification cctbx/examples/site_symmetry_constraints.py -> build/lib.linux-x86_64-3.10/examples/site_symmetry_constraints.py copying with modification cctbx/examples/site_symmetry_table.py -> build/lib.linux-x86_64-3.10/examples/site_symmetry_table.py copying with modification cctbx/examples/space_group_matrices.py -> build/lib.linux-x86_64-3.10/examples/space_group_matrices.py copying with modification cctbx/examples/space_subgroups.py -> build/lib.linux-x86_64-3.10/examples/space_subgroups.py copying with modification cctbx/examples/steve_collins.py -> build/lib.linux-x86_64-3.10/examples/steve_collins.py copying with modification cctbx/examples/structure_factor_derivatives.py -> build/lib.linux-x86_64-3.10/examples/structure_factor_derivatives.py copying with modification cctbx/examples/structure_factor_derivatives_2.py -> build/lib.linux-x86_64-3.10/examples/structure_factor_derivatives_2.py copying with modification cctbx/examples/structure_factor_derivatives_3.py -> build/lib.linux-x86_64-3.10/examples/structure_factor_derivatives_3.py copying with modification cctbx/examples/structure_factor_derivatives_4.py -> build/lib.linux-x86_64-3.10/examples/structure_factor_derivatives_4.py copying with modification cctbx/examples/sub_group_graph.py -> build/lib.linux-x86_64-3.10/examples/sub_group_graph.py copying with modification cctbx/examples/symops_530.py -> build/lib.linux-x86_64-3.10/examples/symops_530.py copying with modification cctbx/examples/trigonal_r_vs_tetragonal_i.py -> build/lib.linux-x86_64-3.10/examples/trigonal_r_vs_tetragonal_i.py copying with modification cctbx/examples/tst_exp_i_alpha_derivatives.py -> build/lib.linux-x86_64-3.10/examples/tst_exp_i_alpha_derivatives.py copying with modification cctbx/examples/tst_g_exp_i_alpha_derivatives.py -> build/lib.linux-x86_64-3.10/examples/tst_g_exp_i_alpha_derivatives.py copying with modification cctbx/examples/tst_phase_o_phrenia.py -> build/lib.linux-x86_64-3.10/examples/tst_phase_o_phrenia.py copying with modification cctbx/examples/tst_space_subgroups.py -> build/lib.linux-x86_64-3.10/examples/tst_space_subgroups.py copying with modification cctbx/examples/tst_structure_factor_derivatives.py -> build/lib.linux-x86_64-3.10/examples/tst_structure_factor_derivatives.py copying with modification cctbx/examples/tst_structure_factor_derivatives_2.py -> build/lib.linux-x86_64-3.10/examples/tst_structure_factor_derivatives_2.py copying with modification cctbx/examples/tst_structure_factor_derivatives_3.py -> build/lib.linux-x86_64-3.10/examples/tst_structure_factor_derivatives_3.py copying with modification cctbx/examples/tst_structure_factor_derivatives_4.py -> build/lib.linux-x86_64-3.10/examples/tst_structure_factor_derivatives_4.py copying with modification cctbx/examples/unit_cell_minimizers.py -> build/lib.linux-x86_64-3.10/examples/unit_cell_minimizers.py copying with modification cctbx/examples/unit_cell_refinement.py -> build/lib.linux-x86_64-3.10/examples/unit_cell_refinement.py copying with modification cctbx/examples/view_fft_map.py -> build/lib.linux-x86_64-3.10/examples/view_fft_map.py creating build/lib.linux-x86_64-3.10/geometry copying with modification cctbx/geometry/__init__.py -> build/lib.linux-x86_64-3.10/geometry/__init__.py creating build/lib.linux-x86_64-3.10/geometry_restraints copying with modification cctbx/geometry_restraints/__init__.py -> build/lib.linux-x86_64-3.10/geometry_restraints/__init__.py copying with modification cctbx/geometry_restraints/auto_linking_types.py -> build/lib.linux-x86_64-3.10/geometry_restraints/auto_linking_types.py copying with modification cctbx/geometry_restraints/base_geometry.py -> build/lib.linux-x86_64-3.10/geometry_restraints/base_geometry.py copying with modification cctbx/geometry_restraints/distance_least_squares.py -> build/lib.linux-x86_64-3.10/geometry_restraints/distance_least_squares.py copying with modification cctbx/geometry_restraints/energies.py -> build/lib.linux-x86_64-3.10/geometry_restraints/energies.py copying with modification cctbx/geometry_restraints/flags.py -> build/lib.linux-x86_64-3.10/geometry_restraints/flags.py copying with modification cctbx/geometry_restraints/lbfgs.py -> build/lib.linux-x86_64-3.10/geometry_restraints/lbfgs.py copying with modification cctbx/geometry_restraints/linking_class.py -> build/lib.linux-x86_64-3.10/geometry_restraints/linking_class.py copying with modification cctbx/geometry_restraints/manager.py -> build/lib.linux-x86_64-3.10/geometry_restraints/manager.py copying with modification cctbx/geometry_restraints/nonbonded_overlaps.py -> build/lib.linux-x86_64-3.10/geometry_restraints/nonbonded_overlaps.py copying with modification cctbx/geometry_restraints/process_nonbonded_proxies.py -> build/lib.linux-x86_64-3.10/geometry_restraints/process_nonbonded_proxies.py copying with modification cctbx/geometry_restraints/standard_cif_links.py -> build/lib.linux-x86_64-3.10/geometry_restraints/standard_cif_links.py copying with modification cctbx/geometry_restraints/tst_angle_derivs.py -> build/lib.linux-x86_64-3.10/geometry_restraints/tst_angle_derivs.py copying with modification cctbx/geometry_restraints/tst_ext.py -> build/lib.linux-x86_64-3.10/geometry_restraints/tst_ext.py copying with modification cctbx/geometry_restraints/tst_motif.py -> build/lib.linux-x86_64-3.10/geometry_restraints/tst_motif.py copying with modification cctbx/geometry_restraints/tst_nonbonded_overlaps.py -> build/lib.linux-x86_64-3.10/geometry_restraints/tst_nonbonded_overlaps.py copying with modification cctbx/geometry_restraints/tst_process_nonbonded_proxies.py -> build/lib.linux-x86_64-3.10/geometry_restraints/tst_process_nonbonded_proxies.py copying with modification cctbx/geometry_restraints/tst_proxy_registry.py -> build/lib.linux-x86_64-3.10/geometry_restraints/tst_proxy_registry.py creating build/lib.linux-x86_64-3.10/macro_mol copying cctbx/macro_mol/__init__.py -> build/lib.linux-x86_64-3.10/macro_mol copying with modification cctbx/macro_mol/rotation_parameters.py -> build/lib.linux-x86_64-3.10/macro_mol/rotation_parameters.py creating build/lib.linux-x86_64-3.10/maptbx copying with modification cctbx/maptbx/__init__.py -> build/lib.linux-x86_64-3.10/maptbx/__init__.py copying with modification cctbx/maptbx/auto_sharpen.py -> build/lib.linux-x86_64-3.10/maptbx/auto_sharpen.py copying with modification cctbx/maptbx/bcr.py -> build/lib.linux-x86_64-3.10/maptbx/bcr.py copying with modification cctbx/maptbx/box.py -> build/lib.linux-x86_64-3.10/maptbx/box.py copying with modification cctbx/maptbx/map_symmetry.py -> build/lib.linux-x86_64-3.10/maptbx/map_symmetry.py copying with modification cctbx/maptbx/mask.py -> build/lib.linux-x86_64-3.10/maptbx/mask.py copying with modification cctbx/maptbx/mem.py -> build/lib.linux-x86_64-3.10/maptbx/mem.py copying with modification cctbx/maptbx/minimization.py -> build/lib.linux-x86_64-3.10/maptbx/minimization.py copying with modification cctbx/maptbx/prepare_map_for_docking.py -> build/lib.linux-x86_64-3.10/maptbx/prepare_map_for_docking.py copying with modification cctbx/maptbx/real_space_refinement_simple.py -> build/lib.linux-x86_64-3.10/maptbx/real_space_refinement_simple.py copying with modification cctbx/maptbx/refine_scales_errors.py -> build/lib.linux-x86_64-3.10/maptbx/refine_scales_errors.py copying with modification cctbx/maptbx/refine_sharpening.py -> build/lib.linux-x86_64-3.10/maptbx/refine_sharpening.py copying with modification cctbx/maptbx/resolution_from_map_and_model.py -> build/lib.linux-x86_64-3.10/maptbx/resolution_from_map_and_model.py copying with modification cctbx/maptbx/segment_and_split_map.py -> build/lib.linux-x86_64-3.10/maptbx/segment_and_split_map.py copying with modification cctbx/maptbx/tst_asymmetric_map.py -> build/lib.linux-x86_64-3.10/maptbx/tst_asymmetric_map.py copying with modification cctbx/maptbx/tst_atom_curves.py -> build/lib.linux-x86_64-3.10/maptbx/tst_atom_curves.py copying with modification cctbx/maptbx/tst_atom_radius_as_central_peak_width.py -> build/lib.linux-x86_64-3.10/maptbx/tst_atom_radius_as_central_peak_width.py copying with modification cctbx/maptbx/tst_bcr.py -> build/lib.linux-x86_64-3.10/maptbx/tst_bcr.py copying with modification cctbx/maptbx/tst_ccp.py -> build/lib.linux-x86_64-3.10/maptbx/tst_ccp.py copying with modification cctbx/maptbx/tst_get_percentile_cutoffs.py -> build/lib.linux-x86_64-3.10/maptbx/tst_get_percentile_cutoffs.py copying with modification cctbx/maptbx/tst_interpolation.py -> build/lib.linux-x86_64-3.10/maptbx/tst_interpolation.py copying with modification cctbx/maptbx/tst_interpolation_2.py -> build/lib.linux-x86_64-3.10/maptbx/tst_interpolation_2.py copying with modification cctbx/maptbx/tst_map_peak_3d_as_2d.py -> build/lib.linux-x86_64-3.10/maptbx/tst_map_peak_3d_as_2d.py copying with modification cctbx/maptbx/tst_mask.py -> build/lib.linux-x86_64-3.10/maptbx/tst_mask.py copying with modification cctbx/maptbx/tst_peak_volume_estimate.py -> build/lib.linux-x86_64-3.10/maptbx/tst_peak_volume_estimate.py copying with modification cctbx/maptbx/tst_real_space_refinement_simple.py -> build/lib.linux-x86_64-3.10/maptbx/tst_real_space_refinement_simple.py copying with modification cctbx/maptbx/tst_resolution_from_map_and_model.py -> build/lib.linux-x86_64-3.10/maptbx/tst_resolution_from_map_and_model.py copying with modification cctbx/maptbx/tst_target_and_gradients.py -> build/lib.linux-x86_64-3.10/maptbx/tst_target_and_gradients.py creating build/lib.linux-x86_64-3.10/masks copying with modification cctbx/masks/__init__.py -> build/lib.linux-x86_64-3.10/masks/__init__.py creating build/lib.linux-x86_64-3.10/merging copying with modification cctbx/merging/__init__.py -> build/lib.linux-x86_64-3.10/merging/__init__.py copying with modification cctbx/merging/brehm_diederichs.py -> build/lib.linux-x86_64-3.10/merging/brehm_diederichs.py creating build/lib.linux-x86_64-3.10/miller copying with modification cctbx/miller/__init__.py -> build/lib.linux-x86_64-3.10/miller/__init__.py copying with modification cctbx/miller/display.py -> build/lib.linux-x86_64-3.10/miller/display.py copying with modification cctbx/miller/display2.py -> build/lib.linux-x86_64-3.10/miller/display2.py copying with modification cctbx/miller/reindexing.py -> build/lib.linux-x86_64-3.10/miller/reindexing.py copying with modification cctbx/miller/tst_map_to_asu_isym.py -> build/lib.linux-x86_64-3.10/miller/tst_map_to_asu_isym.py copying with modification cctbx/miller/tst_reindexing.py -> build/lib.linux-x86_64-3.10/miller/tst_reindexing.py creating build/lib.linux-x86_64-3.10/neutron copying with modification cctbx/neutron/__init__.py -> build/lib.linux-x86_64-3.10/neutron/__init__.py creating build/lib.linux-x86_64-3.10/omz copying with modification cctbx/omz/__init__.py -> build/lib.linux-x86_64-3.10/omz/__init__.py copying with modification cctbx/omz/bfgs.py -> build/lib.linux-x86_64-3.10/omz/bfgs.py copying with modification cctbx/omz/cif_refine.py -> build/lib.linux-x86_64-3.10/omz/cif_refine.py copying with modification cctbx/omz/cod_refine.py -> build/lib.linux-x86_64-3.10/omz/cod_refine.py copying with modification cctbx/omz/cod_select_and_pickle.py -> build/lib.linux-x86_64-3.10/omz/cod_select_and_pickle.py copying with modification cctbx/omz/dev.py -> build/lib.linux-x86_64-3.10/omz/dev.py copying with modification cctbx/omz/eval_iso_vs_refined.py -> build/lib.linux-x86_64-3.10/omz/eval_iso_vs_refined.py copying with modification cctbx/omz/pdb_dev.py -> build/lib.linux-x86_64-3.10/omz/pdb_dev.py copying with modification cctbx/omz/tardy_adaptor.py -> build/lib.linux-x86_64-3.10/omz/tardy_adaptor.py copying with modification cctbx/omz/tst_bfgs.py -> build/lib.linux-x86_64-3.10/omz/tst_bfgs.py copying with modification cctbx/omz/tst_dev.py -> build/lib.linux-x86_64-3.10/omz/tst_dev.py creating build/lib.linux-x86_64-3.10/regression copying cctbx/regression/__init__.py -> build/lib.linux-x86_64-3.10/regression copying with modification cctbx/regression/tst_adp_aniso_restraints.py -> build/lib.linux-x86_64-3.10/regression/tst_adp_aniso_restraints.py copying with modification cctbx/regression/tst_adp_constraints.py -> build/lib.linux-x86_64-3.10/regression/tst_adp_constraints.py copying with modification cctbx/regression/tst_adp_constraints_cartesian.py -> build/lib.linux-x86_64-3.10/regression/tst_adp_constraints_cartesian.py copying with modification cctbx/regression/tst_amplitude_normalisation.py -> build/lib.linux-x86_64-3.10/regression/tst_amplitude_normalisation.py copying with modification cctbx/regression/tst_change_basis.py -> build/lib.linux-x86_64-3.10/regression/tst_change_basis.py copying with modification cctbx/regression/tst_connectivity.py -> build/lib.linux-x86_64-3.10/regression/tst_connectivity.py copying with modification cctbx/regression/tst_connectivity_allsym.py -> build/lib.linux-x86_64-3.10/regression/tst_connectivity_allsym.py copying with modification cctbx/regression/tst_coordination_sequences.py -> build/lib.linux-x86_64-3.10/regression/tst_coordination_sequences.py copying with modification cctbx/regression/tst_create_models_or_maps.py -> build/lib.linux-x86_64-3.10/regression/tst_create_models_or_maps.py copying with modification cctbx/regression/tst_crystal.py -> build/lib.linux-x86_64-3.10/regression/tst_crystal.py copying with modification cctbx/regression/tst_crystal_asu_clusters.py -> build/lib.linux-x86_64-3.10/regression/tst_crystal_asu_clusters.py copying with modification cctbx/regression/tst_crystal_close_packing.py -> build/lib.linux-x86_64-3.10/regression/tst_crystal_close_packing.py copying with modification cctbx/regression/tst_diffuse.py -> build/lib.linux-x86_64-3.10/regression/tst_diffuse.py copying with modification cctbx/regression/tst_direct_scaling.py -> build/lib.linux-x86_64-3.10/regression/tst_direct_scaling.py copying with modification cctbx/regression/tst_direct_space_asu.py -> build/lib.linux-x86_64-3.10/regression/tst_direct_space_asu.py copying with modification cctbx/regression/tst_emma.py -> build/lib.linux-x86_64-3.10/regression/tst_emma.py copying with modification cctbx/regression/tst_expand_to_p1.py -> build/lib.linux-x86_64-3.10/regression/tst_expand_to_p1.py copying with modification cctbx/regression/tst_f_model.py -> build/lib.linux-x86_64-3.10/regression/tst_f_model.py copying with modification cctbx/regression/tst_fast_nv1995.py -> build/lib.linux-x86_64-3.10/regression/tst_fast_nv1995.py copying with modification cctbx/regression/tst_fcalc_fft_stability.py -> build/lib.linux-x86_64-3.10/regression/tst_fcalc_fft_stability.py copying with modification cctbx/regression/tst_find_best_cell.py -> build/lib.linux-x86_64-3.10/regression/tst_find_best_cell.py copying with modification cctbx/regression/tst_fourier_transform_real_part_at_x.py -> build/lib.linux-x86_64-3.10/regression/tst_fourier_transform_real_part_at_x.py copying with modification cctbx/regression/tst_french_wilson.py -> build/lib.linux-x86_64-3.10/regression/tst_french_wilson.py copying with modification cctbx/regression/tst_geometry_restraints.py -> build/lib.linux-x86_64-3.10/regression/tst_geometry_restraints.py copying with modification cctbx/regression/tst_geometry_restraints_2.py -> build/lib.linux-x86_64-3.10/regression/tst_geometry_restraints_2.py copying with modification cctbx/regression/tst_geometry_restraints_lbfgs.py -> build/lib.linux-x86_64-3.10/regression/tst_geometry_restraints_lbfgs.py copying with modification cctbx/regression/tst_grm_modifications.py -> build/lib.linux-x86_64-3.10/regression/tst_grm_modifications.py copying with modification cctbx/regression/tst_grm_pickling.py -> build/lib.linux-x86_64-3.10/regression/tst_grm_pickling.py copying with modification cctbx/regression/tst_grouped_data.py -> build/lib.linux-x86_64-3.10/regression/tst_grouped_data.py copying with modification cctbx/regression/tst_itvb_2001_table_a1427_hall_symbols.py -> build/lib.linux-x86_64-3.10/regression/tst_itvb_2001_table_a1427_hall_symbols.py copying with modification cctbx/regression/tst_krivy_gruber.py -> build/lib.linux-x86_64-3.10/regression/tst_krivy_gruber.py copying with modification cctbx/regression/tst_loc_res.py -> build/lib.linux-x86_64-3.10/regression/tst_loc_res.py copying with modification cctbx/regression/tst_map_is_periodic.py -> build/lib.linux-x86_64-3.10/regression/tst_map_is_periodic.py copying with modification cctbx/regression/tst_map_weights_for_symmetry_summation.py -> build/lib.linux-x86_64-3.10/regression/tst_map_weights_for_symmetry_summation.py copying with modification cctbx/regression/tst_maptbx_box.py -> build/lib.linux-x86_64-3.10/regression/tst_maptbx_box.py copying with modification cctbx/regression/tst_maptbx_mask.py -> build/lib.linux-x86_64-3.10/regression/tst_maptbx_mask.py copying with modification cctbx/regression/tst_maptbx_structure_factors.py -> build/lib.linux-x86_64-3.10/regression/tst_maptbx_structure_factors.py copying with modification cctbx/regression/tst_math_module.py -> build/lib.linux-x86_64-3.10/regression/tst_math_module.py copying with modification cctbx/regression/tst_mem.py -> build/lib.linux-x86_64-3.10/regression/tst_mem.py copying with modification cctbx/regression/tst_mem_2.py -> build/lib.linux-x86_64-3.10/regression/tst_mem_2.py copying with modification cctbx/regression/tst_miller.py -> build/lib.linux-x86_64-3.10/regression/tst_miller.py copying with modification cctbx/regression/tst_miller_data_manipulation.py -> build/lib.linux-x86_64-3.10/regression/tst_miller_data_manipulation.py copying with modification cctbx/regression/tst_miller_double_step_filtration.py -> build/lib.linux-x86_64-3.10/regression/tst_miller_double_step_filtration.py copying with modification cctbx/regression/tst_miller_fft_map.py -> build/lib.linux-x86_64-3.10/regression/tst_miller_fft_map.py copying with modification cctbx/regression/tst_miller_lookup_utils.py -> build/lib.linux-x86_64-3.10/regression/tst_miller_lookup_utils.py copying with modification cctbx/regression/tst_miller_merge_equivalents.py -> build/lib.linux-x86_64-3.10/regression/tst_miller_merge_equivalents.py copying with modification cctbx/regression/tst_miller_statistics.py -> build/lib.linux-x86_64-3.10/regression/tst_miller_statistics.py copying with modification cctbx/regression/tst_pair_asu_table.py -> build/lib.linux-x86_64-3.10/regression/tst_pair_asu_table.py copying with modification cctbx/regression/tst_pointgroup_tools.py -> build/lib.linux-x86_64-3.10/regression/tst_pointgroup_tools.py copying with modification cctbx/regression/tst_prepare_map_for_docking.py -> build/lib.linux-x86_64-3.10/regression/tst_prepare_map_for_docking.py copying with modification cctbx/regression/tst_r_free_utils.py -> build/lib.linux-x86_64-3.10/regression/tst_r_free_utils.py copying with modification cctbx/regression/tst_reciprocal_space_asu.py -> build/lib.linux-x86_64-3.10/regression/tst_reciprocal_space_asu.py copying with modification cctbx/regression/tst_refine_xray_curvs.py -> build/lib.linux-x86_64-3.10/regression/tst_refine_xray_curvs.py copying with modification cctbx/regression/tst_reflection_statistics.py -> build/lib.linux-x86_64-3.10/regression/tst_reflection_statistics.py copying with modification cctbx/regression/tst_sampled_model_density.py -> build/lib.linux-x86_64-3.10/regression/tst_sampled_model_density.py copying with modification cctbx/regression/tst_sf_low_res_accuracy.py -> build/lib.linux-x86_64-3.10/regression/tst_sf_low_res_accuracy.py copying with modification cctbx/regression/tst_sgtbx.py -> build/lib.linux-x86_64-3.10/regression/tst_sgtbx.py copying with modification cctbx/regression/tst_sgtbx_denominators.py -> build/lib.linux-x86_64-3.10/regression/tst_sgtbx_denominators.py copying with modification cctbx/regression/tst_sgtbx_harker.py -> build/lib.linux-x86_64-3.10/regression/tst_sgtbx_harker.py copying with modification cctbx/regression/tst_sgtbx_lattice_symmetry.py -> build/lib.linux-x86_64-3.10/regression/tst_sgtbx_lattice_symmetry.py copying with modification cctbx/regression/tst_sgtbx_site_constraints.py -> build/lib.linux-x86_64-3.10/regression/tst_sgtbx_site_constraints.py copying with modification cctbx/regression/tst_sgtbx_special_op_simplifier.py -> build/lib.linux-x86_64-3.10/regression/tst_sgtbx_special_op_simplifier.py copying with modification cctbx/regression/tst_sgtbx_subgroups.py -> build/lib.linux-x86_64-3.10/regression/tst_sgtbx_subgroups.py copying with modification cctbx/regression/tst_sgtbx_tidy_pickling.py -> build/lib.linux-x86_64-3.10/regression/tst_sgtbx_tidy_pickling.py copying with modification cctbx/regression/tst_show_cosets.py -> build/lib.linux-x86_64-3.10/regression/tst_show_cosets.py copying with modification cctbx/regression/tst_space_group_type_tidy_cb_op_t.py -> build/lib.linux-x86_64-3.10/regression/tst_space_group_type_tidy_cb_op_t.py copying with modification cctbx/regression/tst_sphericity.py -> build/lib.linux-x86_64-3.10/regression/tst_sphericity.py copying with modification cctbx/regression/tst_statistics_graphs.py -> build/lib.linux-x86_64-3.10/regression/tst_statistics_graphs.py copying with modification cctbx/regression/tst_triplet_generator.py -> build/lib.linux-x86_64-3.10/regression/tst_triplet_generator.py copying with modification cctbx/regression/tst_twin_target.py -> build/lib.linux-x86_64-3.10/regression/tst_twin_target.py copying with modification cctbx/regression/tst_web_change_basis.py -> build/lib.linux-x86_64-3.10/regression/tst_web_change_basis.py copying with modification cctbx/regression/tst_weighting_schemes.py -> build/lib.linux-x86_64-3.10/regression/tst_weighting_schemes.py copying with modification cctbx/regression/tst_wilson_plot.py -> build/lib.linux-x86_64-3.10/regression/tst_wilson_plot.py copying with modification cctbx/regression/tst_xray.py -> build/lib.linux-x86_64-3.10/regression/tst_xray.py copying with modification cctbx/regression/tst_xray_derivatives.py -> build/lib.linux-x86_64-3.10/regression/tst_xray_derivatives.py copying with modification cctbx/regression/tst_xray_fast_gradients.py -> build/lib.linux-x86_64-3.10/regression/tst_xray_fast_gradients.py copying with modification cctbx/regression/tst_xray_minimization.py -> build/lib.linux-x86_64-3.10/regression/tst_xray_minimization.py copying with modification cctbx/regression/tst_xray_minimization_failure.py -> build/lib.linux-x86_64-3.10/regression/tst_xray_minimization_failure.py copying with modification cctbx/regression/tst_xray_target_functors.py -> build/lib.linux-x86_64-3.10/regression/tst_xray_target_functors.py creating build/lib.linux-x86_64-3.10/sgtbx copying with modification cctbx/sgtbx/__init__.py -> build/lib.linux-x86_64-3.10/sgtbx/__init__.py copying with modification cctbx/sgtbx/bravais_types.py -> build/lib.linux-x86_64-3.10/sgtbx/bravais_types.py copying with modification cctbx/sgtbx/cosets.py -> build/lib.linux-x86_64-3.10/sgtbx/cosets.py copying with modification cctbx/sgtbx/harker.py -> build/lib.linux-x86_64-3.10/sgtbx/harker.py copying with modification cctbx/sgtbx/lattice_symmetry.py -> build/lib.linux-x86_64-3.10/sgtbx/lattice_symmetry.py copying with modification cctbx/sgtbx/literal_description.py -> build/lib.linux-x86_64-3.10/sgtbx/literal_description.py copying with modification cctbx/sgtbx/plane_groups.py -> build/lib.linux-x86_64-3.10/sgtbx/plane_groups.py copying with modification cctbx/sgtbx/pointgroup_tools.py -> build/lib.linux-x86_64-3.10/sgtbx/pointgroup_tools.py copying with modification cctbx/sgtbx/rational_matrices_point_groups.py -> build/lib.linux-x86_64-3.10/sgtbx/rational_matrices_point_groups.py copying with modification cctbx/sgtbx/reticular_pg_tools.py -> build/lib.linux-x86_64-3.10/sgtbx/reticular_pg_tools.py copying with modification cctbx/sgtbx/reticular_twin_laws.py -> build/lib.linux-x86_64-3.10/sgtbx/reticular_twin_laws.py copying with modification cctbx/sgtbx/show_cosets.py -> build/lib.linux-x86_64-3.10/sgtbx/show_cosets.py copying with modification cctbx/sgtbx/sub_lattice_tools.py -> build/lib.linux-x86_64-3.10/sgtbx/sub_lattice_tools.py copying with modification cctbx/sgtbx/subgroups.py -> build/lib.linux-x86_64-3.10/sgtbx/subgroups.py copying with modification cctbx/sgtbx/symbol_confidence.py -> build/lib.linux-x86_64-3.10/sgtbx/symbol_confidence.py copying with modification cctbx/sgtbx/sys_abs_equiv.py -> build/lib.linux-x86_64-3.10/sgtbx/sys_abs_equiv.py creating build/lib.linux-x86_64-3.10/source_generators copying cctbx/source_generators/__init__.py -> build/lib.linux-x86_64-3.10/source_generators copying with modification cctbx/source_generators/flex_fwd_h.py -> build/lib.linux-x86_64-3.10/source_generators/flex_fwd_h.py creating build/lib.linux-x86_64-3.10/uctbx copying with modification cctbx/uctbx/__init__.py -> build/lib.linux-x86_64-3.10/uctbx/__init__.py copying with modification cctbx/uctbx/gruber_1973.py -> build/lib.linux-x86_64-3.10/uctbx/gruber_1973.py copying with modification cctbx/uctbx/gruber_1973_table_1.py -> build/lib.linux-x86_64-3.10/uctbx/gruber_1973_table_1.py copying with modification cctbx/uctbx/krivy_gruber_1976.py -> build/lib.linux-x86_64-3.10/uctbx/krivy_gruber_1976.py copying with modification cctbx/uctbx/reduction_base.py -> build/lib.linux-x86_64-3.10/uctbx/reduction_base.py creating build/lib.linux-x86_64-3.10/web copying cctbx/web/__init__.py -> build/lib.linux-x86_64-3.10/web copying with modification cctbx/web/all_axes.py -> build/lib.linux-x86_64-3.10/web/all_axes.py copying with modification cctbx/web/browse_settings.py -> build/lib.linux-x86_64-3.10/web/browse_settings.py copying with modification cctbx/web/cgi_utils.py -> build/lib.linux-x86_64-3.10/web/cgi_utils.py copying with modification cctbx/web/change_basis.py -> build/lib.linux-x86_64-3.10/web/change_basis.py copying with modification cctbx/web/change_hand.py -> build/lib.linux-x86_64-3.10/web/change_hand.py copying with modification cctbx/web/change_setting.py -> build/lib.linux-x86_64-3.10/web/change_setting.py copying with modification cctbx/web/dispatcher.py -> build/lib.linux-x86_64-3.10/web/dispatcher.py copying with modification cctbx/web/emma.py -> build/lib.linux-x86_64-3.10/web/emma.py copying with modification cctbx/web/explore_symmetry.py -> build/lib.linux-x86_64-3.10/web/explore_symmetry.py copying with modification cctbx/web/frac_cart.py -> build/lib.linux-x86_64-3.10/web/frac_cart.py copying with modification cctbx/web/io_utils.py -> build/lib.linux-x86_64-3.10/web/io_utils.py copying with modification cctbx/web/iotbx_cif_validate.py -> build/lib.linux-x86_64-3.10/web/iotbx_cif_validate.py copying with modification cctbx/web/lattice_symmetry.py -> build/lib.linux-x86_64-3.10/web/lattice_symmetry.py copying with modification cctbx/web/libtbx_help.py -> build/lib.linux-x86_64-3.10/web/libtbx_help.py copying with modification cctbx/web/multiple_cell.py -> build/lib.linux-x86_64-3.10/web/multiple_cell.py copying with modification cctbx/web/phase_o_phrenia.py -> build/lib.linux-x86_64-3.10/web/phase_o_phrenia.py copying with modification cctbx/web/replay.py -> build/lib.linux-x86_64-3.10/web/replay.py copying with modification cctbx/web/shelx.py -> build/lib.linux-x86_64-3.10/web/shelx.py copying with modification cctbx/web/structure_factors.py -> build/lib.linux-x86_64-3.10/web/structure_factors.py copying with modification cctbx/web/structure_factors_pdb.py -> build/lib.linux-x86_64-3.10/web/structure_factors_pdb.py copying with modification cctbx/web/wyckoff.py -> build/lib.linux-x86_64-3.10/web/wyckoff.py creating build/lib.linux-x86_64-3.10/xray copying with modification cctbx/xray/__init__.py -> build/lib.linux-x86_64-3.10/xray/__init__.py copying with modification cctbx/xray/ext.py -> build/lib.linux-x86_64-3.10/xray/ext.py copying with modification cctbx/xray/minimization.py -> build/lib.linux-x86_64-3.10/xray/minimization.py copying with modification cctbx/xray/observation_types.py -> build/lib.linux-x86_64-3.10/xray/observation_types.py copying with modification cctbx/xray/scatterer.py -> build/lib.linux-x86_64-3.10/xray/scatterer.py copying with modification cctbx/xray/structure.py -> build/lib.linux-x86_64-3.10/xray/structure.py copying with modification cctbx/xray/target_functors.py -> build/lib.linux-x86_64-3.10/xray/target_functors.py copying with modification cctbx/xray/weighting_schemes.py -> build/lib.linux-x86_64-3.10/xray/weighting_schemes.py creating build/lib.linux-x86_64-3.10/eltbx/development copying cctbx/eltbx/development/__init__.py -> build/lib.linux-x86_64-3.10/eltbx/development copying with modification cctbx/eltbx/development/combine_fits.py -> build/lib.linux-x86_64-3.10/eltbx/development/combine_fits.py copying with modification cctbx/eltbx/development/create_n_gaussian_raw_cpp.py -> build/lib.linux-x86_64-3.10/eltbx/development/create_n_gaussian_raw_cpp.py copying with modification cctbx/eltbx/development/e_scattering_plots.py -> build/lib.linux-x86_64-3.10/eltbx/development/e_scattering_plots.py copying with modification cctbx/eltbx/development/format_gaussian_fits.py -> build/lib.linux-x86_64-3.10/eltbx/development/format_gaussian_fits.py copying with modification cctbx/eltbx/development/hydrogen_plots.py -> build/lib.linux-x86_64-3.10/eltbx/development/hydrogen_plots.py copying with modification cctbx/eltbx/development/itvc_approx.py -> build/lib.linux-x86_64-3.10/eltbx/development/itvc_approx.py copying with modification cctbx/eltbx/development/itvc_cross_validation.py -> build/lib.linux-x86_64-3.10/eltbx/development/itvc_cross_validation.py copying with modification cctbx/eltbx/development/itvc_fits.py -> build/lib.linux-x86_64-3.10/eltbx/development/itvc_fits.py copying with modification cctbx/eltbx/development/itvc_kissel.py -> build/lib.linux-x86_64-3.10/eltbx/development/itvc_kissel.py copying with modification cctbx/eltbx/development/itvc_section61_io.py -> build/lib.linux-x86_64-3.10/eltbx/development/itvc_section61_io.py copying with modification cctbx/eltbx/development/kissel_fits.py -> build/lib.linux-x86_64-3.10/eltbx/development/kissel_fits.py copying with modification cctbx/eltbx/development/kissel_io.py -> build/lib.linux-x86_64-3.10/eltbx/development/kissel_io.py copying with modification cctbx/eltbx/development/rez_rez_grant.py -> build/lib.linux-x86_64-3.10/eltbx/development/rez_rez_grant.py creating build/lib.linux-x86_64-3.10/eltbx/xray_scattering copying with modification cctbx/eltbx/xray_scattering/__init__.py -> build/lib.linux-x86_64-3.10/eltbx/xray_scattering/__init__.py creating build/lib.linux-x86_64-3.10/examples/merging copying with modification cctbx/examples/merging/__init__.py -> build/lib.linux-x86_64-3.10/examples/merging/__init__.py copying with modification cctbx/examples/merging/data_subset.py -> build/lib.linux-x86_64-3.10/examples/merging/data_subset.py copying with modification cctbx/examples/merging/data_utilities.py -> build/lib.linux-x86_64-3.10/examples/merging/data_utilities.py copying with modification cctbx/examples/merging/show_results.py -> build/lib.linux-x86_64-3.10/examples/merging/show_results.py copying with modification cctbx/examples/merging/sigma_correction.py -> build/lib.linux-x86_64-3.10/examples/merging/sigma_correction.py copying with modification cctbx/examples/merging/task4.py -> build/lib.linux-x86_64-3.10/examples/merging/task4.py copying with modification cctbx/examples/merging/test1.py -> build/lib.linux-x86_64-3.10/examples/merging/test1.py copying with modification cctbx/examples/merging/test_cc_half.py -> build/lib.linux-x86_64-3.10/examples/merging/test_cc_half.py copying with modification cctbx/examples/merging/test_levenberg_sparse.py -> build/lib.linux-x86_64-3.10/examples/merging/test_levenberg_sparse.py copying with modification cctbx/examples/merging/tst_permutations.py -> build/lib.linux-x86_64-3.10/examples/merging/tst_permutations.py creating build/lib.linux-x86_64-3.10/examples/structure_factor_calculus copying cctbx/examples/structure_factor_calculus/__init__.py -> build/lib.linux-x86_64-3.10/examples/structure_factor_calculus copying with modification cctbx/examples/structure_factor_calculus/site_derivatives.py -> build/lib.linux-x86_64-3.10/examples/structure_factor_calculus/site_derivatives.py copying with modification cctbx/examples/structure_factor_calculus/sites_derivatives.py -> build/lib.linux-x86_64-3.10/examples/structure_factor_calculus/sites_derivatives.py copying with modification cctbx/examples/structure_factor_calculus/sites_least_squares_derivatives.py -> build/lib.linux-x86_64-3.10/examples/structure_factor_calculus/sites_least_squares_derivatives.py copying with modification cctbx/examples/structure_factor_calculus/u_star_derivatives.py -> build/lib.linux-x86_64-3.10/examples/structure_factor_calculus/u_star_derivatives.py creating build/lib.linux-x86_64-3.10/sgtbx/direct_space_asu copying with modification cctbx/sgtbx/direct_space_asu/__init__.py -> build/lib.linux-x86_64-3.10/sgtbx/direct_space_asu/__init__.py copying with modification cctbx/sgtbx/direct_space_asu/check_redundancies.py -> build/lib.linux-x86_64-3.10/sgtbx/direct_space_asu/check_redundancies.py copying with modification cctbx/sgtbx/direct_space_asu/cut_plane.py -> build/lib.linux-x86_64-3.10/sgtbx/direct_space_asu/cut_plane.py copying with modification cctbx/sgtbx/direct_space_asu/facet_analysis.py -> build/lib.linux-x86_64-3.10/sgtbx/direct_space_asu/facet_analysis.py copying with modification cctbx/sgtbx/direct_space_asu/plane_group_reference_table.py -> build/lib.linux-x86_64-3.10/sgtbx/direct_space_asu/plane_group_reference_table.py copying with modification cctbx/sgtbx/direct_space_asu/reference_table.py -> build/lib.linux-x86_64-3.10/sgtbx/direct_space_asu/reference_table.py copying with modification cctbx/sgtbx/direct_space_asu/short_cuts.py -> build/lib.linux-x86_64-3.10/sgtbx/direct_space_asu/short_cuts.py creating build/lib.linux-x86_64-3.10/source_generators/eltbx copying cctbx/source_generators/eltbx/__init__.py -> build/lib.linux-x86_64-3.10/source_generators/eltbx copying with modification cctbx/source_generators/eltbx/generate_henke_cpp.py -> build/lib.linux-x86_64-3.10/source_generators/eltbx/generate_henke_cpp.py copying with modification cctbx/source_generators/eltbx/generate_sasaki_cpp.py -> build/lib.linux-x86_64-3.10/source_generators/eltbx/generate_sasaki_cpp.py creating build/lib.linux-x86_64-3.10/uctbx/determine_unit_cell copying with modification cctbx/uctbx/determine_unit_cell/__init__.py -> build/lib.linux-x86_64-3.10/uctbx/determine_unit_cell/__init__.py creating build/lib.linux-x86_64-3.10/web/asu_gallery copying with modification cctbx/web/asu_gallery/__init__.py -> build/lib.linux-x86_64-3.10/web/asu_gallery/__init__.py copying with modification cctbx/web/asu_gallery/guide_to_notation.py -> build/lib.linux-x86_64-3.10/web/asu_gallery/guide_to_notation.py copying with modification cctbx/web/asu_gallery/jv_asu.py -> build/lib.linux-x86_64-3.10/web/asu_gallery/jv_asu.py copying with modification cctbx/web/asu_gallery/jv_index.py -> build/lib.linux-x86_64-3.10/web/asu_gallery/jv_index.py copying with modification cctbx/web/asu_gallery/jvx.py -> build/lib.linux-x86_64-3.10/web/asu_gallery/jvx.py copying with modification cctbx/web/asu_gallery/web_links.py -> build/lib.linux-x86_64-3.10/web/asu_gallery/web_links.py creating build/lib.linux-x86_64-3.10/xray/observations copying with modification cctbx/xray/observations/__init__.py -> build/lib.linux-x86_64-3.10/xray/observations/__init__.py copying with modification cctbx/xray/observations/tst_observations.py -> build/lib.linux-x86_64-3.10/xray/observations/tst_observations.py creating build/lib.linux-x86_64-3.10/xray/structure_factors copying with modification cctbx/xray/structure_factors/__init__.py -> build/lib.linux-x86_64-3.10/xray/structure_factors/__init__.py copying with modification cctbx/xray/structure_factors/from_scatterers.py -> build/lib.linux-x86_64-3.10/xray/structure_factors/from_scatterers.py copying with modification cctbx/xray/structure_factors/from_scatterers_direct.py -> build/lib.linux-x86_64-3.10/xray/structure_factors/from_scatterers_direct.py copying with modification cctbx/xray/structure_factors/from_scatterers_direct_parallel.py -> build/lib.linux-x86_64-3.10/xray/structure_factors/from_scatterers_direct_parallel.py copying with modification cctbx/xray/structure_factors/from_scatterers_fft.py -> build/lib.linux-x86_64-3.10/xray/structure_factors/from_scatterers_fft.py copying with modification cctbx/xray/structure_factors/global_counters.py -> build/lib.linux-x86_64-3.10/xray/structure_factors/global_counters.py copying with modification cctbx/xray/structure_factors/gradient_flags.py -> build/lib.linux-x86_64-3.10/xray/structure_factors/gradient_flags.py copying with modification cctbx/xray/structure_factors/gradients.py -> build/lib.linux-x86_64-3.10/xray/structure_factors/gradients.py copying with modification cctbx/xray/structure_factors/gradients_base.py -> build/lib.linux-x86_64-3.10/xray/structure_factors/gradients_base.py copying with modification cctbx/xray/structure_factors/gradients_direct.py -> build/lib.linux-x86_64-3.10/xray/structure_factors/gradients_direct.py copying with modification cctbx/xray/structure_factors/gradients_fft.py -> build/lib.linux-x86_64-3.10/xray/structure_factors/gradients_fft.py copying with modification cctbx/xray/structure_factors/manager.py -> build/lib.linux-x86_64-3.10/xray/structure_factors/manager.py copying with modification cctbx/xray/structure_factors/misc.py -> build/lib.linux-x86_64-3.10/xray/structure_factors/misc.py creating build/lib.linux-x86_64-3.10/xray/targets copying with modification cctbx/xray/targets/__init__.py -> build/lib.linux-x86_64-3.10/xray/targets/__init__.py copying with modification cctbx/xray/targets/r1.py -> build/lib.linux-x86_64-3.10/xray/targets/r1.py copying with modification cctbx/xray/targets/tst_r1.py -> build/lib.linux-x86_64-3.10/xray/targets/tst_r1.py copying with modification cctbx/xray/targets/tst_shelxl_wght_ls.py -> build/lib.linux-x86_64-3.10/xray/targets/tst_shelxl_wght_ls.py creating build/lib.linux-x86_64-3.10/examples/merging/samosa copying cctbx/examples/merging/samosa/__init__.py -> build/lib.linux-x86_64-3.10/examples/merging/samosa copying with modification cctbx/examples/merging/samosa/join.py -> build/lib.linux-x86_64-3.10/examples/merging/samosa/join.py copying with modification cctbx/examples/merging/samosa/per_lattice_postrefinement.py -> build/lib.linux-x86_64-3.10/examples/merging/samosa/per_lattice_postrefinement.py copying with modification cctbx/examples/merging/samosa/scale.py -> build/lib.linux-x86_64-3.10/examples/merging/samosa/scale.py creating build/lib.linux-x86_64-3.10/sgtbx/direct_space_asu/proto copying with modification cctbx/sgtbx/direct_space_asu/proto/__init__.py -> build/lib.linux-x86_64-3.10/sgtbx/direct_space_asu/proto/__init__.py copying with modification cctbx/sgtbx/direct_space_asu/proto/generate_cpp_asu_table.py -> build/lib.linux-x86_64-3.10/sgtbx/direct_space_asu/proto/generate_cpp_asu_table.py copying with modification cctbx/sgtbx/direct_space_asu/proto/tst_asu.py -> build/lib.linux-x86_64-3.10/sgtbx/direct_space_asu/proto/tst_asu.py file cctbx/stdlib.py (for module stdlib) not found running build_ext /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( Python: 3.10.4 "/usr/bin/python3" Compiler: default Build mode: release Warning level: 0 Precompiled Headers: False Static libraries: False Static exe: False Scan Boost headers: False Write full flex_fwd.h files: False Build Boost.Python extensions: True Define BOOST_PYTHON_NO_PY_SIGNATURES: False Define BOOST_PYTHON_BOOL_INT_STRICT: True Enable OpenMP if possible: False Boost threads enabled: True Enable CUDA: False Use conda: False Use opt_resources if available: False Use environment flags: False Enable C++11: False command_version_suffix: None Relocatable paths anchored at: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/temp.linux-x86_64-3.10/cctbx-build Top-down list of all modules involved: Creating files in build directory: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/temp.linux-x86_64-3.10/cctbx-build" dispatcher_include_template.sh dispatcher_head.sh setpaths.sh setpaths.csh setpaths_all.sh setpaths_all.csh setpaths_debug.sh unsetpaths.sh setpaths_debug.csh unsetpaths.csh SConstruct Makefile Regenerating module files in /build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/temp.linux-x86_64-3.10/base Base directory '/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/temp.linux-x86_64-3.10/base' does not exist. Assuming base-less installation, skipping module file regeneration /usr/bin/python3 /usr/bin/scons scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... scons: `.' is up to date. scons: done building targets. cd /build/cctbx-TO2hyq/cctbx-2021.12+ds1/build && python3 ../libtbx/configure.py --build=debug --use_environment_flags cctbx cbflib scitbx crys3d libtbx iotbx wxtbx smtbx Python: 3.10.4 "/usr/bin/python3" Compiler: default Build mode: debug Warning level: 0 Precompiled Headers: False Static libraries: False Static exe: False Scan Boost headers: False Write full flex_fwd.h files: False Build Boost.Python extensions: True Define BOOST_PYTHON_NO_PY_SIGNATURES: False Define BOOST_PYTHON_BOOL_INT_STRICT: True Enable OpenMP if possible: False Boost threads enabled: True Enable CUDA: False Use conda: False Use opt_resources if available: False Use environment flags: True Enable C++11: False CXXFLAGS = -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security CFLAGS = -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS = -Wdate-time -D_FORTIFY_SOURCE=2 LDFLAGS = -Wl,-z,relro command_version_suffix: None Relocatable paths anchored at: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/build Top-down list of all modules involved: wxtbx "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/wxtbx" iotbx "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx" smtbx "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx" ucif "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/ucif" crys3d "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/crys3d" cctbx "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx" scitbx "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx" fable "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable" omptbx "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/omptbx" boost+adaptbx "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost" "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx" tbxx "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/tbxx" chiltbx "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/chiltbx" libtbx "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/libtbx" Creating files in build directory: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build" dispatcher_include_template.sh dispatcher_head.sh setpaths.sh setpaths.csh setpaths_all.sh setpaths_all.csh setpaths_debug.sh unsetpaths.sh setpaths_debug.csh unsetpaths.csh SConstruct Makefile run_tests.csh Processing: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/libtbx/command_line" Processing: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/command_line" Processing: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable/command_line" Processing: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/command_line" Processing: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/command_line" Processing: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/crys3d/command_line" Processing: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/command_line" Processing: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/command_line" Processing: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/wxtbx/command_line" Processing: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/libtbx/libtbx_refresh.py" Processing: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/libtbx_refresh.py" Processing: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/libtbx_refresh.py" Generating C++ header files in: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include/scitbx/array_family" Generating C++ files in: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include/scitbx/array_family/boost_python" Using fable to convert scitbx/lbfgs.f Updating entry points for scitbx 1 entries for entry point pytest_randomly.random_seeder /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( Processing: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/libtbx_refresh.py" Generating C++ files in: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/cctbx/eltbx" Generating C++ files in: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include/cctbx/boost_python" Processing: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/crys3d/libtbx_refresh.py" Processing: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/libtbx_refresh.py" Generating C++ files in: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include/smtbx/boost_python" Processing: "/build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/libtbx_refresh.py" Using fable to convert iotbx/pdb/hybrid_36_f.f Writing: iotbx/pdb/hybrid_36_fem.cpp Regenerating module files in /build/cctbx-TO2hyq/cctbx-2021.12+ds1/base Base directory '/build/cctbx-TO2hyq/cctbx-2021.12+ds1/base' does not exist. Assuming base-less installation, skipping module file regeneration Done. cd /build/cctbx-TO2hyq/cctbx-2021.12+ds1/build && ./bin/libtbx.scons -j "10" scons: Reading SConscript files ... libtbx.scons: using flags from initial environment: CXXFLAGS = -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security CFLAGS = -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS = -Wdate-time -D_FORTIFY_SOURCE=2 LDFLAGS = -Wl,-z,relro libtbx.scons: OpenMP is disabled. BOOST_PYTHON_LIB_VERSION: boost_python310 BOOST_NUMPY_LIB_VERSION: boost_numpy310 BOOST_VERSION: 107400 Ignored: [Errno 2] No such file or directory: '/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/exe_dev/cctbx.getting_started' Ignored: [Errno 2] No such file or directory: '/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/exe_dev/cctbx.sym_equiv_sites' Ignored: [Errno 2] No such file or directory: '/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/exe_dev/cctbx.convert_ccp4_symop_lib' Ignored: [Errno 2] No such file or directory: '/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/exe_dev/cctbx.lattice_symmetry' Ignored: [Errno 2] No such file or directory: '/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/exe_dev/cctbx.find_distances' Ignored: [Errno 2] No such file or directory: '/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/exe_dev/cctbx.sys_abs_equiv_space_groups' scons: done reading SConscript files. scons: Building targets ... g++ -o boost_adaptbx/graph/breadth_first_search_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/breadth_first_search_ext.cpp g++ -o boost_adaptbx/graph/clustering_algorithm_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/clustering_algorithm_ext.cpp g++ -o boost_adaptbx/graph/connected_component_algorithm_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/connected_component_algorithm_ext.cpp g++ -o boost_adaptbx/graph/graph_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/graph_ext.cpp g++ -o boost_adaptbx/graph/graph_structure_comparison_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/graph_structure_comparison_ext.cpp g++ -o boost_adaptbx/graph/maximum_clique_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/maximum_clique_ext.cpp g++ -o boost_adaptbx/graph/metric_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/metric_ext.cpp g++ -o boost_adaptbx/graph/min_cut_max_flow_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/min_cut_max_flow_ext.cpp g++ -o boost_adaptbx/graph/utility_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/utility_ext.cpp g++ -o boost_adaptbx/hybrid_times_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/hybrid_times_ext.cpp g++ -o boost_adaptbx/meta_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/meta_ext.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/graph_type.hpp:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/connected_component_algorithm_ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/graph_type.hpp:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/graph_structure_comparison_ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/graph_type.hpp:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/clustering_algorithm_ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/graph_type.hpp:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/maximum_clique_ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/graph_type.hpp:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/breadth_first_search_ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/graph_type.hpp:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/graph_ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/graph_type.hpp:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/utility_ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/graph_type.hpp:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/metric_ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/graph_type.hpp:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/graph/min_cut_max_flow_ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ g++ -o boost_adaptbx/optional_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/optional_ext.cpp g++ -o boost_adaptbx/rational_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/rational_ext.cpp g++ -o boost_adaptbx/std_pair_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/std_pair_ext.cpp g++ -o boost_adaptbx/tests/boost_thread_test.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/tests/boost_thread_test.cpp g++ -o boost_adaptbx/tests/python_streambuf_test_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/tests/python_streambuf_test_ext.cpp g++ -o boost_adaptbx/tests/tst_optional_copy.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/tests/tst_optional_copy.cpp g++ -o boost_adaptbx/tuple_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/tuple_ext.cpp g++ -o boost_adaptbx/tests/tst_optional_copy -rdynamic -Wl,-z,relro -pthread boost_adaptbx/tests/tst_optional_copy.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system g++ -o cctbx/adp_restraints/adp_restraints_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/adp_restraints/adp_restraints_bpl.cpp g++ -o cctbx/adp_restraints/adp_restraints_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/adp_restraints/adp_restraints_ext.cpp g++ -o cctbx/adp_restraints/adp_similarity_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/adp_restraints/adp_similarity_bpl.cpp g++ -o cctbx/adp_restraints/aniso_restraints_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/adp_restraints/aniso_restraints_bpl.cpp g++ -o cctbx/adp_restraints/fixed_u_eq_adp_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/adp_restraints/fixed_u_eq_adp_bpl.cpp g++ -o cctbx/adp_restraints/isotropic_adp_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/adp_restraints/isotropic_adp_bpl.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/to_python_value.hpp:20, from /usr/include/boost/python/default_call_policies.hpp:10, from /usr/include/boost/python/make_function.hpp:10, from /usr/include/boost/python/def.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/boost_adaptbx/tests/python_streambuf_test_ext.cpp:2: /usr/include/boost/timer.hpp:21:1: note: ‘#pragma message: This header is deprecated. Use the facilities in instead.’ 21 | BOOST_HEADER_DEPRECATED( "the facilities in " ) | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o cctbx/adp_restraints/rigid_bond_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/adp_restraints/rigid_bond_bpl.cpp g++ -o cctbx/adp_restraints/rigu_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/adp_restraints/rigu_bpl.cpp g++ -o cctbx/adptbx/boost_python/adptbx_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/adptbx/boost_python/adptbx_ext.cpp g++ -o cctbx/adptbx/boost_python/anharmonic_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/adptbx/boost_python/anharmonic_ext.cpp g++ -o cctbx/adptbx/boost_python/hirshfeld.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/adptbx/boost_python/hirshfeld.cpp g++ -o cctbx/array_family/boost_python/flex_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/array_family/boost_python/flex_ext.cpp g++ -o cctbx/array_family/boost_python/flex_hendrickson_lattman.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/array_family/boost_python/flex_hendrickson_lattman.cpp g++ -o cctbx/array_family/boost_python/flex_miller_index.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/array_family/boost_python/flex_miller_index.cpp g++ -o cctbx/array_family/boost_python/flex_xray_scatterer.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/array_family/boost_python/flex_xray_scatterer.cpp g++ -o cctbx/boost_python/emma_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/boost_python/emma_ext.cpp g++ -o cctbx/boost_python/french_wilson_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/boost_python/french_wilson_ext.cpp g++ -o cctbx/boost_python/orientation_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/boost_python/orientation_ext.cpp g++ -o cctbx/boost_python/statistics_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/boost_python/statistics_ext.cpp g++ -o cctbx/covariance/boost_python/covariance_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/covariance/boost_python/covariance_ext.cpp g++ -o cctbx/crystal/asu_clusters_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/crystal/asu_clusters_bpl.cpp g++ -o cctbx/crystal/close_packing_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/crystal/close_packing_bpl.cpp g++ -o cctbx/crystal/coordination_sequences_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/crystal/coordination_sequences_bpl.cpp g++ -o cctbx/crystal/crystal_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/crystal/crystal_ext.cpp g++ -o cctbx/crystal/direct_space_asu_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/crystal/direct_space_asu_bpl.cpp g++ -o cctbx/crystal/incremental_pairs_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/crystal/incremental_pairs_bpl.cpp g++ -o cctbx/crystal/neighbors_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/crystal/neighbors_bpl.cpp g++ -o cctbx/crystal/pair_tables_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/crystal/pair_tables_bpl.cpp g++ -o cctbx/crystal/site_cluster_analysis_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/crystal/site_cluster_analysis_bpl.cpp g++ -o cctbx/crystal/symmetry_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/crystal/symmetry_bpl.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/crystal/incremental_pairs_bpl.cpp:3: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o cctbx/dmtbx/boost_python/dmtbx_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/dmtbx/boost_python/dmtbx_ext.cpp g++ -o cctbx/dmtbx/boost_python/triplet_generator.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/dmtbx/boost_python/triplet_generator.cpp g++ -o cctbx/dmtbx/boost_python/triplet_phase_relation.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/dmtbx/boost_python/triplet_phase_relation.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/crystal/site_cluster_analysis_bpl.cpp:3: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/crystal/symmetry_bpl.cpp:3: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o cctbx/eltbx/attenuation_coefficient.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/attenuation_coefficient.cpp g++ -o cctbx/eltbx/basic.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/basic.cpp g++ -o cctbx/eltbx/boost_python/attenuation_coefficient_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/boost_python/attenuation_coefficient_ext.cpp g++ -o cctbx/eltbx/boost_python/chemical_elements_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/boost_python/chemical_elements_ext.cpp g++ -o cctbx/eltbx/boost_python/covalent_radii_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/boost_python/covalent_radii_ext.cpp g++ -o cctbx/eltbx/boost_python/fp_fdp_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/boost_python/fp_fdp_ext.cpp g++ -o cctbx/eltbx/boost_python/henke_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/boost_python/henke_ext.cpp g++ -o cctbx/eltbx/boost_python/icsd_radii_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/boost_python/icsd_radii_ext.cpp g++ -o cctbx/eltbx/boost_python/neutron_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/boost_python/neutron_ext.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/boost_python/attenuation_coefficient_ext.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o cctbx/eltbx/boost_python/sasaki_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/boost_python/sasaki_ext.cpp g++ -o cctbx/eltbx/boost_python/tiny_pse_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/boost_python/tiny_pse_ext.cpp g++ -o cctbx/eltbx/boost_python/wavelengths_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/boost_python/wavelengths_ext.cpp g++ -o cctbx/eltbx/boost_python/xray_scattering_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/boost_python/xray_scattering_ext.cpp g++ -o cctbx/eltbx/covalent_radii.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/covalent_radii.cpp g++ -o cctbx/eltbx/electron_scattering/peng1996.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/electron_scattering/peng1996.cpp g++ -o cctbx/eltbx/fp_fdp.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/fp_fdp.cpp g++ -o cctbx/eltbx/henke.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include cctbx/eltbx/henke.cpp g++ -o cctbx/eltbx/henke_tables_01_12.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include cctbx/eltbx/henke_tables_01_12.cpp g++ -o cctbx/eltbx/henke_tables_13_24.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include cctbx/eltbx/henke_tables_13_24.cpp g++ -o cctbx/eltbx/henke_tables_25_36.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include cctbx/eltbx/henke_tables_25_36.cpp g++ -o cctbx/eltbx/henke_tables_37_48.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include cctbx/eltbx/henke_tables_37_48.cpp g++ -o cctbx/eltbx/henke_tables_49_60.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include cctbx/eltbx/henke_tables_49_60.cpp g++ -o cctbx/eltbx/henke_tables_61_72.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include cctbx/eltbx/henke_tables_61_72.cpp g++ -o cctbx/eltbx/henke_tables_73_84.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include cctbx/eltbx/henke_tables_73_84.cpp g++ -o cctbx/eltbx/henke_tables_85_92.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include cctbx/eltbx/henke_tables_85_92.cpp g++ -o cctbx/eltbx/icsd_radii.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/icsd_radii.cpp g++ -o cctbx/eltbx/neutron.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/neutron.cpp g++ -o cctbx/eltbx/sasaki.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include cctbx/eltbx/sasaki.cpp g++ -o cctbx/eltbx/sasaki_tables_01_12.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include cctbx/eltbx/sasaki_tables_01_12.cpp g++ -o cctbx/eltbx/sasaki_tables_13_24.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include cctbx/eltbx/sasaki_tables_13_24.cpp g++ -o cctbx/eltbx/sasaki_tables_25_36.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include cctbx/eltbx/sasaki_tables_25_36.cpp g++ -o cctbx/eltbx/sasaki_tables_37_48.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include cctbx/eltbx/sasaki_tables_37_48.cpp g++ -o cctbx/eltbx/sasaki_tables_49_60.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include cctbx/eltbx/sasaki_tables_49_60.cpp g++ -o cctbx/eltbx/sasaki_tables_61_72.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include cctbx/eltbx/sasaki_tables_61_72.cpp g++ -o cctbx/eltbx/sasaki_tables_73_82.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include cctbx/eltbx/sasaki_tables_73_82.cpp g++ -o cctbx/eltbx/tiny_pse.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/tiny_pse.cpp g++ -o cctbx/eltbx/wavelengths.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/wavelengths.cpp g++ -o cctbx/eltbx/xray_scattering/it1992.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/xray_scattering/it1992.cpp g++ -o cctbx/eltbx/xray_scattering/n_gaussian.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/xray_scattering/n_gaussian.cpp g++ -o cctbx/eltbx/xray_scattering/n_gaussian_raw.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/xray_scattering/n_gaussian_raw.cpp g++ -o cctbx/eltbx/xray_scattering/wk1995.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/eltbx/xray_scattering/wk1995.cpp g++ -o cctbx/examples/convert_ccp4_symop_lib.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Icctbx/examples -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/examples /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/examples/convert_ccp4_symop_lib.cpp g++ -o cctbx/examples/find_distances.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Icctbx/examples -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/examples /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/examples/find_distances.cpp g++ -o cctbx/examples/getting_started.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Icctbx/examples -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/examples /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/examples/getting_started.cpp g++ -o cctbx/examples/lattice_symmetry.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Icctbx/examples -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/examples /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/examples/lattice_symmetry.cpp g++ -o cctbx/examples/sym_equiv_sites.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Icctbx/examples -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/examples /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/examples/sym_equiv_sites.cpp g++ -o cctbx/examples/sys_abs_equiv_space_groups.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Icctbx/examples -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/examples /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/examples/sys_abs_equiv_space_groups.cpp g++ -o cctbx/geometry/boost_python/geometry_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/geometry/boost_python/geometry_ext.cpp g++ -o cctbx/geometry_restraints/angle_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/geometry_restraints/angle_bpl.cpp g++ -o cctbx/geometry_restraints/bond_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/geometry_restraints/bond_bpl.cpp g++ -o cctbx/geometry_restraints/bond_similarity_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/geometry_restraints/bond_similarity_bpl.cpp g++ -o cctbx/geometry_restraints/bond_sorted_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/geometry_restraints/bond_sorted_bpl.cpp g++ -o cctbx/geometry_restraints/chirality_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/geometry_restraints/chirality_bpl.cpp g++ -o cctbx/geometry_restraints/dihedral_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/geometry_restraints/dihedral_bpl.cpp g++ -o cctbx/geometry_restraints/geometry_restraints_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/geometry_restraints/geometry_restraints_ext.cpp g++ -o cctbx/geometry_restraints/motif_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/geometry_restraints/motif_bpl.cpp g++ -o cctbx/geometry_restraints/nonbonded_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/geometry_restraints/nonbonded_bpl.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/geometry_restraints/bond_sorted_bpl.cpp:3: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /usr/include/boost/python/tuple.hpp:10, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/geometry_restraints/shared_wrapper_pickle.hpp:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/geometry_restraints/bond_bpl.cpp:2: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o cctbx/geometry_restraints/nonbonded_sorted_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/geometry_restraints/nonbonded_sorted_bpl.cpp g++ -o cctbx/geometry_restraints/parallelity_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/geometry_restraints/parallelity_bpl.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/geometry_restraints/motif_bpl.cpp:3: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o cctbx/geometry_restraints/planarity_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/geometry_restraints/planarity_bpl.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/geometry_restraints/nonbonded_sorted_bpl.cpp:3: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o cctbx/maptbx/asymmetric_map.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/maptbx/asymmetric_map.cpp g++ -o cctbx/maptbx/asymmetric_map_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/maptbx/asymmetric_map_ext.cpp g++ -o cctbx/maptbx/boost_python/coordinate_transformers.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/maptbx/boost_python/coordinate_transformers.cpp g++ -o cctbx/maptbx/boost_python/grid_indices_around_sites.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/maptbx/boost_python/grid_indices_around_sites.cpp g++ -o cctbx/maptbx/boost_python/grid_tags.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/maptbx/boost_python/grid_tags.cpp g++ -o cctbx/maptbx/boost_python/gridding.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/maptbx/boost_python/gridding.cpp g++ -o cctbx/maptbx/boost_python/maptbx_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/maptbx/boost_python/maptbx_ext.cpp g++ -o cctbx/maptbx/boost_python/misc.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/maptbx/boost_python/misc.cpp g++ -o cctbx/maptbx/boost_python/peak_search.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/maptbx/boost_python/peak_search.cpp g++ -o cctbx/maptbx/boost_python/pymol_interface.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/maptbx/boost_python/pymol_interface.cpp g++ -o cctbx/maptbx/boost_python/statistics.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/maptbx/boost_python/statistics.cpp g++ -o cctbx/maptbx/boost_python/structure_factors.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/maptbx/boost_python/structure_factors.cpp g++ -o cctbx/masks/boost_python/masks_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/masks/boost_python/masks_ext.cpp g++ -o cctbx/math/boost_python/math_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/math/boost_python/math_ext.cpp g++ -o cctbx/math/time_trigonometry.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/math/time_trigonometry.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/smart_ptr/shared_array.hpp:24, from /usr/include/boost/shared_array.hpp:17, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/math/cos_sin_table.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/math/time_trigonometry.cpp:1: /usr/include/boost/timer.hpp:21:1: note: ‘#pragma message: This header is deprecated. Use the facilities in instead.’ 21 | BOOST_HEADER_DEPRECATED( "the facilities in " ) | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o cctbx/miller/asu.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/asu.cpp g++ -o cctbx/miller/bins.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/bins.cpp g++ -o cctbx/miller/index_generator.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/index_generator.cpp g++ -o cctbx/miller/index_span.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/index_span.cpp g++ -o cctbx/miller/match_bijvoet_mates.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/match_bijvoet_mates.cpp g++ -o cctbx/miller/match_indices.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/match_indices.cpp g++ -o cctbx/miller/match_multi_indices.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/match_multi_indices.cpp g++ -o cctbx/miller/sym_equiv.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/sym_equiv.cpp g++ -o cctbx/sgtbx/bricks.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/bricks.cpp g++ -o cctbx/sgtbx/change_of_basis_op.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/change_of_basis_op.cpp g++ -o cctbx/sgtbx/find_affine.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/find_affine.cpp g++ -o cctbx/sgtbx/group_codes.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/group_codes.cpp g++ -o cctbx/sgtbx/hall_in.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/hall_in.cpp g++ -o cctbx/sgtbx/lattice_tr.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/lattice_tr.cpp g++ -o cctbx/sgtbx/lattice_symmetry.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/lattice_symmetry.cpp g++ -o cctbx/sgtbx/miller.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/miller.cpp g++ -o cctbx/sgtbx/reciprocal_space_asu.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/reciprocal_space_asu.cpp g++ -o cctbx/sgtbx/reciprocal_space_ref_asu.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/reciprocal_space_ref_asu.cpp g++ -o cctbx/sgtbx/rot_mx.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/rot_mx.cpp g++ -o cctbx/sgtbx/rot_mx_info.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/rot_mx_info.cpp g++ -o cctbx/sgtbx/row_echelon_solve.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/row_echelon_solve.cpp g++ -o cctbx/sgtbx/rt_mx.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/rt_mx.cpp g++ -o cctbx/sgtbx/select_generators.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/select_generators.cpp g++ -o cctbx/sgtbx/seminvariant.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/seminvariant.cpp g++ -o cctbx/sgtbx/site_symmetry.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/site_symmetry.cpp g++ -o cctbx/sgtbx/space_group.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/space_group.cpp g++ -o cctbx/sgtbx/space_group_type.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/space_group_type.cpp g++ -o cctbx/sgtbx/symbols.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/symbols.cpp g++ -o cctbx/sgtbx/tensor_rank_2.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/tensor_rank_2.cpp g++ -o cctbx/sgtbx/tr_group.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/tr_group.cpp g++ -o cctbx/sgtbx/tr_vec.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/tr_vec.cpp g++ -o cctbx/sgtbx/utils.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/utils.cpp g++ -o cctbx/sgtbx/wyckoff.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/wyckoff.cpp g++ -o cctbx/sgtbx/reference_settings/hall_symbol_table.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/reference_settings/hall_symbol_table.cpp g++ -o cctbx/sgtbx/reference_settings/matrix_group_code_table.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/reference_settings/matrix_group_code_table.cpp g++ -o cctbx/sgtbx/reference_settings/normalizer.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/reference_settings/normalizer.cpp g++ -o cctbx/sgtbx/reference_settings/wyckoff.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/reference_settings/wyckoff.cpp g++ -o cctbx/uctbx/uctbx.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/uctbx/uctbx.cpp g++ -o cctbx/uctbx/spoil_optimization.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/uctbx/spoil_optimization.cpp g++ -o cctbx/uctbx/crystal_orientation.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/uctbx/crystal_orientation.cpp g++ -o cctbx/merging/ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/merging/ext.cpp g++ -o cctbx/miller/boost_python/amplitude_normalisation.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/boost_python/amplitude_normalisation.cpp g++ -o cctbx/miller/boost_python/asu.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/boost_python/asu.cpp g++ -o cctbx/miller/boost_python/bins.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/boost_python/bins.cpp g++ -o cctbx/miller/boost_python/change_basis.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/boost_python/change_basis.cpp g++ -o cctbx/miller/boost_python/expand_to_p1.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/boost_python/expand_to_p1.cpp g++ -o cctbx/miller/boost_python/f_calc_map.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/boost_python/f_calc_map.cpp g++ -o cctbx/miller/boost_python/index_generator.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/boost_python/index_generator.cpp g++ -o lib/libcctbx.so.0.0.1 -shared -rdynamic -Wl,-z,relro -Wl,-soname=libcctbx.so.0 cctbx/eltbx/basic.o cctbx/eltbx/xray_scattering/it1992.o cctbx/eltbx/xray_scattering/wk1995.o cctbx/eltbx/xray_scattering/n_gaussian_raw.o cctbx/eltbx/xray_scattering/n_gaussian.o cctbx/eltbx/fp_fdp.o cctbx/eltbx/henke.o cctbx/eltbx/henke_tables_01_12.o cctbx/eltbx/henke_tables_13_24.o cctbx/eltbx/henke_tables_25_36.o cctbx/eltbx/henke_tables_37_48.o cctbx/eltbx/henke_tables_49_60.o cctbx/eltbx/henke_tables_61_72.o cctbx/eltbx/henke_tables_73_84.o cctbx/eltbx/henke_tables_85_92.o cctbx/eltbx/icsd_radii.o cctbx/eltbx/covalent_radii.o cctbx/eltbx/neutron.o cctbx/eltbx/sasaki.o cctbx/eltbx/sasaki_tables_01_12.o cctbx/eltbx/sasaki_tables_13_24.o cctbx/eltbx/sasaki_tables_25_36.o cctbx/eltbx/sasaki_tables_37_48.o cctbx/eltbx/sasaki_tables_49_60.o cctbx/eltbx/sasaki_tables_61_72.o cctbx/eltbx/sasaki_tables_73_82.o cctbx/eltbx/tiny_pse.o cctbx/eltbx/wavelengths.o cctbx/eltbx/electron_scattering/peng1996.o cctbx/eltbx/attenuation_coefficient.o cctbx/miller/asu.o cctbx/miller/bins.o cctbx/miller/index_generator.o cctbx/miller/index_span.o cctbx/miller/match_bijvoet_mates.o cctbx/miller/match_indices.o cctbx/miller/match_multi_indices.o cctbx/miller/sym_equiv.o cctbx/sgtbx/bricks.o cctbx/sgtbx/change_of_basis_op.o cctbx/sgtbx/find_affine.o cctbx/sgtbx/group_codes.o cctbx/sgtbx/hall_in.o cctbx/sgtbx/lattice_tr.o cctbx/sgtbx/lattice_symmetry.o cctbx/sgtbx/miller.o cctbx/sgtbx/reciprocal_space_asu.o cctbx/sgtbx/reciprocal_space_ref_asu.o cctbx/sgtbx/rot_mx.o cctbx/sgtbx/rot_mx_info.o cctbx/sgtbx/row_echelon_solve.o cctbx/sgtbx/rt_mx.o cctbx/sgtbx/select_generators.o cctbx/sgtbx/seminvariant.o cctbx/sgtbx/site_symmetry.o cctbx/sgtbx/space_group.o cctbx/sgtbx/space_group_type.o cctbx/sgtbx/symbols.o cctbx/sgtbx/tensor_rank_2.o cctbx/sgtbx/tr_group.o cctbx/sgtbx/tr_vec.o cctbx/sgtbx/utils.o cctbx/sgtbx/wyckoff.o cctbx/sgtbx/reference_settings/hall_symbol_table.o cctbx/sgtbx/reference_settings/matrix_group_code_table.o cctbx/sgtbx/reference_settings/normalizer.o cctbx/sgtbx/reference_settings/wyckoff.o cctbx/uctbx/uctbx.o cctbx/uctbx/spoil_optimization.o cctbx/uctbx/crystal_orientation.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lm Create symlinks for: 'lib/libcctbx.so.0.0.1': 'lib/libcctbx.so.0'->'lib/libcctbx.so.0.0.1', 'lib/libcctbx.so'->'lib/libcctbx.so.0.0.1' g++ -o cctbx/math/time_trigonometry -rdynamic -Wl,-z,relro -pthread cctbx/math/time_trigonometry.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lboost_thread -lboost_system -lm g++ -o cctbx/miller/boost_python/index_span.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/boost_python/index_span.cpp g++ -o cctbx/miller/boost_python/lookup_utils.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/boost_python/lookup_utils.cpp g++ -o cctbx/miller/boost_python/match_bijvoet_mates.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/boost_python/match_bijvoet_mates.cpp g++ -o cctbx/miller/boost_python/match_indices.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/boost_python/match_indices.cpp g++ -o cctbx/miller/boost_python/match_multi_indices.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/boost_python/match_multi_indices.cpp g++ -o cctbx/miller/boost_python/merge_equivalents.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/boost_python/merge_equivalents.cpp g++ -o cctbx/miller/boost_python/miller_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/boost_python/miller_ext.cpp g++ -o cctbx/miller/boost_python/phase_integrator.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/boost_python/phase_integrator.cpp g++ -o cctbx/miller/boost_python/phase_transfer.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/boost_python/phase_transfer.cpp g++ -o cctbx/miller/boost_python/randomize_amplitude_and_phase.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/boost_python/randomize_amplitude_and_phase.cpp g++ -o cctbx/miller/boost_python/slices.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/boost_python/slices.cpp g++ -o cctbx/miller/boost_python/sym_equiv.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/boost_python/sym_equiv.cpp In file included from /usr/include/boost/math/tools/cxx03_warn.hpp:9, from /usr/include/boost/math/constants/constants.hpp:11, from /usr/include/boost/math/special_functions/gamma.hpp:24, from /usr/include/boost/math/special_functions/detail/bessel_jy.hpp:14, from /usr/include/boost/math/special_functions/bessel.hpp:20, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/bessel.h:9, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/hendrickson_lattman.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/sym_equiv.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/miller/boost_python/miller_ext.cpp:3: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o cctbx/multipolar/aspherical_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/multipolar/aspherical_ext.cpp g++ -o cctbx/sgtbx/boost_python/brick.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/brick.cpp g++ -o cctbx/sgtbx/boost_python/change_of_basis.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/change_of_basis.cpp g++ -o cctbx/sgtbx/boost_python/find_affine.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/find_affine.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/multipolar/aspherical.h:12, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/multipolar/aspherical_ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o cctbx/sgtbx/boost_python/lattice_symmetry.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/lattice_symmetry.cpp g++ -o cctbx/sgtbx/boost_python/phase_info.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/phase_info.cpp g++ -o cctbx/sgtbx/boost_python/reciprocal_space_asu.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/reciprocal_space_asu.cpp g++ -o cctbx/sgtbx/boost_python/rot_mx.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/rot_mx.cpp g++ -o cctbx/sgtbx/boost_python/rt_mx.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/rt_mx.cpp g++ -o cctbx/sgtbx/boost_python/search_symmetry.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/search_symmetry.cpp g++ -o cctbx/sgtbx/boost_python/select_generators.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/select_generators.cpp g++ -o cctbx/sgtbx/boost_python/seminvariant.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/seminvariant.cpp g++ -o cctbx/sgtbx/boost_python/sgtbx_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/sgtbx_ext.cpp g++ -o cctbx/sgtbx/boost_python/site_symmetry.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/site_symmetry.cpp g++ -o cctbx/sgtbx/boost_python/space_group.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/space_group.cpp g++ -o cctbx/sgtbx/boost_python/space_group_type.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/space_group_type.cpp g++ -o cctbx/sgtbx/boost_python/sym_equiv_sites.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/sym_equiv_sites.cpp g++ -o cctbx/sgtbx/boost_python/symbols.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/symbols.cpp g++ -o cctbx/sgtbx/boost_python/tensor_rank_2.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/tensor_rank_2.cpp g++ -o cctbx/sgtbx/boost_python/tensors.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/tensors.cpp g++ -o cctbx/sgtbx/boost_python/tr_vec.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/tr_vec.cpp g++ -o cctbx/sgtbx/boost_python/wyckoff.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/boost_python/wyckoff.cpp g++ -o cctbx/sgtbx/direct_space_asu/proto/asu_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/direct_space_asu/proto/asu_ext.cpp g++ -o cctbx/sgtbx/direct_space_asu/proto/cut.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/direct_space_asu/proto/cut.cpp g++ -o cctbx/sgtbx/direct_space_asu/proto/direct_space_asu.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/direct_space_asu/proto/direct_space_asu.cpp g++ -o cctbx/sgtbx/direct_space_asu/proto/reference_table.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/direct_space_asu/proto/reference_table.cpp g++ -o cctbx/sgtbx/direct_space_asu/proto/tst_asu.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/sgtbx/direct_space_asu/proto/tst_asu.cpp g++ -o cctbx/symmetry_search/boost_python/symmetry_search_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/symmetry_search/boost_python/symmetry_search_ext.cpp g++ -o cctbx/translation_search/boost_python/fast_nv1995.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/translation_search/boost_python/fast_nv1995.cpp g++ -o cctbx/translation_search/boost_python/fast_terms.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/translation_search/boost_python/fast_terms.cpp g++ -o cctbx/translation_search/boost_python/symmetry_flags.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/translation_search/boost_python/symmetry_flags.cpp g++ -o cctbx/translation_search/boost_python/translation_search_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/translation_search/boost_python/translation_search_ext.cpp g++ -o cctbx/uctbx/boost_python/fast_minimum_reduction.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/uctbx/boost_python/fast_minimum_reduction.cpp g++ -o cctbx/uctbx/boost_python/uctbx_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/uctbx/boost_python/uctbx_ext.cpp g++ -o cctbx/uctbx/determine_unit_cell/ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_SINGLEFILE_NCDIST -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/uctbx/determine_unit_cell/ext.cpp g++ -o cctbx/xray/boost_python/conversions.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/conversions.cpp g++ -o cctbx/xray/boost_python/curvatures_simple.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/curvatures_simple.cpp g++ -o cctbx/xray/boost_python/each_hkl_gradients_direct.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/each_hkl_gradients_direct.cpp g++ -o cctbx/xray/boost_python/extinction.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/extinction.cpp g++ -o cctbx/xray/boost_python/f_model_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/f_model_bpl.cpp g++ -o cctbx/xray/boost_python/fast_gradients.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/fast_gradients.cpp g++ -o cctbx/xray/boost_python/gradient_flags.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/gradient_flags.cpp g++ -o cctbx/xray/boost_python/gradients_direct.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/gradients_direct.cpp g++ -o cctbx/xray/boost_python/grouped_data.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/grouped_data.cpp g++ -o cctbx/xray/boost_python/minimization.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/minimization.cpp g++ -o cctbx/xray/boost_python/parameter_map.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/parameter_map.cpp g++ -o cctbx/xray/boost_python/sampled_model_density.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/sampled_model_density.cpp g++ -o cctbx/xray/boost_python/sampling_base.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/sampling_base.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object/class.hpp:9, from /usr/include/boost/python/class.hpp:13, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/parameter_map.cpp:3: /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ g++ -o cctbx/xray/boost_python/scatterer.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/scatterer.cpp g++ -o cctbx/xray/boost_python/scatterer_flags.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/scatterer_flags.cpp g++ -o cctbx/xray/boost_python/scattering_type_registry.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/scattering_type_registry.cpp g++ -o cctbx/xray/boost_python/sigmaa.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/sigmaa.cpp g++ -o cctbx/xray/boost_python/structure_factors_direct.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/structure_factors_direct.cpp g++ -o cctbx/xray/boost_python/structure_factors_simple.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/structure_factors_simple.cpp g++ -o cctbx/xray/boost_python/targets.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/targets.cpp g++ -o cctbx/xray/boost_python/twin_components.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/twin_components.cpp /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/scattering_type_registry.cpp:49:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 49 | std::auto_ptr | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/misc.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/vec3.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/mat3.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/sym_mat3.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/scatterer_flags.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/scatterer.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/scattering_type_registry.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/scattering_type_registry.cpp:3: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/scattering_type_registry.cpp: In static member function ‘static std::auto_ptr cctbx::xray::boost_python::{anonymous}::scattering_type_registry_wrappers::constructor_for_pickle(const boost::python::dict&, const boost::python::list&, const unique_counts_t&)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/scattering_type_registry.cpp:55:12: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 55 | std::auto_ptr self(new w_t); | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/misc.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/vec3.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/mat3.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/sym_mat3.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/scatterer_flags.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/scatterer.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/scattering_type_registry.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/scattering_type_registry.cpp:3: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -o cctbx/xray/boost_python/twin_targets.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/twin_targets.cpp g++ -o cctbx/xray/boost_python/xray_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/boost_python/xray_ext.cpp g++ -o cctbx/xray/observations/boost_python/observations.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/observations/boost_python/observations.cpp g++ -o cctbx/xray/observations/boost_python/observations_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/observations/boost_python/observations_ext.cpp g++ -o cctbx/xray/targets/shelxl_wght_ls_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/targets/shelxl_wght_ls_bpl.cpp g++ -o chiltbx/handle_test.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/chiltbx/handle_test.cpp g++ -o chiltbx/handle_test -rdynamic -Wl,-z,relro chiltbx/handle_test.o -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib g++ -o fable/ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable/ext.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/targets/shelxl_wght_ls_bpl.cpp:22: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o iotbx/detectors/bruker.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/detectors/bruker.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable/ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o iotbx/detectors/bruker_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/detectors/bruker_ext.cpp g++ -o iotbx/detectors/detectors_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/detectors/detectors_ext.cpp g++ -o iotbx/detectors/image_divider.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/detectors/image_divider.cpp g++ -o iotbx/dsn6/ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/dsn6/ext.cpp g++ -o iotbx/misc/boost_python/dtrek_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/misc/boost_python/dtrek_ext.cpp g++ -o lib/libcctbx_sgtbx_asu.so.0.0.1 -rdynamic -Wl,-z,relro -pthread -shared -Wl,-z,relro -Wl,-soname=libcctbx_sgtbx_asu.so.0 cctbx/sgtbx/direct_space_asu/proto/cut.o cctbx/sgtbx/direct_space_asu/proto/reference_table.o cctbx/sgtbx/direct_space_asu/proto/direct_space_asu.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lm Create symlinks for: 'lib/libcctbx_sgtbx_asu.so.0.0.1': 'lib/libcctbx_sgtbx_asu.so.0'->'lib/libcctbx_sgtbx_asu.so.0.0.1', 'lib/libcctbx_sgtbx_asu.so'->'lib/libcctbx_sgtbx_asu.so.0.0.1' g++ -o iotbx/misc/boost_python/scalepack_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/misc/boost_python/scalepack_ext.cpp g++ -o exe_dev/cctbx.sym_equiv_sites -rdynamic -Wl,-z,relro -pthread cctbx/examples/sym_equiv_sites.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lboost_thread -lboost_system -lm g++ -o exe_dev/cctbx.find_distances -rdynamic -Wl,-z,relro -pthread cctbx/examples/find_distances.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lboost_thread -lboost_system -lm g++ -o exe_dev/cctbx.convert_ccp4_symop_lib -rdynamic -Wl,-z,relro -pthread cctbx/examples/convert_ccp4_symop_lib.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lboost_thread -lboost_system -lm g++ -o exe_dev/cctbx.getting_started -rdynamic -Wl,-z,relro -pthread cctbx/examples/getting_started.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lboost_thread -lboost_system -lm In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/detectors/bruker_ext.cpp:18: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o exe_dev/cctbx.sys_abs_equiv_space_groups -rdynamic -Wl,-z,relro -pthread cctbx/examples/sys_abs_equiv_space_groups.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lboost_thread -lboost_system -lm g++ -o exe_dev/cctbx.lattice_symmetry -rdynamic -Wl,-z,relro -pthread cctbx/examples/lattice_symmetry.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lboost_thread -lboost_system -lm g++ -o cctbx/sgtbx/direct_space_asu/proto/tst_asu -rdynamic -Wl,-z,relro -pthread cctbx/sgtbx/direct_space_asu/proto/tst_asu.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lm g++ -o iotbx/pdb/atom_selection.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/atom_selection.cpp g++ -o iotbx/pdb/common_residue_names_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/common_residue_names_bpl.cpp g++ -o iotbx/pdb/construct_hierarchy.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/construct_hierarchy.cpp g++ -o iotbx/pdb/ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/ext.cpp In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:31, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/namespace.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/atom_selection.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/detectors/scanbox.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/detectors/image_divider.h:2, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/detectors/detectors_ext.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:31, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/namespace.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/input.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/construct_hierarchy.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o iotbx/pdb/hierarchy.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy.cpp g++ -o iotbx/pdb/hierarchy_atom_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atom_bpl.cpp g++ -o iotbx/pdb/hierarchy_atoms.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.cpp g++ -o iotbx/pdb/hierarchy_atoms_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp g++ -o iotbx/pdb/hierarchy_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_ext.cpp g++ -o iotbx/pdb/hierarchy_select.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_select.cpp In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:31, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/namespace.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:31, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/namespace.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.h: At global scope: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.h:157:8: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 157 | std::auto_ptr | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/misc.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:31, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/namespace.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.cpp:1: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.h:163:8: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 163 | std::auto_ptr | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/misc.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:31, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/namespace.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.cpp:1: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.cpp:242:8: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 242 | std::auto_ptr | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/misc.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:31, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/namespace.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.cpp:1: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.cpp: In function ‘std::auto_ptr iotbx::pdb::hierarchy::atoms::reset_tmp(const scitbx::af::const_ref&, int, int)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.cpp:248:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 248 | std::auto_ptr result(new atom_tmp_sentinel(atoms)); | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/misc.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:31, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/namespace.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.cpp:1: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.cpp: At global scope: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.cpp:257:8: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 257 | std::auto_ptr | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/misc.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:31, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/namespace.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.cpp:1: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.cpp: In function ‘std::auto_ptr iotbx::pdb::hierarchy::atoms::reset_tmp_for_occupancy_groups_simple(const scitbx::af::const_ref&)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.cpp:261:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 261 | std::auto_ptr result(new atom_tmp_sentinel(atoms)); | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/misc.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:31, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/namespace.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.cpp:1: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -o iotbx/pdb/hierarchy_write.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_write.cpp In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:31, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/namespace.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_select.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o iotbx/pdb/hybrid_36_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hybrid_36_bpl.cpp In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:31, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/namespace.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_write.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_write.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.h: At global scope: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.h:157:8: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 157 | std::auto_ptr | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/misc.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:31, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/namespace.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_write.cpp:1: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_write.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.h:163:8: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 163 | std::auto_ptr | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/misc.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:31, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/namespace.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_write.cpp:1: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_ext.cpp:11: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.h:157:8: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 157 | std::auto_ptr | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from /usr/include/boost/config/no_tr1/memory.hpp:21, from /usr/include/boost/get_pointer.hpp:14, from /usr/include/boost/python/object/pointer_holder.hpp:11, from /usr/include/boost/python/to_python_indirect.hpp:10, from /usr/include/boost/python/converter/arg_to_python.hpp:10, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object/class.hpp:9, from /usr/include/boost/python/class.hpp:13, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_ext.cpp:4: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_ext.cpp:11: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.h:163:8: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 163 | std::auto_ptr | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from /usr/include/boost/config/no_tr1/memory.hpp:21, from /usr/include/boost/get_pointer.hpp:14, from /usr/include/boost/python/object/pointer_holder.hpp:11, from /usr/include/boost/python/to_python_indirect.hpp:10, from /usr/include/boost/python/converter/arg_to_python.hpp:10, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object/class.hpp:9, from /usr/include/boost/python/class.hpp:13, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_ext.cpp:4: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ gcc -o iotbx/pdb/hybrid_36_c.o -c -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hybrid_36_c.c g++ -o iotbx/pdb/hybrid_36_cpp.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hybrid_36_cpp.cpp g++ -o iotbx/pdb/hybrid_36_fem.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable iotbx/pdb/hybrid_36_fem.cpp g++ -o iotbx/pdb/input.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/input.cpp g++ -o iotbx/pdb/input_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/input_bpl.cpp g++ -o iotbx/pdb/input_write.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/input_write.cpp In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:13: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.h:157:8: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 157 | std::auto_ptr | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/misc.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/vec3.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/mat3.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/sym_mat3.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/scatterer_flags.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/scatterer.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:2: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:13: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms.h:163:8: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 163 | std::auto_ptr | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/misc.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/vec3.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/mat3.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/sym_mat3.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/scatterer_flags.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/scatterer.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:2: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp: In function ‘void iotbx::pdb::hierarchy::atoms::bpl_wrap()’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:84:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 84 | std::auto_ptr, | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/misc.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/vec3.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/mat3.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/sym_mat3.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/scatterer_flags.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/cctbx/xray/scatterer.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:2: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:31, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/namespace.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/input.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/input_write.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o iotbx/pdb/overall_counts.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/overall_counts.cpp In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:31, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/namespace.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/input.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/input.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:31, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/namespace.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/hierarchy.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/overall_counts.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o iotbx/pdb/rna_dna_atom_names_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/rna_dna_atom_names_bpl.cpp /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o iotbx/pdb/hybrid_36_fem -rdynamic -Wl,-z,relro -pthread iotbx/pdb/hybrid_36_fem.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system g++ -o iotbx/pdb/utils.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/utils.cpp g++ -o iotbx/pdb/write_utils.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/write_utils.cpp In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:31, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/namespace.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/write_utils.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/write_utils.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/write_utils.cpp: In destructor ‘iotbx::pdb::write_utils::fstream_open_close::~fstream_open_close()’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/write_utils.cpp:42:7: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 42 | throw std::runtime_error( | ^~~~~~~~~~~~~~~~~~~~~~~~~ 43 | "Failure writing to file: \"" + file_name + "\""); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/write_utils.cpp:42:7: note: in C++11 destructors default to ‘noexcept’ g++ -o iotbx/pdb/xray_structure_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/pdb/xray_structure_bpl.cpp g++ -o iotbx/shelx/shelx_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/shelx/shelx_ext.cpp g++ -o iotbx/wildcard_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/wildcard_ext.cpp g++ -o iotbx/xplor/boost_python/xplor_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/xplor/boost_python/xplor_ext.cpp g++ -o iotbx/xplor/map_reader.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/xplor/map_reader.cpp g++ -o iotbx/xplor/map_writer.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/iotbx/xplor/map_writer.cpp g++ -o lib/boost_adaptbx_boost_thread_test_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=boost_adaptbx_boost_thread_test_ext.so.0 boost_adaptbx/tests/boost_thread_test.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/boost_adaptbx_boost_thread_test_ext.so.0.0.1': 'lib/boost_adaptbx_boost_thread_test_ext.so.0'->'lib/boost_adaptbx_boost_thread_test_ext.so.0.0.1', 'lib/boost_adaptbx_boost_thread_test_ext.so'->'lib/boost_adaptbx_boost_thread_test_ext.so.0.0.1' g++ -o lib/boost_adaptbx_graph_breadth_first_search_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=boost_adaptbx_graph_breadth_first_search_ext.so.0 boost_adaptbx/graph/breadth_first_search_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/boost_adaptbx_graph_breadth_first_search_ext.so.0.0.1': 'lib/boost_adaptbx_graph_breadth_first_search_ext.so.0'->'lib/boost_adaptbx_graph_breadth_first_search_ext.so.0.0.1', 'lib/boost_adaptbx_graph_breadth_first_search_ext.so'->'lib/boost_adaptbx_graph_breadth_first_search_ext.so.0.0.1' g++ -o lib/boost_adaptbx_graph_clustering_algorithm_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=boost_adaptbx_graph_clustering_algorithm_ext.so.0 boost_adaptbx/graph/clustering_algorithm_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/boost_adaptbx_graph_clustering_algorithm_ext.so.0.0.1': 'lib/boost_adaptbx_graph_clustering_algorithm_ext.so.0'->'lib/boost_adaptbx_graph_clustering_algorithm_ext.so.0.0.1', 'lib/boost_adaptbx_graph_clustering_algorithm_ext.so'->'lib/boost_adaptbx_graph_clustering_algorithm_ext.so.0.0.1' g++ -o lib/boost_adaptbx_graph_connected_component_algorithm_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=boost_adaptbx_graph_connected_component_algorithm_ext.so.0 boost_adaptbx/graph/connected_component_algorithm_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/boost_adaptbx_graph_connected_component_algorithm_ext.so.0.0.1': 'lib/boost_adaptbx_graph_connected_component_algorithm_ext.so.0'->'lib/boost_adaptbx_graph_connected_component_algorithm_ext.so.0.0.1', 'lib/boost_adaptbx_graph_connected_component_algorithm_ext.so'->'lib/boost_adaptbx_graph_connected_component_algorithm_ext.so.0.0.1' g++ -o lib/boost_adaptbx_graph_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=boost_adaptbx_graph_ext.so.0 boost_adaptbx/graph/graph_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=boost_adaptbx_graph_graph_structure_comparison_ext.so.0 boost_adaptbx/graph/graph_structure_comparison_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/boost_adaptbx_graph_maximum_clique_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=boost_adaptbx_graph_maximum_clique_ext.so.0 boost_adaptbx/graph/maximum_clique_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/boost_adaptbx_graph_ext.so.0.0.1': 'lib/boost_adaptbx_graph_ext.so.0'->'lib/boost_adaptbx_graph_ext.so.0.0.1', 'lib/boost_adaptbx_graph_ext.so'->'lib/boost_adaptbx_graph_ext.so.0.0.1' Create symlinks for: 'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1': 'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0'->'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1', 'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so'->'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1' g++ -o lib/boost_adaptbx_graph_metric_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=boost_adaptbx_graph_metric_ext.so.0 boost_adaptbx/graph/metric_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=boost_adaptbx_graph_min_cut_max_flow_ext.so.0 boost_adaptbx/graph/min_cut_max_flow_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/boost_adaptbx_graph_utility_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=boost_adaptbx_graph_utility_ext.so.0 boost_adaptbx/graph/utility_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/boost_adaptbx_graph_maximum_clique_ext.so.0.0.1': 'lib/boost_adaptbx_graph_maximum_clique_ext.so.0'->'lib/boost_adaptbx_graph_maximum_clique_ext.so.0.0.1', 'lib/boost_adaptbx_graph_maximum_clique_ext.so'->'lib/boost_adaptbx_graph_maximum_clique_ext.so.0.0.1' g++ -o lib/boost_adaptbx_python_streambuf_test_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=boost_adaptbx_python_streambuf_test_ext.so.0 boost_adaptbx/tests/python_streambuf_test_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/boost_optional_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=boost_optional_ext.so.0 boost_adaptbx/optional_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/boost_adaptbx_python_streambuf_test_ext.so.0.0.1': 'lib/boost_adaptbx_python_streambuf_test_ext.so.0'->'lib/boost_adaptbx_python_streambuf_test_ext.so.0.0.1', 'lib/boost_adaptbx_python_streambuf_test_ext.so'->'lib/boost_adaptbx_python_streambuf_test_ext.so.0.0.1' g++ -o lib/boost_python_hybrid_times_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=boost_python_hybrid_times_ext.so.0 boost_adaptbx/hybrid_times_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/boost_python_meta_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=boost_python_meta_ext.so.0 boost_adaptbx/meta_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/boost_adaptbx_graph_utility_ext.so.0.0.1': 'lib/boost_adaptbx_graph_utility_ext.so.0'->'lib/boost_adaptbx_graph_utility_ext.so.0.0.1', 'lib/boost_adaptbx_graph_utility_ext.so'->'lib/boost_adaptbx_graph_utility_ext.so.0.0.1' Create symlinks for: 'lib/boost_optional_ext.so.0.0.1': 'lib/boost_optional_ext.so.0'->'lib/boost_optional_ext.so.0.0.1', 'lib/boost_optional_ext.so'->'lib/boost_optional_ext.so.0.0.1' Create symlinks for: 'lib/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1': 'lib/boost_adaptbx_graph_min_cut_max_flow_ext.so.0'->'lib/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1', 'lib/boost_adaptbx_graph_min_cut_max_flow_ext.so'->'lib/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1' g++ -o lib/boost_rational_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=boost_rational_ext.so.0 boost_adaptbx/rational_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/boost_python_hybrid_times_ext.so.0.0.1': 'lib/boost_python_hybrid_times_ext.so.0'->'lib/boost_python_hybrid_times_ext.so.0.0.1', 'lib/boost_python_hybrid_times_ext.so'->'lib/boost_python_hybrid_times_ext.so.0.0.1' g++ -o lib/boost_tuple_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=boost_tuple_ext.so.0 boost_adaptbx/tuple_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/boost_tuple_ext.so.0.0.1': 'lib/boost_tuple_ext.so.0'->'lib/boost_tuple_ext.so.0.0.1', 'lib/boost_tuple_ext.so'->'lib/boost_tuple_ext.so.0.0.1' Create symlinks for: 'lib/boost_adaptbx_graph_metric_ext.so.0.0.1': 'lib/boost_adaptbx_graph_metric_ext.so.0'->'lib/boost_adaptbx_graph_metric_ext.so.0.0.1', 'lib/boost_adaptbx_graph_metric_ext.so'->'lib/boost_adaptbx_graph_metric_ext.so.0.0.1' g++ -o scitbx/boost_python/utils.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/boost_python/utils.cpp Create symlinks for: 'lib/boost_python_meta_ext.so.0.0.1': 'lib/boost_python_meta_ext.so.0'->'lib/boost_python_meta_ext.so.0.0.1', 'lib/boost_python_meta_ext.so'->'lib/boost_python_meta_ext.so.0.0.1' g++ -o scitbx/boost_python/slice.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/boost_python/slice.cpp Create symlinks for: 'lib/boost_rational_ext.so.0.0.1': 'lib/boost_rational_ext.so.0'->'lib/boost_rational_ext.so.0.0.1', 'lib/boost_rational_ext.so'->'lib/boost_rational_ext.so.0.0.1' g++ -o scitbx/array_family/boost_python/utils.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/utils.cpp g++ -o lib/libiotbx_xplor.so.0.0.1 -shared -rdynamic -Wl,-z,relro -Wl,-soname=libiotbx_xplor.so.0 iotbx/xplor/map_reader.o iotbx/xplor/map_writer.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lm g++ -o omptbx/stubs.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/omptbx/stubs.cpp Create symlinks for: 'lib/libiotbx_xplor.so.0.0.1': 'lib/libiotbx_xplor.so.0'->'lib/libiotbx_xplor.so.0.0.1', 'lib/libiotbx_xplor.so'->'lib/libiotbx_xplor.so.0.0.1' g++ -o lib/fable_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=fable_ext.so.0 fable/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/iotbx_detectors_bruker_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=iotbx_detectors_bruker_ext.so.0 iotbx/detectors/bruker_ext.o iotbx/detectors/bruker.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/iotbx_detectors_bruker_ext.so.0.0.1': 'lib/iotbx_detectors_bruker_ext.so.0'->'lib/iotbx_detectors_bruker_ext.so.0.0.1', 'lib/iotbx_detectors_bruker_ext.so'->'lib/iotbx_detectors_bruker_ext.so.0.0.1' g++ -o lib/iotbx_detectors_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=iotbx_detectors_ext.so.0 iotbx/detectors/detectors_ext.o iotbx/detectors/image_divider.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/fable_ext.so.0.0.1': 'lib/fable_ext.so.0'->'lib/fable_ext.so.0.0.1', 'lib/fable_ext.so'->'lib/fable_ext.so.0.0.1' g++ -o lib/iotbx_dsn6_map_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=iotbx_dsn6_map_ext.so.0 iotbx/dsn6/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/libomptbx.so.0.0.1 -shared -rdynamic -Wl,-z,relro -Wl,-soname=libomptbx.so.0 omptbx/stubs.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system Create symlinks for: 'lib/iotbx_dsn6_map_ext.so.0.0.1': 'lib/iotbx_dsn6_map_ext.so.0'->'lib/iotbx_dsn6_map_ext.so.0.0.1', 'lib/iotbx_dsn6_map_ext.so'->'lib/iotbx_dsn6_map_ext.so.0.0.1' g++ -o lib/iotbx_dtrek_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=iotbx_dtrek_ext.so.0 iotbx/misc/boost_python/dtrek_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/iotbx_dtrek_ext.so.0.0.1': 'lib/iotbx_dtrek_ext.so.0'->'lib/iotbx_dtrek_ext.so.0.0.1', 'lib/iotbx_dtrek_ext.so'->'lib/iotbx_dtrek_ext.so.0.0.1' g++ -o lib/libiotbx_pdb.so.0.0.1 -shared -rdynamic -Wl,-z,relro -Wl,-soname=libiotbx_pdb.so.0 iotbx/pdb/hybrid_36_c.o iotbx/pdb/hybrid_36_cpp.o iotbx/pdb/utils.o iotbx/pdb/write_utils.o iotbx/pdb/hierarchy.o iotbx/pdb/hierarchy_select.o iotbx/pdb/hierarchy_atoms.o iotbx/pdb/construct_hierarchy.o iotbx/pdb/overall_counts.o iotbx/pdb/hierarchy_write.o iotbx/pdb/atom_selection.o iotbx/pdb/input.o iotbx/pdb/input_write.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system Create symlinks for: 'lib/libomptbx.so.0.0.1': 'lib/libomptbx.so.0'->'lib/libomptbx.so.0.0.1', 'lib/libomptbx.so'->'lib/libomptbx.so.0.0.1' g++ -o lib/libasymmetric_map.so.0.0.1 -shared -rdynamic -Wl,-z,relro -Wl,-soname=libasymmetric_map.so.0 cctbx/maptbx/asymmetric_map.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -liotbx_xplor -lcctbx_sgtbx_asu -lcctbx -lomptbx -lm Create symlinks for: 'lib/iotbx_detectors_ext.so.0.0.1': 'lib/iotbx_detectors_ext.so.0'->'lib/iotbx_detectors_ext.so.0.0.1', 'lib/iotbx_detectors_ext.so'->'lib/iotbx_detectors_ext.so.0.0.1' g++ -o lib/iotbx_scalepack_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=iotbx_scalepack_ext.so.0 iotbx/misc/boost_python/scalepack_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/libasymmetric_map.so.0.0.1': 'lib/libasymmetric_map.so.0'->'lib/libasymmetric_map.so.0.0.1', 'lib/libasymmetric_map.so'->'lib/libasymmetric_map.so.0.0.1' g++ -o lib/iotbx_wildcard_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=iotbx_wildcard_ext.so.0 iotbx/wildcard_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/iotbx_scalepack_ext.so.0.0.1': 'lib/iotbx_scalepack_ext.so.0'->'lib/iotbx_scalepack_ext.so.0.0.1', 'lib/iotbx_scalepack_ext.so'->'lib/iotbx_scalepack_ext.so.0.0.1' g++ -o scitbx/minpack/raw.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/minpack/raw.cpp Create symlinks for: 'lib/iotbx_wildcard_ext.so.0.0.1': 'lib/iotbx_wildcard_ext.so.0'->'lib/iotbx_wildcard_ext.so.0.0.1', 'lib/iotbx_wildcard_ext.so'->'lib/iotbx_wildcard_ext.so.0.0.1' In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/accessors/flex_grid.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/utils.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/utils.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -o scitbx/slatec/lib_c.o -c -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/slatec/lib_c.c /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘const ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h: In member function ‘ElementType& scitbx::af::versa_plain::at(scitbx::af::versa_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h: In member function ‘const ElementType& scitbx::af::versa_plain::at(scitbx::af::versa_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Create symlinks for: 'lib/libiotbx_pdb.so.0.0.1': 'lib/libiotbx_pdb.so.0'->'lib/libiotbx_pdb.so.0.0.1', 'lib/libiotbx_pdb.so'->'lib/libiotbx_pdb.so.0.0.1' g++ -o lib/libscitbx_slatec.so.0.0.1 -shared -rdynamic -Wl,-z,relro -Wl,-soname=libscitbx_slatec.so.0 scitbx/slatec/lib_c.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lm Create symlinks for: 'lib/libscitbx_slatec.so.0.0.1': 'lib/libscitbx_slatec.so.0'->'lib/libscitbx_slatec.so.0.0.1', 'lib/libscitbx_slatec.so'->'lib/libscitbx_slatec.so.0.0.1' g++ -o smtbx/refinement/constraints/affine.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/affine.cpp g++ -o lib/iotbx_shelx_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=iotbx_shelx_ext.so.0 iotbx/shelx/shelx_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/iotbx_shelx_ext.so.0.0.1': 'lib/iotbx_shelx_ext.so.0'->'lib/iotbx_shelx_ext.so.0.0.1', 'lib/iotbx_shelx_ext.so'->'lib/iotbx_shelx_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/geometrical_hydrogens.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/geometrical_hydrogens.cpp g++ -o smtbx/refinement/constraints/occupancy.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/occupancy.cpp g++ -o smtbx/refinement/constraints/reparametrisation.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/reparametrisation.cpp g++ -o smtbx/refinement/constraints/rigid.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/rigid.cpp g++ -o lib/libscitbx_minpack.so.0.0.1 -shared -rdynamic -Wl,-z,relro -Wl,-soname=libscitbx_minpack.so.0 scitbx/minpack/raw.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lm Create symlinks for: 'lib/libscitbx_minpack.so.0.0.1': 'lib/libscitbx_minpack.so.0'->'lib/libscitbx_minpack.so.0.0.1', 'lib/libscitbx_minpack.so'->'lib/libscitbx_minpack.so.0.0.1' g++ -o smtbx/refinement/constraints/same_group.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/same_group.cpp g++ -o lib/iotbx_xplor_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=iotbx_xplor_ext.so.0 iotbx/xplor/boost_python/xplor_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -liotbx_xplor -lcctbx -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/iotbx_xplor_ext.so.0.0.1': 'lib/iotbx_xplor_ext.so.0'->'lib/iotbx_xplor_ext.so.0.0.1', 'lib/iotbx_xplor_ext.so'->'lib/iotbx_xplor_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/shared.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/shared.cpp g++ -o smtbx/refinement/constraints/special_position.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/special_position.cpp g++ -o lib/libscitbx_boost_python.so.0.0.1 -shared -rdynamic -Wl,-z,relro -shared -rdynamic -Wl,-soname=libscitbx_boost_python.so.0 scitbx/boost_python/utils.o scitbx/boost_python/slice.o scitbx/array_family/boost_python/utils.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 Create symlinks for: 'lib/libscitbx_boost_python.so.0.0.1': 'lib/libscitbx_boost_python.so.0'->'lib/libscitbx_boost_python.so.0.0.1', 'lib/libscitbx_boost_python.so'->'lib/libscitbx_boost_python.so.0.0.1' g++ -o lib/cctbx_eltbx_wavelengths_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_eltbx_wavelengths_ext.so.0 cctbx/eltbx/boost_python/wavelengths_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_eltbx_wavelengths_ext.so.0.0.1': 'lib/cctbx_eltbx_wavelengths_ext.so.0'->'lib/cctbx_eltbx_wavelengths_ext.so.0.0.1', 'lib/cctbx_eltbx_wavelengths_ext.so'->'lib/cctbx_eltbx_wavelengths_ext.so.0.0.1' g++ -o lib/cctbx_adp_restraints_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_adp_restraints_ext.so.0 cctbx/adp_restraints/adp_restraints_bpl.o cctbx/adp_restraints/adp_restraints_ext.o cctbx/adp_restraints/rigid_bond_bpl.o cctbx/adp_restraints/rigu_bpl.o cctbx/adp_restraints/adp_similarity_bpl.o cctbx/adp_restraints/isotropic_adp_bpl.o cctbx/adp_restraints/aniso_restraints_bpl.o cctbx/adp_restraints/fixed_u_eq_adp_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_adp_restraints_ext.so.0.0.1': 'lib/cctbx_adp_restraints_ext.so.0'->'lib/cctbx_adp_restraints_ext.so.0.0.1', 'lib/cctbx_adp_restraints_ext.so'->'lib/cctbx_adp_restraints_ext.so.0.0.1' g++ -o lib/cctbx_sgtbx_asu_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_sgtbx_asu_ext.so.0 cctbx/sgtbx/direct_space_asu/proto/asu_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_sgtbx_asu_ext.so.0.0.1': 'lib/cctbx_sgtbx_asu_ext.so.0'->'lib/cctbx_sgtbx_asu_ext.so.0.0.1', 'lib/cctbx_sgtbx_asu_ext.so'->'lib/cctbx_sgtbx_asu_ext.so.0.0.1' g++ -o lib/cctbx_multipolar_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_multipolar_ext.so.0 cctbx/multipolar/aspherical_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_multipolar_ext.so.0.0.1': 'lib/cctbx_multipolar_ext.so.0'->'lib/cctbx_multipolar_ext.so.0.0.1', 'lib/cctbx_multipolar_ext.so'->'lib/cctbx_multipolar_ext.so.0.0.1' g++ -o lib/cctbx_eltbx_tiny_pse_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_eltbx_tiny_pse_ext.so.0 cctbx/eltbx/boost_python/tiny_pse_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_eltbx_tiny_pse_ext.so.0.0.1': 'lib/cctbx_eltbx_tiny_pse_ext.so.0'->'lib/cctbx_eltbx_tiny_pse_ext.so.0.0.1', 'lib/cctbx_eltbx_tiny_pse_ext.so'->'lib/cctbx_eltbx_tiny_pse_ext.so.0.0.1' g++ -o lib/cctbx_crystal_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_crystal_ext.so.0 cctbx/crystal/crystal_ext.o cctbx/crystal/asu_clusters_bpl.o cctbx/crystal/close_packing_bpl.o cctbx/crystal/coordination_sequences_bpl.o cctbx/crystal/direct_space_asu_bpl.o cctbx/crystal/incremental_pairs_bpl.o cctbx/crystal/neighbors_bpl.o cctbx/crystal/pair_tables_bpl.o cctbx/crystal/site_cluster_analysis_bpl.o cctbx/crystal/symmetry_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/cctbx_french_wilson_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_french_wilson_ext.so.0 cctbx/boost_python/french_wilson_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_french_wilson_ext.so.0.0.1': 'lib/cctbx_french_wilson_ext.so.0'->'lib/cctbx_french_wilson_ext.so.0.0.1', 'lib/cctbx_french_wilson_ext.so'->'lib/cctbx_french_wilson_ext.so.0.0.1' g++ -o lib/cctbx_symmetry_search_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_symmetry_search_ext.so.0 cctbx/symmetry_search/boost_python/symmetry_search_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_symmetry_search_ext.so.0.0.1': 'lib/cctbx_symmetry_search_ext.so.0'->'lib/cctbx_symmetry_search_ext.so.0.0.1', 'lib/cctbx_symmetry_search_ext.so'->'lib/cctbx_symmetry_search_ext.so.0.0.1' g++ -o lib/determine_unit_cell_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=determine_unit_cell_ext.so.0 cctbx/uctbx/determine_unit_cell/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/determine_unit_cell_ext.so.0.0.1': 'lib/determine_unit_cell_ext.so.0'->'lib/determine_unit_cell_ext.so.0.0.1', 'lib/determine_unit_cell_ext.so'->'lib/determine_unit_cell_ext.so.0.0.1' g++ -o lib/cctbx_statistics_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_statistics_ext.so.0 cctbx/boost_python/statistics_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_statistics_ext.so.0.0.1': 'lib/cctbx_statistics_ext.so.0'->'lib/cctbx_statistics_ext.so.0.0.1', 'lib/cctbx_statistics_ext.so'->'lib/cctbx_statistics_ext.so.0.0.1' g++ -o lib/cctbx_eltbx_icsd_radii_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_eltbx_icsd_radii_ext.so.0 cctbx/eltbx/boost_python/icsd_radii_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_eltbx_icsd_radii_ext.so.0.0.1': 'lib/cctbx_eltbx_icsd_radii_ext.so.0'->'lib/cctbx_eltbx_icsd_radii_ext.so.0.0.1', 'lib/cctbx_eltbx_icsd_radii_ext.so'->'lib/cctbx_eltbx_icsd_radii_ext.so.0.0.1' g++ -o lib/cctbx_translation_search_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_translation_search_ext.so.0 cctbx/translation_search/boost_python/translation_search_ext.o cctbx/translation_search/boost_python/fast_nv1995.o cctbx/translation_search/boost_python/fast_terms.o cctbx/translation_search/boost_python/symmetry_flags.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/cctbx_miller_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_miller_ext.so.0 cctbx/miller/boost_python/miller_ext.o cctbx/miller/boost_python/asu.o cctbx/miller/boost_python/bins.o cctbx/miller/boost_python/change_basis.o cctbx/miller/boost_python/expand_to_p1.o cctbx/miller/boost_python/index_generator.o cctbx/miller/boost_python/index_span.o cctbx/miller/boost_python/match_bijvoet_mates.o cctbx/miller/boost_python/match_indices.o cctbx/miller/boost_python/match_multi_indices.o cctbx/miller/boost_python/merge_equivalents.o cctbx/miller/boost_python/phase_integrator.o cctbx/miller/boost_python/phase_transfer.o cctbx/miller/boost_python/sym_equiv.o cctbx/miller/boost_python/f_calc_map.o cctbx/miller/boost_python/lookup_utils.o cctbx/miller/boost_python/amplitude_normalisation.o cctbx/miller/boost_python/randomize_amplitude_and_phase.o cctbx/miller/boost_python/slices.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_translation_search_ext.so.0.0.1': 'lib/cctbx_translation_search_ext.so.0'->'lib/cctbx_translation_search_ext.so.0.0.1', 'lib/cctbx_translation_search_ext.so'->'lib/cctbx_translation_search_ext.so.0.0.1' g++ -o lib/cctbx_sgtbx_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_sgtbx_ext.so.0 cctbx/sgtbx/boost_python/sgtbx_ext.o cctbx/sgtbx/boost_python/brick.o cctbx/sgtbx/boost_python/change_of_basis.o cctbx/sgtbx/boost_python/find_affine.o cctbx/sgtbx/boost_python/lattice_symmetry.o cctbx/sgtbx/boost_python/phase_info.o cctbx/sgtbx/boost_python/reciprocal_space_asu.o cctbx/sgtbx/boost_python/rot_mx.o cctbx/sgtbx/boost_python/rt_mx.o cctbx/sgtbx/boost_python/search_symmetry.o cctbx/sgtbx/boost_python/seminvariant.o cctbx/sgtbx/boost_python/site_symmetry.o cctbx/sgtbx/boost_python/space_group.o cctbx/sgtbx/boost_python/space_group_type.o cctbx/sgtbx/boost_python/sym_equiv_sites.o cctbx/sgtbx/boost_python/symbols.o cctbx/sgtbx/boost_python/tensor_rank_2.o cctbx/sgtbx/boost_python/tensors.o cctbx/sgtbx/boost_python/tr_vec.o cctbx/sgtbx/boost_python/wyckoff.o cctbx/sgtbx/boost_python/select_generators.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/cctbx_eltbx_attenuation_coefficient_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_eltbx_attenuation_coefficient_ext.so.0 cctbx/eltbx/boost_python/attenuation_coefficient_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/cctbx_covariance_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_covariance_ext.so.0 cctbx/covariance/boost_python/covariance_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_covariance_ext.so.0.0.1': 'lib/cctbx_covariance_ext.so.0'->'lib/cctbx_covariance_ext.so.0.0.1', 'lib/cctbx_covariance_ext.so'->'lib/cctbx_covariance_ext.so.0.0.1' g++ -o lib/cctbx_emma_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_emma_ext.so.0 cctbx/boost_python/emma_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_crystal_ext.so.0.0.1': 'lib/cctbx_crystal_ext.so.0'->'lib/cctbx_crystal_ext.so.0.0.1', 'lib/cctbx_crystal_ext.so'->'lib/cctbx_crystal_ext.so.0.0.1' Create symlinks for: 'lib/cctbx_eltbx_attenuation_coefficient_ext.so.0.0.1': 'lib/cctbx_eltbx_attenuation_coefficient_ext.so.0'->'lib/cctbx_eltbx_attenuation_coefficient_ext.so.0.0.1', 'lib/cctbx_eltbx_attenuation_coefficient_ext.so'->'lib/cctbx_eltbx_attenuation_coefficient_ext.so.0.0.1' g++ -o lib/cctbx_array_family_flex_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_array_family_flex_ext.so.0 cctbx/array_family/boost_python/flex_ext.o cctbx/array_family/boost_python/flex_hendrickson_lattman.o cctbx/array_family/boost_python/flex_miller_index.o cctbx/array_family/boost_python/flex_xray_scatterer.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_emma_ext.so.0.0.1': 'lib/cctbx_emma_ext.so.0'->'lib/cctbx_emma_ext.so.0.0.1', 'lib/cctbx_emma_ext.so'->'lib/cctbx_emma_ext.so.0.0.1' g++ -o lib/cctbx_eltbx_chemical_elements_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_eltbx_chemical_elements_ext.so.0 cctbx/eltbx/boost_python/chemical_elements_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/cctbx_xray_observations_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_xray_observations_ext.so.0 cctbx/xray/observations/boost_python/observations.o cctbx/xray/observations/boost_python/observations_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_eltbx_chemical_elements_ext.so.0.0.1': 'lib/cctbx_eltbx_chemical_elements_ext.so.0'->'lib/cctbx_eltbx_chemical_elements_ext.so.0.0.1', 'lib/cctbx_eltbx_chemical_elements_ext.so'->'lib/cctbx_eltbx_chemical_elements_ext.so.0.0.1' g++ -o lib/iotbx_pdb_hierarchy_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=iotbx_pdb_hierarchy_ext.so.0 iotbx/pdb/hierarchy_ext.o iotbx/pdb/hierarchy_atom_bpl.o iotbx/pdb/hierarchy_atoms_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -liotbx_pdb -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/cctbx_eltbx_covalent_radii_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_eltbx_covalent_radii_ext.so.0 cctbx/eltbx/boost_python/covalent_radii_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/cctbx_dmtbx_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_dmtbx_ext.so.0 cctbx/dmtbx/boost_python/dmtbx_ext.o cctbx/dmtbx/boost_python/triplet_phase_relation.o cctbx/dmtbx/boost_python/triplet_generator.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/cctbx_geometry_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_geometry_ext.so.0 cctbx/geometry/boost_python/geometry_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/cctbx_maptbx_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_maptbx_ext.so.0 cctbx/maptbx/boost_python/maptbx_ext.o cctbx/maptbx/boost_python/grid_indices_around_sites.o cctbx/maptbx/boost_python/grid_tags.o cctbx/maptbx/boost_python/gridding.o cctbx/maptbx/boost_python/misc.o cctbx/maptbx/boost_python/peak_search.o cctbx/maptbx/boost_python/pymol_interface.o cctbx/maptbx/boost_python/statistics.o cctbx/maptbx/boost_python/structure_factors.o cctbx/maptbx/boost_python/coordinate_transformers.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_eltbx_covalent_radii_ext.so.0.0.1': 'lib/cctbx_eltbx_covalent_radii_ext.so.0'->'lib/cctbx_eltbx_covalent_radii_ext.so.0.0.1', 'lib/cctbx_eltbx_covalent_radii_ext.so'->'lib/cctbx_eltbx_covalent_radii_ext.so.0.0.1' g++ -o lib/cctbx_asymmetric_map_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_asymmetric_map_ext.so.0 cctbx/maptbx/asymmetric_map_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lasymmetric_map -liotbx_xplor -lcctbx_sgtbx_asu -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_asymmetric_map_ext.so.0.0.1': 'lib/cctbx_asymmetric_map_ext.so.0'->'lib/cctbx_asymmetric_map_ext.so.0.0.1', 'lib/cctbx_asymmetric_map_ext.so'->'lib/cctbx_asymmetric_map_ext.so.0.0.1' g++ -o lib/cctbx_eltbx_neutron_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_eltbx_neutron_ext.so.0 cctbx/eltbx/boost_python/neutron_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_dmtbx_ext.so.0.0.1': 'lib/cctbx_dmtbx_ext.so.0'->'lib/cctbx_dmtbx_ext.so.0.0.1', 'lib/cctbx_dmtbx_ext.so'->'lib/cctbx_dmtbx_ext.so.0.0.1' g++ -o lib/cctbx_eltbx_henke_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_eltbx_henke_ext.so.0 cctbx/eltbx/boost_python/henke_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_eltbx_neutron_ext.so.0.0.1': 'lib/cctbx_eltbx_neutron_ext.so.0'->'lib/cctbx_eltbx_neutron_ext.so.0.0.1', 'lib/cctbx_eltbx_neutron_ext.so'->'lib/cctbx_eltbx_neutron_ext.so.0.0.1' g++ -o lib/iotbx_pdb_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=iotbx_pdb_ext.so.0 iotbx/pdb/ext.o iotbx/pdb/hybrid_36_bpl.o iotbx/pdb/common_residue_names_bpl.o iotbx/pdb/rna_dna_atom_names_bpl.o iotbx/pdb/input_bpl.o iotbx/pdb/xray_structure_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -liotbx_pdb -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_geometry_ext.so.0.0.1': 'lib/cctbx_geometry_ext.so.0'->'lib/cctbx_geometry_ext.so.0.0.1', 'lib/cctbx_geometry_ext.so'->'lib/cctbx_geometry_ext.so.0.0.1' g++ -o lib/cctbx_masks_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_masks_ext.so.0 cctbx/masks/boost_python/masks_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_xray_observations_ext.so.0.0.1': 'lib/cctbx_xray_observations_ext.so.0'->'lib/cctbx_xray_observations_ext.so.0.0.1', 'lib/cctbx_xray_observations_ext.so'->'lib/cctbx_xray_observations_ext.so.0.0.1' g++ -o lib/cctbx_xray_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_xray_ext.so.0 cctbx/xray/boost_python/xray_ext.o cctbx/xray/boost_python/conversions.o cctbx/xray/boost_python/gradient_flags.o cctbx/xray/boost_python/gradients_direct.o cctbx/xray/boost_python/each_hkl_gradients_direct.o cctbx/xray/boost_python/fast_gradients.o cctbx/xray/boost_python/minimization.o cctbx/xray/boost_python/scatterer_flags.o cctbx/xray/boost_python/scatterer.o cctbx/xray/boost_python/scattering_type_registry.o cctbx/xray/boost_python/sampling_base.o cctbx/xray/boost_python/sampled_model_density.o cctbx/xray/boost_python/structure_factors_direct.o cctbx/xray/boost_python/structure_factors_simple.o cctbx/xray/boost_python/curvatures_simple.o cctbx/xray/boost_python/targets.o cctbx/xray/boost_python/f_model_bpl.o cctbx/xray/boost_python/twin_targets.o cctbx/xray/boost_python/grouped_data.o cctbx/xray/boost_python/parameter_map.o cctbx/xray/boost_python/twin_components.o cctbx/xray/boost_python/extinction.o cctbx/xray/boost_python/sigmaa.o cctbx/xray/targets/shelxl_wght_ls_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/cctbx_merging_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_merging_ext.so.0 cctbx/merging/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_masks_ext.so.0.0.1': 'lib/cctbx_masks_ext.so.0'->'lib/cctbx_masks_ext.so.0.0.1', 'lib/cctbx_masks_ext.so'->'lib/cctbx_masks_ext.so.0.0.1' g++ -o lib/cctbx_math_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_math_ext.so.0 cctbx/math/boost_python/math_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_eltbx_henke_ext.so.0.0.1': 'lib/cctbx_eltbx_henke_ext.so.0'->'lib/cctbx_eltbx_henke_ext.so.0.0.1', 'lib/cctbx_eltbx_henke_ext.so'->'lib/cctbx_eltbx_henke_ext.so.0.0.1' g++ -o lib/cctbx_uctbx_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_uctbx_ext.so.0 cctbx/uctbx/boost_python/uctbx_ext.o cctbx/uctbx/boost_python/fast_minimum_reduction.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/iotbx_pdb_ext.so.0.0.1': 'lib/iotbx_pdb_ext.so.0'->'lib/iotbx_pdb_ext.so.0.0.1', 'lib/iotbx_pdb_ext.so'->'lib/iotbx_pdb_ext.so.0.0.1' Create symlinks for: 'lib/cctbx_array_family_flex_ext.so.0.0.1': 'lib/cctbx_array_family_flex_ext.so.0'->'lib/cctbx_array_family_flex_ext.so.0.0.1', 'lib/cctbx_array_family_flex_ext.so'->'lib/cctbx_array_family_flex_ext.so.0.0.1' Create symlinks for: 'lib/cctbx_math_ext.so.0.0.1': 'lib/cctbx_math_ext.so.0'->'lib/cctbx_math_ext.so.0.0.1', 'lib/cctbx_math_ext.so'->'lib/cctbx_math_ext.so.0.0.1' Create symlinks for: 'lib/cctbx_miller_ext.so.0.0.1': 'lib/cctbx_miller_ext.so.0'->'lib/cctbx_miller_ext.so.0.0.1', 'lib/cctbx_miller_ext.so'->'lib/cctbx_miller_ext.so.0.0.1' Create symlinks for: 'lib/cctbx_merging_ext.so.0.0.1': 'lib/cctbx_merging_ext.so.0'->'lib/cctbx_merging_ext.so.0.0.1', 'lib/cctbx_merging_ext.so'->'lib/cctbx_merging_ext.so.0.0.1' g++ -o lib/cctbx_adptbx_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_adptbx_ext.so.0 cctbx/adptbx/boost_python/adptbx_ext.o cctbx/adptbx/boost_python/hirshfeld.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/cctbx_orientation_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_orientation_ext.so.0 cctbx/boost_python/orientation_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/cctbx_eltbx_fp_fdp_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_eltbx_fp_fdp_ext.so.0 cctbx/eltbx/boost_python/fp_fdp_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/iotbx_pdb_hierarchy_ext.so.0.0.1': 'lib/iotbx_pdb_hierarchy_ext.so.0'->'lib/iotbx_pdb_hierarchy_ext.so.0.0.1', 'lib/iotbx_pdb_hierarchy_ext.so'->'lib/iotbx_pdb_hierarchy_ext.so.0.0.1' Create symlinks for: 'lib/cctbx_uctbx_ext.so.0.0.1': 'lib/cctbx_uctbx_ext.so.0'->'lib/cctbx_uctbx_ext.so.0.0.1', 'lib/cctbx_uctbx_ext.so'->'lib/cctbx_uctbx_ext.so.0.0.1' g++ -o lib/cctbx_eltbx_sasaki_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_eltbx_sasaki_ext.so.0 cctbx/eltbx/boost_python/sasaki_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/cctbx_eltbx_xray_scattering_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_eltbx_xray_scattering_ext.so.0 cctbx/eltbx/boost_python/xray_scattering_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/cctbx_anharmonic_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_anharmonic_ext.so.0 cctbx/adptbx/boost_python/anharmonic_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o lib/cctbx_geometry_restraints_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=cctbx_geometry_restraints_ext.so.0 cctbx/geometry_restraints/geometry_restraints_ext.o cctbx/geometry_restraints/bond_bpl.o cctbx/geometry_restraints/bond_similarity_bpl.o cctbx/geometry_restraints/bond_sorted_bpl.o cctbx/geometry_restraints/nonbonded_bpl.o cctbx/geometry_restraints/nonbonded_sorted_bpl.o cctbx/geometry_restraints/angle_bpl.o cctbx/geometry_restraints/dihedral_bpl.o cctbx/geometry_restraints/chirality_bpl.o cctbx/geometry_restraints/planarity_bpl.o cctbx/geometry_restraints/parallelity_bpl.o cctbx/geometry_restraints/motif_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/cctbx_eltbx_fp_fdp_ext.so.0.0.1': 'lib/cctbx_eltbx_fp_fdp_ext.so.0'->'lib/cctbx_eltbx_fp_fdp_ext.so.0.0.1', 'lib/cctbx_eltbx_fp_fdp_ext.so'->'lib/cctbx_eltbx_fp_fdp_ext.so.0.0.1' Create symlinks for: 'lib/cctbx_sgtbx_ext.so.0.0.1': 'lib/cctbx_sgtbx_ext.so.0'->'lib/cctbx_sgtbx_ext.so.0.0.1', 'lib/cctbx_sgtbx_ext.so'->'lib/cctbx_sgtbx_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/symmetry_equivalent.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/symmetry_equivalent.cpp Create symlinks for: 'lib/cctbx_orientation_ext.so.0.0.1': 'lib/cctbx_orientation_ext.so.0'->'lib/cctbx_orientation_ext.so.0.0.1', 'lib/cctbx_orientation_ext.so'->'lib/cctbx_orientation_ext.so.0.0.1' Create symlinks for: 'lib/cctbx_adptbx_ext.so.0.0.1': 'lib/cctbx_adptbx_ext.so.0'->'lib/cctbx_adptbx_ext.so.0.0.1', 'lib/cctbx_adptbx_ext.so'->'lib/cctbx_adptbx_ext.so.0.0.1' Create symlinks for: 'lib/cctbx_eltbx_sasaki_ext.so.0.0.1': 'lib/cctbx_eltbx_sasaki_ext.so.0'->'lib/cctbx_eltbx_sasaki_ext.so.0.0.1', 'lib/cctbx_eltbx_sasaki_ext.so'->'lib/cctbx_eltbx_sasaki_ext.so.0.0.1' Create symlinks for: 'lib/cctbx_anharmonic_ext.so.0.0.1': 'lib/cctbx_anharmonic_ext.so.0'->'lib/cctbx_anharmonic_ext.so.0.0.1', 'lib/cctbx_anharmonic_ext.so'->'lib/cctbx_anharmonic_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/u_eq_dependent_u_iso.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/u_eq_dependent_u_iso.cpp g++ -o smtbx/refinement/constraints/u_iso_dependent_u_iso.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/u_iso_dependent_u_iso.cpp Create symlinks for: 'lib/cctbx_eltbx_xray_scattering_ext.so.0.0.1': 'lib/cctbx_eltbx_xray_scattering_ext.so.0'->'lib/cctbx_eltbx_xray_scattering_ext.so.0.0.1', 'lib/cctbx_eltbx_xray_scattering_ext.so'->'lib/cctbx_eltbx_xray_scattering_ext.so.0.0.1' g++ -o omptbx/ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/omptbx/ext.cpp g++ -o scitbx/array_family/boost_python/flex_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_ext.cpp g++ -o scitbx/array_family/boost_python/flex_grid.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_grid.cpp g++ -o scitbx/array_family/boost_python/flex_bool.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_bool.cpp Create symlinks for: 'lib/cctbx_maptbx_ext.so.0.0.1': 'lib/cctbx_maptbx_ext.so.0'->'lib/cctbx_maptbx_ext.so.0.0.1', 'lib/cctbx_maptbx_ext.so'->'lib/cctbx_maptbx_ext.so.0.0.1' g++ -o scitbx/array_family/boost_python/flex_size_t.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_size_t.cpp Create symlinks for: 'lib/cctbx_xray_ext.so.0.0.1': 'lib/cctbx_xray_ext.so.0'->'lib/cctbx_xray_ext.so.0.0.1', 'lib/cctbx_xray_ext.so'->'lib/cctbx_xray_ext.so.0.0.1' g++ -o scitbx/array_family/boost_python/flex_int.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_int.cpp Create symlinks for: 'lib/cctbx_geometry_restraints_ext.so.0.0.1': 'lib/cctbx_geometry_restraints_ext.so.0'->'lib/cctbx_geometry_restraints_ext.so.0.0.1', 'lib/cctbx_geometry_restraints_ext.so'->'lib/cctbx_geometry_restraints_ext.so.0.0.1' g++ -o scitbx/array_family/boost_python/flex_float.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_float.cpp g++ -o scitbx/array_family/boost_python/flex_double.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_double.cpp g++ -o scitbx/array_family/boost_python/flex_double_matrix.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_double_matrix.cpp g++ -o lib/libsmtbx_refinement_constraints.so.0.0.1 -rdynamic -Wl,-z,relro -pthread -shared -Wl,-z,relro -Wl,-soname=libsmtbx_refinement_constraints.so.0 smtbx/refinement/constraints/affine.o smtbx/refinement/constraints/geometrical_hydrogens.o smtbx/refinement/constraints/occupancy.o smtbx/refinement/constraints/reparametrisation.o smtbx/refinement/constraints/rigid.o smtbx/refinement/constraints/same_group.o smtbx/refinement/constraints/shared.o smtbx/refinement/constraints/special_position.o smtbx/refinement/constraints/symmetry_equivalent.o smtbx/refinement/constraints/u_eq_dependent_u_iso.o smtbx/refinement/constraints/u_iso_dependent_u_iso.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system Create symlinks for: 'lib/libsmtbx_refinement_constraints.so.0.0.1': 'lib/libsmtbx_refinement_constraints.so.0'->'lib/libsmtbx_refinement_constraints.so.0.0.1', 'lib/libsmtbx_refinement_constraints.so'->'lib/libsmtbx_refinement_constraints.so.0.0.1' In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/to_python_value.hpp:20, from /usr/include/boost/python/default_call_policies.hpp:10, from /usr/include/boost/python/make_function.hpp:10, from /usr/include/boost/python/def.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/array_family/boost_python/flex_complex_double.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_complex_double.cpp g++ -o lib/omptbx_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=omptbx_ext.so.0 omptbx/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lomptbx -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/omptbx_ext.so.0.0.1': 'lib/omptbx_ext.so.0'->'lib/omptbx_ext.so.0.0.1', 'lib/omptbx_ext.so'->'lib/omptbx_ext.so.0.0.1' In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/to_python_value.hpp:20, from /usr/include/boost/python/default_call_policies.hpp:10, from /usr/include/boost/python/make_function.hpp:10, from /usr/include/boost/python/def.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_bool.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/array_family/boost_python/flex_std_string.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_std_string.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/to_python_value.hpp:20, from /usr/include/boost/python/default_call_policies.hpp:10, from /usr/include/boost/python/make_function.hpp:10, from /usr/include/boost/python/def.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_int.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/to_python_value.hpp:20, from /usr/include/boost/python/default_call_policies.hpp:10, from /usr/include/boost/python/make_function.hpp:10, from /usr/include/boost/python/def.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_float.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/to_python_value.hpp:20, from /usr/include/boost/python/default_call_policies.hpp:10, from /usr/include/boost/python/make_function.hpp:10, from /usr/include/boost/python/def.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_double.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/to_python_value.hpp:20, from /usr/include/boost/python/default_call_policies.hpp:10, from /usr/include/boost/python/make_function.hpp:10, from /usr/include/boost/python/def.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_complex_double.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/array_family/boost_python/flex_random.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_random.cpp g++ -o scitbx/array_family/boost_python/flex_sort.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_sort.cpp g++ -o scitbx/array_family/boost_python/flex_histogram.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_histogram.cpp g++ -o scitbx/array_family/boost_python/flex_weighted_histogram.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_weighted_histogram.cpp g++ -o scitbx/array_family/boost_python/flex_mean_and_variance.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_mean_and_variance.cpp g++ -o scitbx/array_family/boost_python/flex_median.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_median.cpp g++ -o scitbx/array_family/boost_python/flex_linear_interpolation.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_linear_interpolation.cpp g++ -o scitbx/array_family/boost_python/flex_vec3_double.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_vec3_double.cpp g++ -o scitbx/array_family/boost_python/flex_vec2_double.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp g++ -o scitbx/array_family/boost_python/flex_vec3_int.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_vec3_int.cpp g++ -o scitbx/array_family/boost_python/flex_sym_mat3_double.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_sym_mat3_double.cpp g++ -o scitbx/array_family/boost_python/flex_mat3_double.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp g++ -o scitbx/array_family/boost_python/flex_tiny_size_t_2.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/flex_tiny_size_t_2.cpp g++ -o scitbx/array_family/boost_python/loops.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/loops.cpp g++ -o scitbx/array_family/boost_python/show_sizes.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/show_sizes.cpp g++ -o scitbx/array_family/boost_python/numpy_bridge.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -DSCITBX_HAVE_NUMPY_INCLUDE -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/numpy_bridge.cpp g++ -o scitbx/array_family/boost_python/shared_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/shared_ext.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /usr/include/boost/python/numpy/dtype.hpp:15, from /usr/include/boost/python/numpy.hpp:10, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/numpy_bridge.cpp:2: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/cubicle_neighbors_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/cubicle_neighbors_ext.cpp g++ -o scitbx/fftpack/boost_python/fftpack_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/fftpack/boost_python/fftpack_ext.cpp g++ -o scitbx/glmtbx/boost_python/ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/glmtbx/boost_python/ext.cc g++ -o scitbx/graphics_utils/ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/graphics_utils/ext.cpp g++ -o scitbx/iso_surface/iso_surface_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/iso_surface/iso_surface_ext.cpp g++ -o scitbx/lbfgs/ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DSCITBX_LBFGS_HAVE_LBFGS_FEM -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgs/ext.cpp g++ -o scitbx/lbfgs/lbfgs_fem.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable scitbx/lbfgs/lbfgs_fem.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/cubicle_neighbors_ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/glmtbx/boost_python/ext.cc:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o lib/scitbx_iso_surface_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_iso_surface_ext.so.0 scitbx/iso_surface/iso_surface_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/scitbx_iso_surface_ext.so.0.0.1': 'lib/scitbx_iso_surface_ext.so.0'->'lib/scitbx_iso_surface_ext.so.0.0.1', 'lib/scitbx_iso_surface_ext.so'->'lib/scitbx_iso_surface_ext.so.0.0.1' g++ -o scitbx/lbfgsb/boost_python/lbfgsb_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/boost_python/lbfgsb_ext.cpp g++ -o scitbx/linalg/boost_python/linalg_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/linalg/boost_python/linalg_ext.cpp g++ -o lib/scitbx_cubicle_neighbors_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_cubicle_neighbors_ext.so.0 scitbx/cubicle_neighbors_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o scitbx/linalg/boost_python/matrix.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/linalg/boost_python/matrix.cpp Create symlinks for: 'lib/scitbx_cubicle_neighbors_ext.so.0.0.1': 'lib/scitbx_cubicle_neighbors_ext.so.0'->'lib/scitbx_cubicle_neighbors_ext.so.0.0.1', 'lib/scitbx_cubicle_neighbors_ext.so'->'lib/scitbx_cubicle_neighbors_ext.so.0.0.1' g++ -o scitbx/linalg/boost_python/cholesky.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/linalg/boost_python/cholesky.cpp In file included from /usr/include/boost/config/header_deprecated.hpp:18, from /usr/include/boost/timer.hpp:20, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/raw.h:9, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/boost_python/lbfgsb_ext.cpp:3: /usr/include/boost/timer.hpp:21:1: note: ‘#pragma message: This header is deprecated. Use the facilities in instead.’ 21 | BOOST_HEADER_DEPRECATED( "the facilities in " ) | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o lib/scitbx_graphics_utils_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_graphics_utils_ext.so.0 scitbx/graphics_utils/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/scitbx_graphics_utils_ext.so.0.0.1': 'lib/scitbx_graphics_utils_ext.so.0'->'lib/scitbx_graphics_utils_ext.so.0.0.1', 'lib/scitbx_graphics_utils_ext.so'->'lib/scitbx_graphics_utils_ext.so.0.0.1' g++ -o scitbx/linalg/boost_python/householder.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/linalg/boost_python/householder.cpp g++ -o lib/scitbx_glmtbx_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_glmtbx_ext.so.0 scitbx/glmtbx/boost_python/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/scitbx_glmtbx_ext.so.0.0.1': 'lib/scitbx_glmtbx_ext.so.0'->'lib/scitbx_glmtbx_ext.so.0.0.1', 'lib/scitbx_glmtbx_ext.so'->'lib/scitbx_glmtbx_ext.so.0.0.1' g++ -o scitbx/linalg/boost_python/svd.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/linalg/boost_python/svd.cpp g++ -o scitbx/linalg/boost_python/eigensystem.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/linalg/boost_python/eigensystem.cpp g++ -o lib/scitbx_lbfgs_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_lbfgs_ext.so.0 scitbx/lbfgs/ext.o scitbx/lbfgs/lbfgs_fem.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/scitbx_lbfgs_ext.so.0.0.1': 'lib/scitbx_lbfgs_ext.so.0'->'lib/scitbx_lbfgs_ext.so.0.0.1', 'lib/scitbx_lbfgs_ext.so'->'lib/scitbx_lbfgs_ext.so.0.0.1' g++ -o scitbx/linalg/boost_python/lapack_fem_bpl.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/linalg/boost_python/lapack_fem_bpl.cpp g++ -o scitbx/lstbx/boost_python/lstbx_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lstbx/boost_python/lstbx_ext.cpp g++ -o lib/scitbx_fftpack_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_fftpack_ext.so.0 scitbx/fftpack/boost_python/fftpack_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o scitbx/lstbx/boost_python/normal_equations.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lstbx/boost_python/normal_equations.cpp Create symlinks for: 'lib/scitbx_fftpack_ext.so.0.0.1': 'lib/scitbx_fftpack_ext.so.0'->'lib/scitbx_fftpack_ext.so.0.0.1', 'lib/scitbx_fftpack_ext.so'->'lib/scitbx_fftpack_ext.so.0.0.1' g++ -o scitbx/math/boost_python/math_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/math_ext.cpp g++ -o lib/scitbx_array_family_flex_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_array_family_flex_ext.so.0 scitbx/array_family/boost_python/flex_ext.o scitbx/array_family/boost_python/flex_grid.o scitbx/array_family/boost_python/flex_bool.o scitbx/array_family/boost_python/flex_size_t.o scitbx/array_family/boost_python/flex_int.o scitbx/array_family/boost_python/flex_float.o scitbx/array_family/boost_python/flex_double.o scitbx/array_family/boost_python/flex_double_matrix.o scitbx/array_family/boost_python/flex_complex_double.o scitbx/array_family/boost_python/flex_std_string.o scitbx/array_family/boost_python/flex_random.o scitbx/array_family/boost_python/flex_sort.o scitbx/array_family/boost_python/flex_histogram.o scitbx/array_family/boost_python/flex_weighted_histogram.o scitbx/array_family/boost_python/flex_mean_and_variance.o scitbx/array_family/boost_python/flex_median.o scitbx/array_family/boost_python/flex_linear_interpolation.o scitbx/array_family/boost_python/flex_vec3_double.o scitbx/array_family/boost_python/flex_vec2_double.o scitbx/array_family/boost_python/flex_vec3_int.o scitbx/array_family/boost_python/flex_sym_mat3_double.o scitbx/array_family/boost_python/flex_mat3_double.o scitbx/array_family/boost_python/flex_tiny_size_t_2.o scitbx/array_family/boost_python/loops.o scitbx/array_family/boost_python/show_sizes.o scitbx/array_family/boost_python/numpy_bridge.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm -lboost_numpy310 g++ -o lib/scitbx_array_family_shared_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_array_family_shared_ext.so.0 scitbx/array_family/boost_python/shared_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm -lboost_numpy310 g++ -o scitbx/math/boost_python/basic_statistics.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/basic_statistics.cpp Create symlinks for: 'lib/scitbx_array_family_shared_ext.so.0.0.1': 'lib/scitbx_array_family_shared_ext.so.0'->'lib/scitbx_array_family_shared_ext.so.0.0.1', 'lib/scitbx_array_family_shared_ext.so'->'lib/scitbx_array_family_shared_ext.so.0.0.1' g++ -o scitbx/math/boost_python/gaussian.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/gaussian.cpp g++ -o lib/scitbx_lbfgsb_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_lbfgsb_ext.so.0 scitbx/lbfgsb/boost_python/lbfgsb_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/scitbx_lbfgsb_ext.so.0.0.1': 'lib/scitbx_lbfgsb_ext.so.0'->'lib/scitbx_lbfgsb_ext.so.0.0.1', 'lib/scitbx_lbfgsb_ext.so'->'lib/scitbx_lbfgsb_ext.so.0.0.1' g++ -o scitbx/math/boost_python/golay.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/golay.cpp g++ -o scitbx/math/boost_python/minimum_covering_sphere.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/minimum_covering_sphere.cpp g++ -o scitbx/math/boost_python/principal_axes_of_inertia.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/principal_axes_of_inertia.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/linalg/boost_python/lapack_fem_bpl.cpp:3: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/math/boost_python/row_echelon.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/row_echelon.cpp g++ -o scitbx/math/boost_python/tensor_rank_2.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/tensor_rank_2.cpp g++ -o lib/scitbx_linalg_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_linalg_ext.so.0 scitbx/linalg/boost_python/linalg_ext.o scitbx/linalg/boost_python/matrix.o scitbx/linalg/boost_python/cholesky.o scitbx/linalg/boost_python/householder.o scitbx/linalg/boost_python/svd.o scitbx/linalg/boost_python/eigensystem.o scitbx/linalg/boost_python/lapack_fem_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o scitbx/math/boost_python/chebyshev.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/chebyshev.cpp Create symlinks for: 'lib/scitbx_linalg_ext.so.0.0.1': 'lib/scitbx_linalg_ext.so.0'->'lib/scitbx_linalg_ext.so.0.0.1', 'lib/scitbx_linalg_ext.so'->'lib/scitbx_linalg_ext.so.0.0.1' g++ -o scitbx/math/boost_python/icosahedron.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/icosahedron.cpp Create symlinks for: 'lib/scitbx_array_family_flex_ext.so.0.0.1': 'lib/scitbx_array_family_flex_ext.so.0'->'lib/scitbx_array_family_flex_ext.so.0.0.1', 'lib/scitbx_array_family_flex_ext.so'->'lib/scitbx_array_family_flex_ext.so.0.0.1' g++ -o scitbx/math/boost_python/slatec.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/slatec.cpp g++ -o scitbx/math/boost_python/line_search.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/line_search.cpp g++ -o scitbx/math/boost_python/r3_rotation.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/r3_rotation.cpp g++ -o scitbx/math/boost_python/resample.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/resample.cpp g++ -o scitbx/math/boost_python/quadrature.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/quadrature.cpp g++ -o lib/scitbx_lstbx_normal_equations_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_lstbx_normal_equations_ext.so.0 scitbx/lstbx/boost_python/lstbx_ext.o scitbx/lstbx/boost_python/normal_equations.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o scitbx/math/boost_python/unimodular_generator.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/unimodular_generator.cpp Create symlinks for: 'lib/scitbx_lstbx_normal_equations_ext.so.0.0.1': 'lib/scitbx_lstbx_normal_equations_ext.so.0'->'lib/scitbx_lstbx_normal_equations_ext.so.0.0.1', 'lib/scitbx_lstbx_normal_equations_ext.so'->'lib/scitbx_lstbx_normal_equations_ext.so.0.0.1' g++ -o scitbx/math/boost_python/halton.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/halton.cpp g++ -o scitbx/math/boost_python/least_squares_plane.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/least_squares_plane.cpp g++ -o scitbx/math/boost_python/continued_fraction.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/continued_fraction.cpp g++ -o scitbx/math/boost_python/numeric_limits.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/numeric_limits.cpp g++ -o scitbx/math/boost_python/distributions.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/distributions.cpp g++ -o scitbx/math/boost_python/exp_functions.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/exp_functions.cpp g++ -o scitbx/math/boost_python/zernike.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/zernike.cpp g++ -o scitbx/math/boost_python/zernike_moments.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/zernike_moments.cpp g++ -o scitbx/math/boost_python/2d_zernike_moments.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/2d_zernike_moments.cpp g++ -o scitbx/math/boost_python/weighted_covariance.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/weighted_covariance.cpp g++ -o scitbx/math/boost_python/rotation.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/rotation.cpp g++ -o scitbx/math/boost_python/interpolation.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/interpolation.cpp g++ -o scitbx/math/boost_python/tetrahedron.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/tetrahedron.cpp g++ -o scitbx/math/boost_python/angle_derivative.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/angle_derivative.cpp g++ -o scitbx/minpack/ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/minpack/ext.cpp g++ -o scitbx/r3_utils_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/r3_utils_ext.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/boost_python/angle_derivative.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/random/boost_python/random_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/random/boost_python/random_ext.cpp g++ -o scitbx/random/boost_python/basic_distributions.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/random/boost_python/basic_distributions.cpp g++ -o scitbx/rigid_body/ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/rigid_body/ext.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/r3_utils_ext.cpp:2: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/sparse/boost_python/vector.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/sparse/boost_python/vector.cpp g++ -o lib/scitbx_minpack_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_minpack_ext.so.0 scitbx/minpack/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_minpack -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/scitbx_minpack_ext.so.0.0.1': 'lib/scitbx_minpack_ext.so.0'->'lib/scitbx_minpack_ext.so.0.0.1', 'lib/scitbx_minpack_ext.so'->'lib/scitbx_minpack_ext.so.0.0.1' g++ -o scitbx/sparse/boost_python/matrix.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/sparse/boost_python/matrix.cpp g++ -o lib/scitbx_r3_utils_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_r3_utils_ext.so.0 scitbx/r3_utils_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/scitbx_r3_utils_ext.so.0.0.1': 'lib/scitbx_r3_utils_ext.so.0'->'lib/scitbx_r3_utils_ext.so.0.0.1', 'lib/scitbx_r3_utils_ext.so'->'lib/scitbx_r3_utils_ext.so.0.0.1' g++ -o scitbx/sparse/boost_python/approx_equal.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/sparse/boost_python/approx_equal.cpp g++ -o scitbx/sparse/boost_python/random.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/sparse/boost_python/random.cpp g++ -o scitbx/sparse/boost_python/lu_factorization.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/sparse/boost_python/lu_factorization.cpp g++ -o scitbx/sparse/boost_python/sparse_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/sparse/boost_python/sparse_ext.cpp g++ -o scitbx/stl/map_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/stl/map_ext.cpp g++ -o scitbx/stl/set_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/stl/set_ext.cpp g++ -o scitbx/stl/vector_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/stl/vector_ext.cpp In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/stl/set_ext.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/stl/set_wrapper.h: In static member function ‘static void scitbx::stl::boost_python::set_wrapper::wrap(const string&)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/stl/set_wrapper.h:52:28: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 52 | bp::class_ >(python_name.c_str()) | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from /usr/include/boost/config/no_tr1/memory.hpp:21, from /usr/include/boost/get_pointer.hpp:14, from /usr/include/boost/python/object/pointer_holder.hpp:11, from /usr/include/boost/python/to_python_indirect.hpp:10, from /usr/include/boost/python/converter/arg_to_python.hpp:10, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object/class.hpp:9, from /usr/include/boost/python/class.hpp:13, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/stl/set_wrapper.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/stl/set_ext.cpp:1: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -o lib/scitbx_math_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_math_ext.so.0 scitbx/math/boost_python/math_ext.o scitbx/math/boost_python/basic_statistics.o scitbx/math/boost_python/gaussian.o scitbx/math/boost_python/golay.o scitbx/math/boost_python/minimum_covering_sphere.o scitbx/math/boost_python/principal_axes_of_inertia.o scitbx/math/boost_python/row_echelon.o scitbx/math/boost_python/tensor_rank_2.o scitbx/math/boost_python/chebyshev.o scitbx/math/boost_python/icosahedron.o scitbx/math/boost_python/slatec.o scitbx/math/boost_python/line_search.o scitbx/math/boost_python/r3_rotation.o scitbx/math/boost_python/resample.o scitbx/math/boost_python/quadrature.o scitbx/math/boost_python/unimodular_generator.o scitbx/math/boost_python/halton.o scitbx/math/boost_python/least_squares_plane.o scitbx/math/boost_python/continued_fraction.o scitbx/math/boost_python/numeric_limits.o scitbx/math/boost_python/distributions.o scitbx/math/boost_python/exp_functions.o scitbx/math/boost_python/zernike.o scitbx/math/boost_python/zernike_moments.o scitbx/math/boost_python/2d_zernike_moments.o scitbx/math/boost_python/weighted_covariance.o scitbx/math/boost_python/rotation.o scitbx/math/boost_python/interpolation.o scitbx/math/boost_python/tetrahedron.o scitbx/math/boost_python/angle_derivative.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_slatec -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o scitbx/suffixtree/boost_python/suffixtree_shared_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/suffixtree/boost_python/suffixtree_shared_ext.cpp g++ -o lib/scitbx_random_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_random_ext.so.0 scitbx/random/boost_python/random_ext.o scitbx/random/boost_python/basic_distributions.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/scitbx_random_ext.so.0.0.1': 'lib/scitbx_random_ext.so.0'->'lib/scitbx_random_ext.so.0.0.1', 'lib/scitbx_random_ext.so'->'lib/scitbx_random_ext.so.0.0.1' In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:307, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_matrix.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/rigid_body/spatial_lib.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/rigid_body/featherstone.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/rigid_body/tardy.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/rigid_body/ext.cpp:14: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/push_back_etc.h: In member function ‘void scitbx::af::shared_plain::resize(const size_type&) [with ElementType = scitbx::af::tiny]’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/push_back_etc.h:175:15: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] 175 | resize(new_size, ElementType()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/push_back_etc.h:165:12: note: by argument 3 of type ‘const scitbx::af::tiny&’ to ‘void scitbx::af::shared_plain::resize(const size_type&, const ElementType&) [with ElementType = scitbx::af::tiny]’ declared here 165 | void resize(size_type const& new_size, ElementType const& x) { | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/push_back_etc.h:175:26: note: ‘’ declared here 175 | resize(new_size, ElementType()); | ^~~~~~~~~~~~~ g++ -o scitbx/suffixtree/boost_python/suffixtree_single_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/suffixtree/boost_python/suffixtree_single_ext.cpp g++ -o scitbx/suffixtree/boost_python/object_extensions.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/suffixtree/boost_python/object_extensions.cpp g++ -o lib/scitbx_stl_set_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_stl_set_ext.so.0 scitbx/stl/set_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/scitbx_stl_set_ext.so.0.0.1': 'lib/scitbx_stl_set_ext.so.0'->'lib/scitbx_stl_set_ext.so.0.0.1', 'lib/scitbx_stl_set_ext.so'->'lib/scitbx_stl_set_ext.so.0.0.1' g++ -o scitbx/wigner/ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/wigner/ext.cpp Create symlinks for: 'lib/scitbx_math_ext.so.0.0.1': 'lib/scitbx_math_ext.so.0'->'lib/scitbx_math_ext.so.0.0.1', 'lib/scitbx_math_ext.so'->'lib/scitbx_math_ext.so.0.0.1' g++ -o smtbx/ab_initio/ab_initio_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/ab_initio/ab_initio_ext.cpp g++ -o smtbx/array_family/af_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/array_family/af_ext.cpp g++ -o lib/scitbx_suffixtree_shared_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_suffixtree_shared_ext.so.0 scitbx/suffixtree/boost_python/suffixtree_shared_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/scitbx_suffixtree_shared_ext.so.0.0.1': 'lib/scitbx_suffixtree_shared_ext.so.0'->'lib/scitbx_suffixtree_shared_ext.so.0.0.1', 'lib/scitbx_suffixtree_shared_ext.so'->'lib/scitbx_suffixtree_shared_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/boost_python/affine.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/boost_python/affine.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object/class.hpp:9, from /usr/include/boost/python/class.hpp:13, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/suffixtree/boost_python/suffixtree_single_ext.cpp:2: /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ g++ -o lib/smtbx_array_family_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=smtbx_array_family_ext.so.0 smtbx/array_family/af_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python310 -lm g++ -o smtbx/refinement/constraints/boost_python/constraints_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/boost_python/constraints_ext.cpp Create symlinks for: 'lib/smtbx_array_family_ext.so.0.0.1': 'lib/smtbx_array_family_ext.so.0'->'lib/smtbx_array_family_ext.so.0.0.1', 'lib/smtbx_array_family_ext.so'->'lib/smtbx_array_family_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/boost_python/direction.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/boost_python/direction.cpp g++ -o lib/scitbx_rigid_body_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_rigid_body_ext.so.0 scitbx/rigid_body/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/scitbx_rigid_body_ext.so.0.0.1': 'lib/scitbx_rigid_body_ext.so.0'->'lib/scitbx_rigid_body_ext.so.0.0.1', 'lib/scitbx_rigid_body_ext.so'->'lib/scitbx_rigid_body_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/boost_python/geometrical_hydrogens.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/boost_python/geometrical_hydrogens.cpp g++ -o lib/smtbx_ab_initio_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=smtbx_ab_initio_ext.so.0 smtbx/ab_initio/ab_initio_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/smtbx_ab_initio_ext.so.0.0.1': 'lib/smtbx_ab_initio_ext.so.0'->'lib/smtbx_ab_initio_ext.so.0.0.1', 'lib/smtbx_ab_initio_ext.so'->'lib/smtbx_ab_initio_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/boost_python/independent_scalar_parameters.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/boost_python/independent_scalar_parameters.cpp g++ -o lib/scitbx_stl_vector_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_stl_vector_ext.so.0 scitbx/stl/vector_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/scitbx_stl_vector_ext.so.0.0.1': 'lib/scitbx_stl_vector_ext.so.0'->'lib/scitbx_stl_vector_ext.so.0.0.1', 'lib/scitbx_stl_vector_ext.so'->'lib/scitbx_stl_vector_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/boost_python/occupancy.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/boost_python/occupancy.cpp g++ -o lib/scitbx_sparse_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_sparse_ext.so.0 scitbx/sparse/boost_python/vector.o scitbx/sparse/boost_python/matrix.o scitbx/sparse/boost_python/approx_equal.o scitbx/sparse/boost_python/random.o scitbx/sparse/boost_python/lu_factorization.o scitbx/sparse/boost_python/sparse_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm g++ -o smtbx/refinement/constraints/boost_python/reparametrisation.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/boost_python/reparametrisation.cpp Create symlinks for: 'lib/scitbx_sparse_ext.so.0.0.1': 'lib/scitbx_sparse_ext.so.0'->'lib/scitbx_sparse_ext.so.0.0.1', 'lib/scitbx_sparse_ext.so'->'lib/scitbx_sparse_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/boost_python/rigid.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/boost_python/rigid.cpp g++ -o lib/scitbx_wigner_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_wigner_ext.so.0 scitbx/wigner/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/scitbx_wigner_ext.so.0.0.1': 'lib/scitbx_wigner_ext.so.0'->'lib/scitbx_wigner_ext.so.0.0.1', 'lib/scitbx_wigner_ext.so'->'lib/scitbx_wigner_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/boost_python/same_group.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/boost_python/same_group.cpp g++ -o lib/scitbx_stl_map_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_stl_map_ext.so.0 scitbx/stl/map_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/scitbx_stl_map_ext.so.0.0.1': 'lib/scitbx_stl_map_ext.so.0'->'lib/scitbx_stl_map_ext.so.0.0.1', 'lib/scitbx_stl_map_ext.so'->'lib/scitbx_stl_map_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/boost_python/scatterer_parameters.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/boost_python/scatterer_parameters.cpp g++ -o smtbx/refinement/constraints/boost_python/shared.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/boost_python/shared.cpp g++ -o smtbx/refinement/constraints/boost_python/special_position.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/boost_python/special_position.cpp g++ -o smtbx/refinement/constraints/boost_python/symmetry_equivalent.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/boost_python/symmetry_equivalent.cpp g++ -o lib/scitbx_suffixtree_single_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=scitbx_suffixtree_single_ext.so.0 scitbx/suffixtree/boost_python/suffixtree_single_ext.o scitbx/suffixtree/boost_python/object_extensions.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/scitbx_suffixtree_single_ext.so.0.0.1': 'lib/scitbx_suffixtree_single_ext.so.0'->'lib/scitbx_suffixtree_single_ext.so.0.0.1', 'lib/scitbx_suffixtree_single_ext.so'->'lib/scitbx_suffixtree_single_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/boost_python/u_eq_dependent_u_iso.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/boost_python/u_eq_dependent_u_iso.cpp g++ -o smtbx/refinement/constraints/boost_python/u_iso_dependent_u_iso.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/boost_python/u_iso_dependent_u_iso.cpp g++ -o smtbx/refinement/boost_python/least_squares_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/boost_python/least_squares_ext.cpp g++ -o smtbx/refinement/boost_python/weighting_schemes.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/boost_python/weighting_schemes.cpp g++ -o smtbx/refinement/boost_python/least_squares.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/boost_python/least_squares.cpp g++ -o smtbx/refinement/restraints/boost_python/origin_fixing.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/restraints/boost_python/origin_fixing.cpp g++ -o smtbx/refinement/restraints/boost_python/restraints_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/restraints/boost_python/restraints_ext.cpp g++ -o smtbx/stl/map_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/stl/map_ext.cpp g++ -o smtbx/structure_factors/direct/boost_python/ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/structure_factors/direct/boost_python/ext.cpp g++ -o smtbx/structure_factors/direct/boost_python/standard_xray.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/structure_factors/direct/boost_python/standard_xray.cpp g++ -o lib/std_pair_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=std_pair_ext.so.0 boost_adaptbx/std_pair_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lboost_python310 -lm g++ -o scitbx/array_family/boost_python/regression_test_ext.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/usr/include/python3.10 /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp g++ -o scitbx/array_family/tst_accessors.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -Iscitbx/array_family -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_accessors.cpp Create symlinks for: 'lib/std_pair_ext.so.0.0.1': 'lib/std_pair_ext.so.0'->'lib/std_pair_ext.so.0.0.1', 'lib/std_pair_ext.so'->'lib/std_pair_ext.so.0.0.1' g++ -o scitbx/array_family/tst_af_1.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -Iscitbx/array_family -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_af_1.cpp In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/accessors/flex_grid.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/flex_types.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_accessors.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘const ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h: In member function ‘ElementType& scitbx::af::versa_plain::at(scitbx::af::versa_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h: In member function ‘const ElementType& scitbx::af::versa_plain::at(scitbx::af::versa_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include/scitbx/array_family/tiny_plain_apply.h:15, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_af_1.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘const ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h: In member function ‘ElementType& scitbx::af::versa_plain::at(scitbx::af::versa_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h: In member function ‘const ElementType& scitbx::af::versa_plain::at(scitbx::af::versa_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_af_1.cpp:15: /usr/include/boost/bind.hpp: At global scope: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/array_family/tst_af_2.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -Iscitbx/array_family -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_af_2.cpp g++ -o scitbx/array_family/tst_accessors -rdynamic -Wl,-z,relro -pthread scitbx/array_family/tst_accessors.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/accessors/flex_grid.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_af_2.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘const ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h: In member function ‘ElementType& scitbx::af::versa_plain::at(scitbx::af::versa_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h: In member function ‘const ElementType& scitbx::af::versa_plain::at(scitbx::af::versa_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/array_family/tst_af_3.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -Iscitbx/array_family -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_af_3.cpp In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/simple_io.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_af_3.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘const ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h: In member function ‘ElementType& scitbx::af::versa_plain::at(scitbx::af::versa_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h: In member function ‘const ElementType& scitbx::af::versa_plain::at(scitbx::af::versa_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/array_family/tst_af_2 -rdynamic -Wl,-z,relro -pthread scitbx/array_family/tst_af_2.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system g++ -o scitbx/array_family/tst_af_4.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -Iscitbx/array_family -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_af_4.cpp g++ -o lib/smtbx_refinement_constraints_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=smtbx_refinement_constraints_ext.so.0 smtbx/refinement/constraints/boost_python/affine.o smtbx/refinement/constraints/boost_python/constraints_ext.o smtbx/refinement/constraints/boost_python/direction.o smtbx/refinement/constraints/boost_python/geometrical_hydrogens.o smtbx/refinement/constraints/boost_python/independent_scalar_parameters.o smtbx/refinement/constraints/boost_python/occupancy.o smtbx/refinement/constraints/boost_python/reparametrisation.o smtbx/refinement/constraints/boost_python/rigid.o smtbx/refinement/constraints/boost_python/same_group.o smtbx/refinement/constraints/boost_python/scatterer_parameters.o smtbx/refinement/constraints/boost_python/shared.o smtbx/refinement/constraints/boost_python/special_position.o smtbx/refinement/constraints/boost_python/symmetry_equivalent.o smtbx/refinement/constraints/boost_python/u_eq_dependent_u_iso.o smtbx/refinement/constraints/boost_python/u_iso_dependent_u_iso.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lsmtbx_refinement_constraints -lscitbx_boost_python -lcctbx -lboost_thread -lboost_system -lboost_python310 -lm g++ -o scitbx/array_family/tst_af_5.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -Iscitbx/array_family -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_af_5.cpp g++ -o scitbx/array_family/tst_af_1 -rdynamic -Wl,-z,relro -pthread scitbx/array_family/tst_af_1.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system g++ -o lib/smtbx_stl_map_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=smtbx_stl_map_ext.so.0 smtbx/stl/map_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/smtbx_stl_map_ext.so.0.0.1': 'lib/smtbx_stl_map_ext.so.0'->'lib/smtbx_stl_map_ext.so.0.0.1', 'lib/smtbx_stl_map_ext.so'->'lib/smtbx_stl_map_ext.so.0.0.1' Create symlinks for: 'lib/smtbx_refinement_constraints_ext.so.0.0.1': 'lib/smtbx_refinement_constraints_ext.so.0'->'lib/smtbx_refinement_constraints_ext.so.0.0.1', 'lib/smtbx_refinement_constraints_ext.so'->'lib/smtbx_refinement_constraints_ext.so.0.0.1' In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/simple_io.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_af_5.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/array_family/tst_mat3.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -Iscitbx/array_family -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_mat3.cpp /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/simple_io.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_af_4.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/array_family/tst_optional_copy.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -Iscitbx/array_family -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_optional_copy.cpp /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘const ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/array_family/tst_rectangular_full_packed.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -Iscitbx/array_family -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_rectangular_full_packed.cpp /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h: In member function ‘ElementType& scitbx::af::versa_plain::at(scitbx::af::versa_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h: In member function ‘const ElementType& scitbx::af::versa_plain::at(scitbx::af::versa_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/array_family/tst_af_3 -rdynamic -Wl,-z,relro -pthread scitbx/array_family/tst_af_3.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system g++ -o scitbx/array_family/tst_ref_matrix_facet.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -Iscitbx/array_family -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_ref_matrix_facet.cpp g++ -o scitbx/array_family/boost_python/regression_test_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=regression_test_ext.so.0 scitbx/array_family/boost_python/regression_test_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python310 -lm -lboost_numpy310 Create symlinks for: 'scitbx/array_family/boost_python/regression_test_ext.so.0.0.1': 'scitbx/array_family/boost_python/regression_test_ext.so.0'->'scitbx/array_family/boost_python/regression_test_ext.so.0.0.1', 'scitbx/array_family/boost_python/regression_test_ext.so'->'scitbx/array_family/boost_python/regression_test_ext.so.0.0.1' g++ -o scitbx/array_family/tst_sym_mat3.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -Iscitbx/array_family -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_sym_mat3.cpp In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/accessors/rectangular_full_packed.h:3, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_rectangular_full_packed.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘const ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h: In member function ‘ElementType& scitbx::af::versa_plain::at(scitbx::af::versa_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h: In member function ‘const ElementType& scitbx::af::versa_plain::at(scitbx::af::versa_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:31, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:5, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_optional_copy.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h: In member function ‘ElementType& scitbx::af::versa_plain::at(scitbx::af::versa_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h: In member function ‘const ElementType& scitbx::af::versa_plain::at(scitbx::af::versa_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘const ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/vec3.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/mat3.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_mat3.cpp:2: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_ref_matrix_facet.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘const ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h: In member function ‘ElementType& scitbx::af::versa_plain::at(scitbx::af::versa_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h: In member function ‘const ElementType& scitbx::af::versa_plain::at(scitbx::af::versa_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/array_family/tst_af_5 -rdynamic -Wl,-z,relro -pthread scitbx/array_family/tst_af_5.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lm g++ -o scitbx/array_family/tst_unsigned_float_arithmetic.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -Iscitbx/array_family -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_unsigned_float_arithmetic.cpp g++ -o scitbx/array_family/tst_rectangular_full_packed -rdynamic -Wl,-z,relro -pthread scitbx/array_family/tst_rectangular_full_packed.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system g++ -o scitbx/array_family/tst_vec3.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/usr/include -Iscitbx/array_family -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_vec3.cpp In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/vec3.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/mat3.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/sym_mat3.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_sym_mat3.cpp:2: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/array_family/tst_ref_matrix_facet -rdynamic -Wl,-z,relro -pthread scitbx/array_family/tst_ref_matrix_facet.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system g++ -o scitbx/error/tst_error.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Iscitbx/error -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/error /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/error/tst_error.cpp g++ -o scitbx/error/tst_error -rdynamic -Wl,-z,relro -pthread scitbx/error/tst_error.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include/scitbx/array_family/tiny_algebra.h:14, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_unsigned_float_arithmetic.cpp:3: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/fftpack/timing/fftpack_timer.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/fftpack/timing/fftpack_timer.cpp g++ -o scitbx/array_family/tst_unsigned_float_arithmetic -rdynamic -Wl,-z,relro -pthread scitbx/array_family/tst_unsigned_float_arithmetic.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system g++ -o scitbx/fftpack/timing/test0.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/fftpack/timing/test0.cpp g++ -o scitbx/array_family/tst_optional_copy -rdynamic -Wl,-z,relro -pthread scitbx/array_family/tst_optional_copy.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system g++ -o scitbx/lbfgs/sdrive_fem.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/fable scitbx/lbfgs/sdrive_fem.cpp g++ -o scitbx/array_family/tst_mat3 -rdynamic -Wl,-z,relro -pthread scitbx/array_family/tst_mat3.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lm In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/vec3.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tst_vec3.cpp:2: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/lbfgs/tst_lbfgs.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgs/tst_lbfgs.cpp In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_types.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/fftpack/factorization.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/fftpack/complex_to_complex.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/fftpack/timing/fftpack_timer.cpp:6: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_types.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/fftpack/factorization.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/fftpack/complex_to_complex.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/fftpack/complex_to_complex_3d.h:4, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/fftpack/timing/test0.cpp:3: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h: In member function ‘ElementType& scitbx::af::versa_plain::at(scitbx::af::versa_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h: In member function ‘const ElementType& scitbx::af::versa_plain::at(scitbx::af::versa_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘const ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/array_family/tst_sym_mat3 -rdynamic -Wl,-z,relro -pthread scitbx/array_family/tst_sym_mat3.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lm g++ -o scitbx/array_family/tst_vec3 -rdynamic -Wl,-z,relro -pthread scitbx/array_family/tst_vec3.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lm g++ -o scitbx/lbfgs/sdrive_fem -rdynamic -Wl,-z,relro -pthread scitbx/lbfgs/sdrive_fem.o scitbx/lbfgs/lbfgs_fem.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lm g++ -o scitbx/lbfgsb/dev/driver1.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/dev/driver1.cpp g++ -o scitbx/lbfgsb/dev/driver2.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/dev/driver2.cpp g++ -o scitbx/lbfgsb/dev/driver3.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/dev/driver3.cpp g++ -o scitbx/lbfgs/tst_lbfgs -rdynamic -Wl,-z,relro -pthread scitbx/lbfgs/tst_lbfgs.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lm g++ -o lib/smtbx_refinement_restraints_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=smtbx_refinement_restraints_ext.so.0 smtbx/refinement/restraints/boost_python/origin_fixing.o smtbx/refinement/restraints/boost_python/restraints_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python310 -lm g++ -o scitbx/math/tests/tst.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Iscitbx/math/tests -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/tests /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/math/tests/tst.cpp In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/raw.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/dev/driver3.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/raw.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/dev/driver2.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘const ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘const ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/config/header_deprecated.hpp:18, from /usr/include/boost/timer.hpp:20, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/raw.h:9, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/dev/driver3.cpp:1: /usr/include/boost/timer.hpp: At global scope: /usr/include/boost/timer.hpp:21:1: note: ‘#pragma message: This header is deprecated. Use the facilities in instead.’ 21 | BOOST_HEADER_DEPRECATED( "the facilities in " ) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/config/header_deprecated.hpp:18, from /usr/include/boost/timer.hpp:20, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/raw.h:9, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/dev/driver2.cpp:1: /usr/include/boost/timer.hpp: At global scope: /usr/include/boost/timer.hpp:21:1: note: ‘#pragma message: This header is deprecated. Use the facilities in instead.’ 21 | BOOST_HEADER_DEPRECATED( "the facilities in " ) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/raw.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/dev/driver2.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/raw.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/dev/driver3.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/fftpack/timing/fftpack_timer -rdynamic -Wl,-z,relro -pthread scitbx/fftpack/timing/fftpack_timer.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lomptbx -lm Create symlinks for: 'lib/smtbx_refinement_restraints_ext.so.0.0.1': 'lib/smtbx_refinement_restraints_ext.so.0'->'lib/smtbx_refinement_restraints_ext.so.0.0.1', 'lib/smtbx_refinement_restraints_ext.so'->'lib/smtbx_refinement_restraints_ext.so.0.0.1' In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/raw.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/dev/driver1.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(scitbx::af::tiny_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h: In member function ‘const ElementType& scitbx::af::small_plain::at(scitbx::af::small_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/config/header_deprecated.hpp:18, from /usr/include/boost/timer.hpp:20, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/raw.h:9, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/dev/driver1.cpp:1: /usr/include/boost/timer.hpp: At global scope: /usr/include/boost/timer.hpp:21:1: note: ‘#pragma message: This header is deprecated. Use the facilities in instead.’ 21 | BOOST_HEADER_DEPRECATED( "the facilities in " ) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/ref.h:8, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/raw.h:6, from /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/lbfgsb/dev/driver1.cpp:1: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type)’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(scitbx::af::shared_plain::size_type) const’: /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 65 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/matrix/tests/tst_cholesky.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Iscitbx/matrix/tests -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/matrix/tests /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/matrix/tests/tst_cholesky.cpp g++ -o scitbx/fftpack/timing/test0 -rdynamic -Wl,-z,relro -pthread scitbx/fftpack/timing/test0.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system -lomptbx -lm g++ -o scitbx/matrix/tests/tst_givens.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Iscitbx/matrix/tests -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/matrix/tests /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/matrix/tests/tst_givens.cpp g++ -o scitbx/matrix/tests/tst_householder.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Iscitbx/matrix/tests -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/matrix/tests /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/matrix/tests/tst_householder.cpp g++ -o scitbx/lbfgsb/dev/driver2 -rdynamic -Wl,-z,relro -pthread scitbx/lbfgsb/dev/driver2.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lm g++ -o scitbx/matrix/tests/tst_svd.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Iscitbx/matrix/tests -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/matrix/tests /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/matrix/tests/tst_svd.cpp g++ -o scitbx/matrix/tests/tst_givens -rdynamic -Wl,-z,relro -pthread scitbx/matrix/tests/tst_givens.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system g++ -o scitbx/math/tests/tst -rdynamic -Wl,-z,relro -pthread scitbx/math/tests/tst.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system g++ -o scitbx/serialization/tst_base_256.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -Wall -Wno-sign-compare -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Iscitbx/serialization -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/serialization /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/serialization/tst_base_256.cpp g++ -o scitbx/lbfgsb/dev/driver3 -rdynamic -Wl,-z,relro -pthread scitbx/lbfgsb/dev/driver3.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lm g++ -o scitbx/sparse/tests/tst_sparse.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Iscitbx/sparse/tests -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/sparse/tests /build/cctbx-TO2hyq/cctbx-2021.12+ds1/scitbx/sparse/tests/tst_sparse.cpp g++ -o smtbx/refinement/constraints/tests/tst_geometrical_hydrogens.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens.cpp g++ -o scitbx/lbfgsb/dev/driver1 -rdynamic -Wl,-z,relro -pthread scitbx/lbfgsb/dev/driver1.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lm g++ -o scitbx/serialization/tst_base_256 -rdynamic -Wl,-z,relro -pthread scitbx/serialization/tst_base_256.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lm g++ -o smtbx/refinement/constraints/tests/tst_reparametrisation.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/tests/tst_reparametrisation.cpp g++ -o smtbx/refinement/constraints/tests/tst_special_position.o -c -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/cctbx-TO2hyq/cctbx-2021.12+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/build/include -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints /build/cctbx-TO2hyq/cctbx-2021.12+ds1/smtbx/refinement/constraints/tests/tst_special_position.cpp g++ -o scitbx/matrix/tests/tst_cholesky -rdynamic -Wl,-z,relro -pthread scitbx/matrix/tests/tst_cholesky.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system g++ -o scitbx/matrix/tests/tst_householder -rdynamic -Wl,-z,relro -pthread scitbx/matrix/tests/tst_householder.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system g++ -o scitbx/matrix/tests/tst_svd -rdynamic -Wl,-z,relro -pthread scitbx/matrix/tests/tst_svd.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system g++ -o scitbx/sparse/tests/tst_sparse -rdynamic -Wl,-z,relro -pthread scitbx/sparse/tests/tst_sparse.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lboost_thread -lboost_system g++ -o smtbx/refinement/constraints/tests/tst_geometrical_hydrogens -rdynamic -Wl,-z,relro -pthread smtbx/refinement/constraints/tests/tst_geometrical_hydrogens.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lsmtbx_refinement_constraints -lboost_thread -lboost_system g++ -o smtbx/refinement/constraints/tests/tst_special_position -rdynamic -Wl,-z,relro -pthread smtbx/refinement/constraints/tests/tst_special_position.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lsmtbx_refinement_constraints -lboost_thread -lboost_system g++ -o scitbx/array_family/tst_af_4 -rdynamic -Wl,-z,relro -pthread scitbx/array_family/tst_af_4.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lm g++ -o lib/smtbx_structure_factors_direct_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=smtbx_structure_factors_direct_ext.so.0 smtbx/structure_factors/direct/boost_python/ext.o smtbx/structure_factors/direct/boost_python/standard_xray.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/smtbx_structure_factors_direct_ext.so.0.0.1': 'lib/smtbx_structure_factors_direct_ext.so.0'->'lib/smtbx_structure_factors_direct_ext.so.0.0.1', 'lib/smtbx_structure_factors_direct_ext.so'->'lib/smtbx_structure_factors_direct_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/tests/tst_reparametrisation -rdynamic -Wl,-z,relro -pthread smtbx/refinement/constraints/tests/tst_reparametrisation.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lcctbx -lsmtbx_refinement_constraints -lboost_thread -lboost_system g++ -o lib/smtbx_refinement_least_squares_ext.so.0.0.1 -shared -rdynamic -Wl,-soname=smtbx_refinement_least_squares_ext.so.0 smtbx/refinement/boost_python/least_squares_ext.o smtbx/refinement/boost_python/weighting_schemes.o smtbx/refinement/boost_python/least_squares.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -Llib -L/build/cctbx-TO2hyq/cctbx-2021.12+ds1/lib -lsmtbx_refinement_constraints -lscitbx_boost_python -lcctbx -lboost_thread -lboost_system -lboost_python310 -lm Create symlinks for: 'lib/smtbx_refinement_least_squares_ext.so.0.0.1': 'lib/smtbx_refinement_least_squares_ext.so.0'->'lib/smtbx_refinement_least_squares_ext.so.0.0.1', 'lib/smtbx_refinement_least_squares_ext.so'->'lib/smtbx_refinement_least_squares_ext.so.0.0.1' scons: done building targets. usr+sys time: 30.35 seconds wall clock time: 16 minutes 17.02 seconds (977.02 seconds total) iconv -f ISO-8859-1 -t UTF-8 cctbx/eltbx/covalent_radii.h > covalent_radii.h mv covalent_radii.h cctbx/eltbx/covalent_radii.h make[1]: Leaving directory '/build/cctbx-TO2hyq/cctbx-2021.12+ds1' dh: command-omitted: The call to "debian/rules override_dh_auto_test" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild W: pybuild base:266: missing command (plugin=custom, method=install, interpreter=python3.9, version=3.9) W: pybuild base:266: missing command (plugin=custom, method=install, interpreter=python3.10, version=3.10) dh_install -a -O--buildsystem=pybuild dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild dh_python3 -a -O--buildsystem=pybuild dh_installsystemduser -a -O--buildsystem=pybuild dh_lintian -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_structure_factors_direct_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_structure_factors_direct_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_structure_factors_direct_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_structure_factors_direct_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_structure_factors_direct_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyComplex_FromDoubles used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_structure_factors_direct_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_structure_factors_direct_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyComplex_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_structure_factors_direct_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_structure_factors_direct_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_least_squares_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_least_squares_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol pthread_condattr_setclock used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_least_squares_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_least_squares_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_least_squares_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_least_squares_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_least_squares_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_least_squares_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_array_family_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_array_family_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_array_family_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_dmtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_dmtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_dmtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_Size used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_dmtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_Occurred used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_dmtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyIter_Next used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_dmtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_dmtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_dmtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_dmtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_Clear used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_dmtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lstbx_normal_equations_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lstbx_normal_equations_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lstbx_normal_equations_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lstbx_normal_equations_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lstbx_normal_equations_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lstbx_normal_equations_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lstbx_normal_equations_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lstbx_normal_equations_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lstbx_normal_equations_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lstbx_normal_equations_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 1 similar warning has been skipped (use -v to see it) dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_maximum_clique_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyList_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_maximum_clique_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyEval_CallFunction used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_maximum_clique_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_maximum_clique_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_maximum_clique_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_maximum_clique_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_GetItem used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_pdb_hierarchy_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_Size used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_pdb_hierarchy_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_pdb_hierarchy_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_Occurred used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_pdb_hierarchy_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_AsUTF8 used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_pdb_hierarchy_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyRange_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_pdb_hierarchy_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PySlice_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_pdb_hierarchy_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _PyBytes_Resize used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_pdb_hierarchy_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_pdb_hierarchy_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyIter_Check used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_pdb_hierarchy_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 24 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_dtrek_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_dtrek_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_covariance_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_covariance_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_covariance_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_covariance_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_crystal_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyDict_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_crystal_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyIter_Check used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_crystal_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_crystal_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyRange_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_crystal_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PySlice_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_crystal_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_GetItem used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_crystal_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_crystal_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_Occurred used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_crystal_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_Size used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_crystal_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 19 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_symmetry_search_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_symmetry_search_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_symmetry_search_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_symmetry_search_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_symmetry_search_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_anharmonic_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyComplex_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_anharmonic_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_anharmonic_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyComplex_FromDoubles used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_anharmonic_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lbfgs_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lbfgs_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lbfgs_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lbfgs_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lbfgs_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lbfgs_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lbfgs_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lbfgs_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lbfgs_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_fp_fdp_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_fp_fdp_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyComplex_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_fp_fdp_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_fp_fdp_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_fp_fdp_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyComplex_FromDoubles used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_fp_fdp_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_fp_fdp_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_fp_fdp_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyImport_ImportModule used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyRange_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_CallFunction used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyEval_CallFunction used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 1 similar warning has been skipped (use -v to see it) dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_array_family_flex_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBytes_AsString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_array_family_flex_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyCapsule_GetPointer used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_array_family_flex_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_Size used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_array_family_flex_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_Print used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_array_family_flex_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyRange_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_array_family_flex_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_TypeError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_array_family_flex_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyList_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_array_family_flex_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBytes_FromStringAndSize used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_array_family_flex_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyComplex_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_array_family_flex_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 41 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/determine_unit_cell_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/determine_unit_cell_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/determine_unit_cell_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/determine_unit_cell_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyCapsule_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_maptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_maptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_maptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyCapsule_GetPointer used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_maptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_maptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_maptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyComplex_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_maptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_maptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_maptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_maptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyUnicode_FromStringAndSize used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_optional_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_optional_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_optional_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_optional_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_FromWideChar used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_optional_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_optional_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_optional_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_optional_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_suffixtree_shared_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_suffixtree_shared_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_suffixtree_shared_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_suffixtree_shared_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_Clear used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_vector_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_IsInstance used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_vector_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyRange_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_vector_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_vector_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_GetIter used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_vector_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PySlice_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_vector_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyIter_Next used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_vector_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_vector_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_HasAttrString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_vector_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_vector_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_ab_initio_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_ab_initio_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_uctbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_uctbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_uctbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_uctbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_uctbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_uctbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_uctbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_uctbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_uctbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_uctbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyExc_StopIteration used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_icsd_radii_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_icsd_radii_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_icsd_radii_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_icsd_radii_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_icsd_radii_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_icsd_radii_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_icsd_radii_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyIter_Next used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_sgtbx_asu_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PySlice_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_sgtbx_asu_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_sgtbx_asu_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyRange_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_sgtbx_asu_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_sgtbx_asu_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_IsInstance used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_sgtbx_asu_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_GetIter used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_sgtbx_asu_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_Clear used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_sgtbx_asu_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_sgtbx_asu_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_Occurred used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_sgtbx_asu_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_glmtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_glmtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_glmtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_glmtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_glmtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_glmtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_glmtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_glmtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_glmtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_IsInstance used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyDict_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_pdb_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_FromStringAndSize used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_pdb_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_pdb_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_pdb_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_pdb_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_Occurred used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_pdb_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_Size used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_pdb_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_pdb_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_pdb_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_pdb_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 4 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_cubicle_neighbors_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_cubicle_neighbors_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_cubicle_neighbors_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_cubicle_neighbors_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_cubicle_neighbors_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_attenuation_coefficient_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_attenuation_coefficient_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_attenuation_coefficient_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_attenuation_coefficient_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_attenuation_coefficient_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_attenuation_coefficient_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_geometry_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_geometry_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_geometry_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_geometry_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_statistics_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_statistics_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyEval_CallFunction used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_french_wilson_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_french_wilson_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_french_wilson_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_french_wilson_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_french_wilson_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_french_wilson_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyEval_CallFunction used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_breadth_first_search_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_breadth_first_search_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_breadth_first_search_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_breadth_first_search_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_clustering_algorithm_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_clustering_algorithm_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyDict_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_clustering_algorithm_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_clustering_algorithm_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_set_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyRange_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_set_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_set_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyIter_Check used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_set_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_GetIter used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_set_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_FromStringAndSize used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_set_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_set_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_HasAttrString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_set_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_Clear used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_set_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_set_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_asymmetric_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_asymmetric_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_merging_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_merging_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_iso_surface_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_iso_surface_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_iso_surface_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_iso_surface_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_python_hybrid_times_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_python_hybrid_times_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_python_hybrid_times_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_python_hybrid_times_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_sparse_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyList_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_sparse_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_sparse_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_sparse_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_sparse_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_sparse_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyDict_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_sparse_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_sparse_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_IsInstance used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_sparse_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_sparse_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 14 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_adp_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyIter_Check used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_adp_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_adp_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyRange_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_adp_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PySlice_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_adp_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_GetItem used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_adp_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_adp_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_Occurred used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_adp_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_Size used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_adp_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_IsInstance used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_adp_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 12 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_boost_thread_test_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_boost_thread_test_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol pthread_condattr_setclock used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_boost_thread_test_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_boost_thread_test_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_boost_thread_test_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_covalent_radii_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_covalent_radii_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_StopIteration used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_covalent_radii_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_covalent_radii_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_covalent_radii_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_covalent_radii_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_covalent_radii_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_linalg_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_linalg_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_linalg_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_linalg_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_linalg_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_linalg_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_linalg_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_linalg_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_IsInstance used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_linalg_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_linalg_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_tiny_pse_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_tiny_pse_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_tiny_pse_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_tiny_pse_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_tiny_pse_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_tiny_pse_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_StopIteration used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_tiny_pse_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_tiny_pse_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_tiny_pse_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_scalepack_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_scalepack_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_minpack_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_minpack_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_minpack_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_minpack_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_minpack_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_minpack_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_minpack_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_minpack_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_graphics_utils_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_graphics_utils_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_graphics_utils_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyList_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_graphics_utils_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_graphics_utils_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_graphics_utils_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_graphics_utils_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_wigner_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_wigner_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_wigner_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_wigner_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/std_pair_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/std_pair_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/std_pair_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/std_pair_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/std_pair_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/std_pair_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_fftpack_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_fftpack_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_fftpack_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_fftpack_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_fftpack_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_fftpack_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_fftpack_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_sasaki_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_sasaki_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_StopIteration used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_sasaki_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_sasaki_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_sasaki_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_sasaki_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_sasaki_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_CheckSignals used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_python_meta_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_python_meta_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBytes_FromStringAndSize used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_python_meta_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyEval_CallFunction used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_python_meta_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_CallFunction used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_python_meta_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _PyBytes_Resize used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_python_meta_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_python_meta_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_python_meta_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyList_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_python_meta_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_python_meta_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 18 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_detectors_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_detectors_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBytes_FromStringAndSize used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_detectors_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_detectors_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_detectors_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_FromStringAndSize used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_detectors_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_detectors_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_detectors_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_detectors_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_detectors_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lbfgsb_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lbfgsb_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lbfgsb_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lbfgsb_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lbfgsb_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lbfgsb_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lbfgsb_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_FromStringAndSize used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lbfgsb_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lbfgsb_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_lbfgsb_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_xray_scattering_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_xray_scattering_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_StopIteration used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_xray_scattering_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_xray_scattering_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_xray_scattering_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_xray_scattering_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_FromStringAndSize used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_xray_scattering_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_xray_scattering_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_xray_scattering_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyList_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_xray_scattering_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_henke_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_henke_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_henke_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_henke_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_henke_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_StopIteration used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_henke_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_henke_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_IsInstance used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_constraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_GetIter used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_constraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_Clear used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_constraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_constraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_HasAttrString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_constraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_constraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_constraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyEval_CallFunction used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_constraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_constraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyIter_Next used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_refinement_constraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 21 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_multipolar_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_multipolar_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyList_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_chemical_elements_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_chemical_elements_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_chemical_elements_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/fable_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/fable_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_FromStringAndSize used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/fable_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/fable_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_Occurred used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/fable_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/fable_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/fable_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_Size used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/fable_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/fable_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/fable_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 2 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyIter_Check used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_array_family_shared_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_array_family_shared_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_array_family_shared_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_HasAttrString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_array_family_shared_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_array_family_shared_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_GetIter used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_array_family_shared_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_IsInstance used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_array_family_shared_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_Clear used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_array_family_shared_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_GetItem used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_array_family_shared_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_Occurred used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_array_family_shared_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_orientation_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_orientation_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_orientation_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_orientation_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_wavelengths_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_wavelengths_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_wavelengths_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_wavelengths_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_StopIteration used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_wavelengths_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_wavelengths_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_wavelengths_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_random_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_random_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_random_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_random_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_random_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_random_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_random_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_random_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_detectors_bruker_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_detectors_bruker_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_detectors_bruker_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_detectors_bruker_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_detectors_bruker_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_detectors_bruker_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_xray_observations_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_xray_observations_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_xray_observations_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_xray_observations_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_xray_observations_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_xray_observations_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_xray_observations_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_xray_observations_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_rational_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_rational_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_rational_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_rational_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_rational_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_rational_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_rational_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_rational_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_rational_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_rational_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyObject_GetIter used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyDict_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_ValueError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_FromStringAndSize used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_KeyError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_stl_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 11 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_suffixtree_single_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_Hash used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_suffixtree_single_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_suffixtree_single_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_suffixtree_single_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_suffixtree_single_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_suffixtree_single_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_KeyError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_suffixtree_single_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_suffixtree_single_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyList_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_suffixtree_single_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_suffixtree_single_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyObject_GetIter used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_stl_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_stl_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_stl_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_KeyError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_stl_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_stl_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_stl_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_Occurred used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_stl_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_stl_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyDict_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_stl_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/smtbx_stl_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_miller_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_miller_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_miller_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_miller_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_miller_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyIter_Next used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_miller_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_miller_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyComplex_FromDoubles used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_miller_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_miller_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_miller_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 17 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/omptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/omptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/omptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/omptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/omptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/omptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/omptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_neutron_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyComplex_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_neutron_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_StopIteration used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_neutron_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_neutron_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_neutron_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyComplex_FromDoubles used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_neutron_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_neutron_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_neutron_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_eltbx_neutron_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_Occurred used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_adptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_adptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_adptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_adptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_adptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_Size used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_adptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyIter_Check used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_adptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_adptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_adptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_adptbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 9 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_shelx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_shelx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_xplor_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_xplor_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_xplor_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_xplor_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_xplor_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_xplor_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyComplex_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_math_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_math_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_math_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyComplex_FromDoubles used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_math_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_math_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_math_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_math_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_math_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_math_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_math_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_sgtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_sgtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_GetIter used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_sgtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_Clear used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_sgtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_sgtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_sgtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_sgtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_FromStringAndSize used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_sgtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_sgtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyIter_Next used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_sgtbx_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 19 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyUnicode_FromStringAndSize used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_python_streambuf_test_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_python_streambuf_test_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_python_streambuf_test_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_python_streambuf_test_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_connected_component_algorithm_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyList_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_connected_component_algorithm_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_connected_component_algorithm_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_connected_component_algorithm_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_connected_component_algorithm_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_array_family_flex_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PySlice_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_array_family_flex_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_array_family_flex_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _PyBytes_Resize used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_array_family_flex_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyIter_Next used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_array_family_flex_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_array_family_flex_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyRange_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_array_family_flex_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_array_family_flex_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_Size used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_array_family_flex_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_array_family_flex_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 21 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_dsn6_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_dsn6_map_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_emma_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_emma_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_emma_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_emma_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_emma_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_emma_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_emma_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_emma_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_tuple_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_tuple_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_tuple_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_tuple_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_tuple_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyEval_CallFunction used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_rigid_body_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_rigid_body_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyList_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_rigid_body_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_rigid_body_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_rigid_body_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_rigid_body_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_rigid_body_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_rigid_body_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_Size used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_rigid_body_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_Occurred used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_rigid_body_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyComplex_FromDoubles used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_math_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_math_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_math_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyComplex_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_math_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_math_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_math_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_masks_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_masks_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_masks_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_masks_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_masks_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_masks_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_masks_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_masks_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_geometry_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_geometry_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyUnicode_FromStringAndSize used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_geometry_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_geometry_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_geometry_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_geometry_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyIter_Next used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_geometry_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_geometry_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_geometry_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_KeyError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_geometry_restraints_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 20 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyFloat_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_r3_utils_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_r3_utils_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_r3_utils_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_r3_utils_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_r3_utils_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/scitbx_r3_utils_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_translation_search_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_translation_search_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_translation_search_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_translation_search_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_translation_search_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_translation_search_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_utility_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyDict_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_utility_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_utility_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_utility_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_Clear used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_xray_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_IsInstance used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_xray_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_GetIter used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_xray_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyList_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_xray_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_HasAttrString used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_xray_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_xray_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_xray_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_xray_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyIter_Next used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_xray_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/cctbx_xray_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: 19 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyBool_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_wildcard_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyBool_FromLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_wildcard_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_wildcard_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/iotbx_wildcard_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_Type used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_metric_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyFloat_FromDouble used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_metric_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyTuple_New used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_metric_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_metric_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_metric_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/libcctbx0/usr/lib/x86_64-linux-gnu/boost_adaptbx_graph_metric_ext.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libcctbx0/usr/lib/x86_64-linux-gnu/libsmtbx_refinement_constraints.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libcctbx_sgtbx_asu.so.0.0.1 were not linked against libpthread.so.0 (they use none of the library's symbols) dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package python3-cctbx: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild dpkg-deb: building package 'libcctbx-dev' in '../libcctbx-dev_2021.12+ds1-4_amd64.deb'. dpkg-deb: building package 'libcctbx0-dbgsym' in '../libcctbx0-dbgsym_2021.12+ds1-4_amd64.deb'. dpkg-deb: building package 'libcctbx0' in '../libcctbx0_2021.12+ds1-4_amd64.deb'. dpkg-deb: building package 'python3-cctbx' in '../python3-cctbx_2021.12+ds1-4_amd64.deb'. dpkg-genbuildinfo --build=any -O../cctbx_2021.12+ds1-4_amd64.buildinfo dpkg-genchanges --build=any -O../cctbx_2021.12+ds1-4_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/cctbx-TO2hyq /tmp/cctbx-2021.12+ds1-46t9gz55i I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.De5lYqQBmC... I: success in 2705.0668 seconds md5: libcctbx-dev_2021.12+ds1-4_amd64.deb: OK md5: libcctbx0-dbgsym_2021.12+ds1-4_amd64.deb: OK md5: libcctbx0_2021.12+ds1-4_amd64.deb: OK md5: python3-cctbx_2021.12+ds1-4_amd64.deb: OK sha1: libcctbx-dev_2021.12+ds1-4_amd64.deb: OK sha1: libcctbx0-dbgsym_2021.12+ds1-4_amd64.deb: OK sha1: libcctbx0_2021.12+ds1-4_amd64.deb: OK sha1: python3-cctbx_2021.12+ds1-4_amd64.deb: OK sha256: libcctbx-dev_2021.12+ds1-4_amd64.deb: OK sha256: libcctbx0-dbgsym_2021.12+ds1-4_amd64.deb: OK sha256: libcctbx0_2021.12+ds1-4_amd64.deb: OK sha256: python3-cctbx_2021.12+ds1-4_amd64.deb: OK Checksums: OK