Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/h/hinge/hinge_0.5.0-7_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/hinge-0.5.0-7ko_w6_66/hinge_0.5.0-7_amd64.buildinfo Get source package info: hinge=0.5.0-7 Source URL: http://snapshot.notset.fr/mr/package/hinge/0.5.0-7/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1.1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-5+b1 binutils=2.37-10 binutils-common=2.37-10 binutils-x86-64-linux-gnu=2.37-10 blt=2.5.3+dfsg-4.1 bsdextrautils=2.37.2-4 bsdutils=1:2.37.2-4 build-essential=12.9 bzip2=1.0.8-5 catch2=2.13.7-1 cmake=3.22.1-1+b1 cmake-data=3.22.1-1 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-13 daligner=1.0+git20200727.ed40ce5-3 dascrubber=1.1-4 dash=0.5.11+git20210903+057cd650a4ed-3 dazzdb=1.0+git20201103.8d98c37-1.1+b1 debconf=1.5.79 debhelper=13.6 debianutils=5.5-1 dh-autoreconf=20 dh-elpa-helper=2.0.10 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dpkg=1.21.1 dpkg-dev=1.21.1 dwz=0.14-1 emacsen-common=3.0.4 file=1:5.41-2 findutils=4.8.0-1 fontconfig-config=2.13.1-4.2 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=11.2.0-13 gcc=4:11.2.0-2 gcc-11=11.2.0-13 gcc-11-base=11.2.0-13 gettext=0.21-4 gettext-base=0.21-4 grep=3.7-1 groff-base=1.22.4-7 gzip=1.10-4 hdf5-helpers=1.10.7+repack-4 hostname=3.23 icu-devtools=67.1-7 init-system-helpers=1.61 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libaec-dev=1.0.6-1 libaec0=1.0.6-1 libarchive-zip-perl=1.68-1 libarchive13=3.4.3-2+b1 libasan6=11.2.0-13 libatomic1=11.2.0-13 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1+b1 libbinutils=2.37-10 libblas3=3.10.0-2 libblkid1=2.37.2-4 libboost-dev=1.74.0.3 libboost-graph-dev=1.74.0.3 libboost-graph1.74-dev=1.74.0-13 libboost-graph1.74.0=1.74.0-13 libboost-regex1.74-dev=1.74.0-13 libboost-regex1.74.0=1.74.0-13 libboost-serialization1.74-dev=1.74.0-13 libboost-serialization1.74.0=1.74.0-13 libboost-test1.74-dev=1.74.0-13 libboost-test1.74.0=1.74.0-13 libboost1.74-dev=1.74.0-13 libbrotli1=1.0.9-2+b3 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-5 libc-bin=2.33-1 libc-dev-bin=2.33-1 libc6=2.33-1 libc6-dev=2.33-1 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-13 libcmark-gfm-extensions0=0.29.0.gfm.0-6 libcmark-gfm0=0.29.0.gfm.0-6 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.27-1 libcrypt1=1:4.4.27-1 libctf-nobfd0=2.37-10 libctf0=2.37-10 libcurl3-gnutls=7.79.1-2 libcurl4=7.79.1-2 libcurl4-openssl-dev=7.79.1-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.6 libdeflate0=1.8-1 libdouble-conversion3=3.1.5-7 libdpkg-perl=1.21.1 libedit2=3.1-20210910-1 libelf1=0.186-1 libexpat1=2.4.1-3 libffi8=3.4.2-3 libfile-stripnondeterminism-perl=1.13.0-1 libfmt-dev=8.0.1+ds1-4 libfmt8=8.0.1+ds1-4 libfontconfig1=2.13.1-4.2 libfreetype6=2.11.0+dfsg-1 libfribidi0=1.0.8-2 libgcc-11-dev=11.2.0-13 libgcc-s1=11.2.0-13 libgcrypt20=1.9.4-5 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgfortran5=11.2.0-13 libglib2.0-0=2.70.2-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.2-4 libgomp1=11.2.0-13 libgpg-error0=1.43-1 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.18.3-7 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 libhts3=1.13+ds-2 libhtscodecs2=1.1.1-3+b1 libicu-dev=67.1-7 libicu67=67.1-7 libidn2-0=2.3.2-2 libimagequant0=2.12.2-1.1 libisl23=0.24-2 libitm1=11.2.0-13 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 libjs-jquery=3.5.1+dfsg+~3.5.5-8 libjs-jquery-ui=1.13.0+dfsg-1 libjsoncpp25=1.9.5-2 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblapack3=3.10.0-2 liblbfgsb0=3.0+dfsg.3-10 liblcms2-2=2.12~rc1-2 libldap-2.4-2=2.4.59+dfsg-1 liblsan0=11.2.0-13 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 libmd0=1.0.4-1 libmount1=2.37.2-4 libmpc3=1.2.1-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncurses6=6.3-1 libncursesw6=6.3-1 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libopenjp2-7=2.4.0-3 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 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.4-1 libpng16-16=1.6.37-3 libprocps8=2:3.3.17-5 libpsl5=0.21.0-1.2 libpython3-stdlib=3.9.8-1 libpython3.10-minimal=3.10.1-2 libpython3.10-stdlib=3.10.1-2 libpython3.9-minimal=3.9.9-2 libpython3.9-stdlib=3.9.9-2 libqhull-r8.0=2020.2-4 libquadmath0=11.2.0-13 libraqm0=0.7.0-4 libreadline8=8.1-2 librhash0=1.4.2-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg2-2 libsasl2-modules-db=2.1.27+dfsg2-2 libseccomp2=2.5.3-2 libselinux1=3.3-1+b1 libsigsegv2=2.13-1 libsmartcols1=2.37.2-4 libspdlog-dev=1:1.9.2+ds-0.2 libspdlog1=1:1.9.2+ds-0.2 libsqlite3-0=3.36.0-2 libssh2-1=1.10.0-2 libssl-dev=1.1.1l-1 libssl1.1=1.1.1l-1 libstdc++-11-dev=11.2.0-13 libstdc++6=11.2.0-13 libsub-override-perl=0.09-2 libsystemd0=249.7-1 libsz2=1.0.6-1 libtasn1-6=4.18.0-4 libtcl8.6=8.6.12+dfsg-1 libtiff5=4.3.0-2 libtinfo6=6.3-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtk8.6=8.6.12-1 libtool=2.4.6-15 libtsan0=11.2.0-13 libubsan1=11.2.0-13 libuchardet0=0.0.7-1 libudev1=249.7-1 libunistring2=0.9.10-6 libuuid1=2.37.2-4 libuv1=1.42.0-1 libwebp6=0.6.1-2.1 libwebpdemux2=0.6.1-2.1 libwebpmux3=0.6.1-2.1 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=2.9.12+dfsg-5+b1 libxrender1=1:0.9.10-1 libxslt1.1=1.1.34-4 libxss1=1:1.2.3-1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.15.5-2 login=1:4.8.1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 ncurses-base=6.3-1 ncurses-bin=6.3-1 pandoc=2.9.2.1-1+b2 pandoc-data=2.9.2.1-1 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 po-debconf=1.0.21+nmu1 procps=2:3.3.17-5 python-matplotlib-data=3.5.0-5 python3=3.9.8-1 python3-appdirs=1.4.4-1 python3-attr=21.2.0-1 python3-biopython=1.79+dfsg-1+b1 python3-brotli=1.0.9-2+b3 python3-colorama=0.4.4-1 python3-colorlog=6.4.1-1 python3-colormap=1.0.4-2 python3-cycler=0.11.0-1 python3-dateutil=2.8.1-6 python3-decorator=4.4.2-2 python3-easydev=0.12.0+dfsg-1 python3-fonttools=4.28.3-1 python3-fs=2.4.12-1 python3-kiwisolver=1.3.2-1+b1 python3-lxml=4.6.4-1 python3-lz4=3.1.3+dfsg-1+b1 python3-matplotlib=3.5.0-5 python3-minimal=3.9.8-1 python3-mpmath=1.2.1-2 python3-networkx=2.5+ds-2 python3-numpy=1:1.21.5-1 python3-packaging=21.3-1 python3-pbcore=1.7.1+git20200430.a127b1e+dfsg-1 python3-pexpect=4.8.0-2 python3-pil=8.4.0-1 python3-pil.imagetk=8.4.0-1 python3-pkg-resources=59.6.0-1 python3-ptyprocess=0.7.0-3 python3-pyparsing=2.4.7-1 python3-pysam=0.17.0+ds-2+b1 python3-renderpm=3.6.2-1 python3-reportlab=3.6.2-1 python3-reportlab-accel=3.6.2-1 python3-scipy=1.7.1-2+b1 python3-six=1.16.0-2 python3-sympy=1.7.1-3 python3-tk=3.9.9-3 python3-tz=2021.3-1 python3-ufolib2=0.12.1+dfsg1-1 python3-ujson=4.2.0-1+b1 python3.10=3.10.1-2 python3.10-minimal=3.10.1-2 python3.9=3.9.9-2 python3.9-minimal=3.9.9-2 readline-common=8.1-2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.01-1 tar=1.34+dfsg-1 tk8.6-blt2.5=2.5.3+dfsg-4.1 tzdata=2021e-1 ucf=3.0043 unicode-data=14.0.0-1.1 util-linux=2.37.2-4 x11-common=1:7.7+23 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211227T152656Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211227T152656Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211222T152232Z/ 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 hinge=0.5.0-7 && mkdir -p /build/hinge-A7WhLP && dpkg-source --no-check -x /*.dsc /build/hinge-A7WhLP/hinge-0.5.0 && chown -R builduser:builduser /build/hinge-A7WhLP" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/hinge-A7WhLP/hinge-0.5.0 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1640157672" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/hinge-A7WhLP /tmp/hinge-0.5.0-7ko_w6_66 bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211222T152232Z 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.hH1snu3RNG 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.hH1snu3RNG Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20211222T152232Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211222T152232Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (907 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 ... 4680 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-1) ... 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/20211227T152656Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211227T152656Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211222T152232Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.hH1snu3RNG Get:1 http://snapshot.notset.fr/archive/debian/20211227T152656Z bookworm InRelease [129 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20211222T152232Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20211227T152656Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211227T152656Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211227T152656Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211227T152656Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211227T152656Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211227T152656Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20211227T152656Z bookworm/main Sources [11.8 MB] Get:4 http://snapshot.notset.fr/archive/debian/20211227T152656Z bookworm/main amd64 Packages [11.2 MB] Fetched 23.1 MB in 20s (1178 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.hH1snu3RNG I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d hinge=0.5.0-7 && mkdir -p /build/hinge-A7WhLP && dpkg-source --no-check -x /*.dsc /build/hinge-A7WhLP/hinge-0.5.0 && chown -R builduser:builduser /build/hinge-A7WhLP"' exec /tmp/mmdebstrap.hH1snu3RNG Reading package lists... NOTICE: 'hinge' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hinge.git Please use: git clone https://salsa.debian.org/med-team/hinge.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 499 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211227T152656Z bookworm/main hinge 0.5.0-7 (dsc) [2141 B] Get:2 http://snapshot.notset.fr/archive/debian/20211227T152656Z bookworm/main hinge 0.5.0-7 (tar) [477 kB] Get:3 http://snapshot.notset.fr/archive/debian/20211227T152656Z bookworm/main hinge 0.5.0-7 (diff) [19.9 kB] Fetched 499 kB in 1s (534 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'hinge_0.5.0-7.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting hinge in /build/hinge-A7WhLP/hinge-0.5.0 dpkg-source: info: unpacking hinge_0.5.0.orig.tar.gz dpkg-source: info: unpacking hinge_0.5.0-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying external-spdlog.patch dpkg-source: info: applying libspdlog-14.0.patch dpkg-source: info: applying libspdlog-1:1.3.0 dpkg-source: info: applying 2to3.patch dpkg-source: info: applying spdlog-1.5.0.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/hinge-A7WhLP/hinge-0.5.0 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1640157672" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.hH1snu3RNG dpkg-buildpackage: info: source package hinge dpkg-buildpackage: info: source version 0.5.0-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu .. -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: graph -- Configuring done CMake Warning (dev) at src/filter/CMakeLists.txt:4 (add_executable): Policy CMP0115 is not set: Source file extensions must be explicit. Run "cmake --help-policy CMP0115" for policy details. Use the cmake_policy command to set the policy and suppress this warning. File: /build/hinge-A7WhLP/hinge-0.5.0/src/filter/filter.cpp This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/maximal/CMakeLists.txt:4 (add_executable): Policy CMP0115 is not set: Source file extensions must be explicit. Run "cmake --help-policy CMP0115" for policy details. Use the cmake_policy command to set the policy and suppress this warning. File: /build/hinge-A7WhLP/hinge-0.5.0/src/maximal/maximal.cpp This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/consensus/CMakeLists.txt:4 (add_executable): Policy CMP0115 is not set: Source file extensions must be explicit. Run "cmake --help-policy CMP0115" for policy details. Use the cmake_policy command to set the policy and suppress this warning. File: /build/hinge-A7WhLP/hinge-0.5.0/src/consensus/draft.cpp This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/layout/CMakeLists.txt:9 (add_executable): Policy CMP0115 is not set: Source file extensions must be explicit. Run "cmake --help-policy CMP0115" for policy details. Use the cmake_policy command to set the policy and suppress this warning. File: /build/hinge-A7WhLP/hinge-0.5.0/src/layout/hinging.cpp This warning is for project developers. Use -Wno-dev to suppress it. -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu dh_auto_build -a cd obj-x86_64-linux-gnu && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/hinge-A7WhLP/hinge-0.5.0 -B/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/CMakeFiles /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/depend make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/depend make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/depend make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/depend make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/depend make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-A7WhLP/hinge-0.5.0 /build/hinge-A7WhLP/hinge-0.5.0/src /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/CMakeFiles/man.dir/DependInfo.cmake --color= make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/depend make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/depend make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-A7WhLP/hinge-0.5.0 /build/hinge-A7WhLP/hinge-0.5.0/src/lib /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/ini.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-A7WhLP/hinge-0.5.0 /build/hinge-A7WhLP/hinge-0.5.0/src/lib /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/DB.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-A7WhLP/hinge-0.5.0 /build/hinge-A7WhLP/hinge-0.5.0/src/lib /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/PAF.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-A7WhLP/hinge-0.5.0 /build/hinge-A7WhLP/hinge-0.5.0/src/lib /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/LA.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-A7WhLP/hinge-0.5.0 /build/hinge-A7WhLP/hinge-0.5.0/src/lib /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/kmer_lookup.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-A7WhLP/hinge-0.5.0 /build/hinge-A7WhLP/hinge-0.5.0/src/lib /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/DW_banded.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/build make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/build make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/build make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/build make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/build make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/build make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/build make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' [ 3%] Building C object bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-A7WhLP/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-A7WhLP/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -MF CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o.d -o CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -c /build/hinge-A7WhLP/hinge-0.5.0/src/lib/kmer_lookup.c [ 6%] Building C object bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-A7WhLP/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-A7WhLP/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o -MF CMakeFiles/DW_banded.dir/DW_banded.c.o.d -o CMakeFiles/DW_banded.dir/DW_banded.c.o -c /build/hinge-A7WhLP/hinge-0.5.0/src/lib/DW_banded.c [ 13%] Building C object bin/lib/CMakeFiles/ini.dir/ini.c.o [ 13%] Generating hinge.1 [ 20%] Building CXX object bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o [ 20%] Building C object bin/lib/CMakeFiles/LA.dir/align.c.o cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-A7WhLP/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-A7WhLP/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/ini.dir/ini.c.o -MF CMakeFiles/ini.dir/ini.c.o.d -o CMakeFiles/ini.dir/ini.c.o -c /build/hinge-A7WhLP/hinge-0.5.0/src/lib/ini.c cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin && /usr/bin/pandoc --from markdown --to man -s /build/hinge-A7WhLP/hinge-0.5.0/src/hinge.1.md -o hinge.1 cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/c++ -I/build/hinge-A7WhLP/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-A7WhLP/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o -MF CMakeFiles/ini.dir/INIReader.cpp.o.d -o CMakeFiles/ini.dir/INIReader.cpp.o -c /build/hinge-A7WhLP/hinge-0.5.0/src/lib/INIReader.cpp cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-A7WhLP/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-A7WhLP/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/LA.dir/align.c.o -MF CMakeFiles/LA.dir/align.c.o.d -o CMakeFiles/LA.dir/align.c.o -c /build/hinge-A7WhLP/hinge-0.5.0/src/lib/align.c [ 27%] Building C object bin/lib/CMakeFiles/DB.dir/DB.c.o [ 27%] Building C object bin/lib/CMakeFiles/DB.dir/QV.c.o cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-A7WhLP/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-A7WhLP/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DB.dir/DB.c.o -MF CMakeFiles/DB.dir/DB.c.o.d -o CMakeFiles/DB.dir/DB.c.o -c /build/hinge-A7WhLP/hinge-0.5.0/src/lib/DB.c cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-A7WhLP/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-A7WhLP/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DB.dir/QV.c.o -MF CMakeFiles/DB.dir/QV.c.o.d -o CMakeFiles/DB.dir/QV.c.o -c /build/hinge-A7WhLP/hinge-0.5.0/src/lib/QV.c [ 31%] Building C object bin/lib/CMakeFiles/PAF.dir/paf.c.o cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-A7WhLP/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-A7WhLP/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/PAF.dir/paf.c.o -MF CMakeFiles/PAF.dir/paf.c.o.d -o CMakeFiles/PAF.dir/paf.c.o -c /build/hinge-A7WhLP/hinge-0.5.0/src/lib/paf.c make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' /build/hinge-A7WhLP/hinge-0.5.0/src/lib/DB.c: In function ‘Load_QVs’: /build/hinge-A7WhLP/hinge-0.5.0/src/lib/DB.c:916:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 916 | fscanf(istub,DB_NFILE,&nfiles); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/hinge-A7WhLP/hinge-0.5.0/src/lib/DB.c:920:13: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 920 | { fscanf(istub,DB_FDATA,&last,fname,prolog); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/hinge-A7WhLP/hinge-0.5.0/src/lib/DB.c:925:13: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 925 | { fscanf(istub,DB_FDATA,&last,fname,prolog); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 34%] Linking C static library libPAF.a cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/PAF.dir/cmake_clean_target.cmake cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/PAF.dir/link.txt --verbose=1 /usr/bin/ar qc libPAF.a CMakeFiles/PAF.dir/paf.c.o /build/hinge-A7WhLP/hinge-0.5.0/src/lib/kmer_lookup.c: In function ‘find_best_aln_range’: /build/hinge-A7WhLP/hinge-0.5.0/src/lib/kmer_lookup.c:347:14: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 347 | q_coor = calloc( km_ptr->count, sizeof(seq_coor_t) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/hinge-A7WhLP/hinge-0.5.0/src/lib/kmer_lookup.c:56: /usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ /build/hinge-A7WhLP/hinge-0.5.0/src/lib/kmer_lookup.c:348:14: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 348 | t_coor = calloc( km_ptr->count, sizeof(seq_coor_t) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/hinge-A7WhLP/hinge-0.5.0/src/lib/kmer_lookup.c:56: /usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ [ 37%] Linking C static library libDW_banded.a cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/DW_banded.dir/cmake_clean_target.cmake cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DW_banded.dir/link.txt --verbose=1 [ 37%] Built target man /usr/bin/ar qc libDW_banded.a CMakeFiles/DW_banded.dir/DW_banded.c.o /build/hinge-A7WhLP/hinge-0.5.0/src/lib/DB.c: In function ‘Open_DB’: /build/hinge-A7WhLP/hinge-0.5.0/src/lib/DB.c:533:11: warning: ‘free’ called on pointer ‘p’ with nonzero offset 40 [-Wfree-nonheap-object] 533 | free(reads); | ^~~~~~~~~~~ /build/hinge-A7WhLP/hinge-0.5.0/src/lib/DB.c:84:12: note: returned from ‘malloc’ 84 | if ((p = malloc(size)) == NULL) | ^~~~~~~~~~~~ /usr/bin/ranlib libPAF.a [ 41%] Linking C static library libkmer_lookup.a cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/kmer_lookup.dir/cmake_clean_target.cmake cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kmer_lookup.dir/link.txt --verbose=1 /usr/bin/ar qc libkmer_lookup.a CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o /usr/bin/ranlib libDW_banded.a make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' /usr/bin/ranlib libkmer_lookup.a make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' /build/hinge-A7WhLP/hinge-0.5.0/src/lib/DB.c: In function ‘Read_All_Sequences’: /build/hinge-A7WhLP/hinge-0.5.0/src/lib/DB.c:1587:15: warning: ‘free’ called on pointer ‘p’ with nonzero offset 1 [-Wfree-nonheap-object] 1587 | free(seq); | ^~~~~~~~~ /build/hinge-A7WhLP/hinge-0.5.0/src/lib/DB.c:84:12: note: returned from ‘malloc’ 84 | if ((p = malloc(size)) == NULL) | ^~~~~~~~~~~~ [ 41%] Built target PAF [ 44%] Linking C static library libDB.a cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/DB.dir/cmake_clean_target.cmake cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DB.dir/link.txt --verbose=1 [ 44%] Built target DW_banded /usr/bin/ar qc libDB.a CMakeFiles/DB.dir/DB.c.o CMakeFiles/DB.dir/QV.c.o [ 44%] Built target kmer_lookup make -f bin/lib/CMakeFiles/falcon.dir/build.make bin/lib/CMakeFiles/falcon.dir/depend make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-A7WhLP/hinge-0.5.0 /build/hinge-A7WhLP/hinge-0.5.0/src/lib /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/falcon.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/lib/CMakeFiles/falcon.dir/build.make bin/lib/CMakeFiles/falcon.dir/build make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' [ 48%] Building C object bin/lib/CMakeFiles/falcon.dir/falcon.c.o cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-A7WhLP/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-A7WhLP/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/falcon.dir/falcon.c.o -MF CMakeFiles/falcon.dir/falcon.c.o.d -o CMakeFiles/falcon.dir/falcon.c.o -c /build/hinge-A7WhLP/hinge-0.5.0/src/lib/falcon.c /usr/bin/ranlib libDB.a make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' [ 51%] Linking CXX static library libini.a cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/ini.dir/cmake_clean_target.cmake cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/ini.dir/link.txt --verbose=1 /usr/bin/ar qc libini.a CMakeFiles/ini.dir/ini.c.o CMakeFiles/ini.dir/INIReader.cpp.o [ 55%] Linking C static library libfalcon.a cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/falcon.dir/cmake_clean_target.cmake cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/falcon.dir/link.txt --verbose=1 /usr/bin/ar qc libfalcon.a CMakeFiles/falcon.dir/falcon.c.o /usr/bin/ranlib libfalcon.a make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' [ 55%] Built target DB /usr/bin/ranlib libini.a make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' [ 55%] Built target falcon [ 55%] Built target ini [ 58%] Linking C static library libLA.a cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/LA.dir/cmake_clean_target.cmake cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/LA.dir/link.txt --verbose=1 /usr/bin/ar qc libLA.a CMakeFiles/LA.dir/align.c.o /usr/bin/ranlib libLA.a make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' [ 58%] Built target LA make -f bin/lib/CMakeFiles/LAInterface.dir/build.make bin/lib/CMakeFiles/LAInterface.dir/depend make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-A7WhLP/hinge-0.5.0 /build/hinge-A7WhLP/hinge-0.5.0/src/lib /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/LAInterface.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/lib/CMakeFiles/LAInterface.dir/build.make bin/lib/CMakeFiles/LAInterface.dir/build make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' [ 62%] Building CXX object bin/lib/CMakeFiles/LAInterface.dir/LAInterface.cpp.o cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/c++ -I/build/hinge-A7WhLP/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-A7WhLP/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/lib/CMakeFiles/LAInterface.dir/LAInterface.cpp.o -MF CMakeFiles/LAInterface.dir/LAInterface.cpp.o.d -o CMakeFiles/LAInterface.dir/LAInterface.cpp.o -c /build/hinge-A7WhLP/hinge-0.5.0/src/lib/LAInterface.cpp /build/hinge-A7WhLP/hinge-0.5.0/src/lib/LAInterface.cpp: In member function ‘void LAInterface::getOverlapw(std::vector&, int, int)’: /build/hinge-A7WhLP/hinge-0.5.0/src/lib/LAInterface.cpp:1666:22: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘int64’ {aka ‘long long int’} [-Wformat=] 1666 | printf("%d percent finished\n", j/(novl/100)); | ~^ ~~~~~~~~~~~~ | | | | int int64 {aka long long int} | %lld [ 65%] Linking CXX static library libLAInterface.a cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/LAInterface.dir/cmake_clean_target.cmake cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/LAInterface.dir/link.txt --verbose=1 /usr/bin/ar qc libLAInterface.a CMakeFiles/LAInterface.dir/LAInterface.cpp.o /usr/bin/ranlib libLAInterface.a make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' [ 65%] Built target LAInterface make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/depend make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/depend make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/depend make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/depend make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/depend make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-A7WhLP/hinge-0.5.0 /build/hinge-A7WhLP/hinge-0.5.0/src/filter /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter/CMakeFiles/Reads_filter.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-A7WhLP/hinge-0.5.0 /build/hinge-A7WhLP/hinge-0.5.0/src/maximal /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal/CMakeFiles/get_maximal_reads.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-A7WhLP/hinge-0.5.0 /build/hinge-A7WhLP/hinge-0.5.0/src/consensus /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus/CMakeFiles/draft_assembly.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-A7WhLP/hinge-0.5.0 /build/hinge-A7WhLP/hinge-0.5.0/src/consensus /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus/CMakeFiles/consensus.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-A7WhLP/hinge-0.5.0 /build/hinge-A7WhLP/hinge-0.5.0/src/layout /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout/CMakeFiles/hinging.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/build make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/build make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/build make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/build make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' [ 72%] Building CXX object bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o [ 72%] Building CXX object bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-A7WhLP/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-A7WhLP/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o -MF CMakeFiles/draft_assembly.dir/draft.cpp.o.d -o CMakeFiles/draft_assembly.dir/draft.cpp.o -c /build/hinge-A7WhLP/hinge-0.5.0/src/consensus/draft.cpp cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-A7WhLP/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-A7WhLP/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o -MF CMakeFiles/Reads_filter.dir/filter.cpp.o.d -o CMakeFiles/Reads_filter.dir/filter.cpp.o -c /build/hinge-A7WhLP/hinge-0.5.0/src/filter/filter.cpp [ 75%] Building CXX object bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-A7WhLP/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-A7WhLP/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -MF CMakeFiles/get_maximal_reads.dir/maximal.cpp.o.d -o CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -c /build/hinge-A7WhLP/hinge-0.5.0/src/maximal/maximal.cpp [ 82%] Building CXX object bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o [ 82%] Building CXX object bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DSPDLOG_FMT_EXTERNAL -I/build/hinge-A7WhLP/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-A7WhLP/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o -MF CMakeFiles/hinging.dir/hinging.cpp.o.d -o CMakeFiles/hinging.dir/hinging.cpp.o -c /build/hinge-A7WhLP/hinge-0.5.0/src/layout/hinging.cpp cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-A7WhLP/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-A7WhLP/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o -MF CMakeFiles/consensus.dir/consensus.cpp.o.d -o CMakeFiles/consensus.dir/consensus.cpp.o -c /build/hinge-A7WhLP/hinge-0.5.0/src/consensus/consensus.cpp [ 86%] Linking CXX executable consensus cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus && /usr/bin/cmake -E cmake_link_script CMakeFiles/consensus.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hinge-A7WhLP/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/consensus.dir/consensus.cpp.o -o consensus -lfmt ../lib/libLAInterface.a ../lib/libfalcon.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz ../lib/libkmer_lookup.a ../lib/libDW_banded.a make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' [ 86%] Built target consensus [ 89%] Linking CXX executable Reads_filter cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter && /usr/bin/cmake -E cmake_link_script CMakeFiles/Reads_filter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hinge-A7WhLP/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/Reads_filter.dir/filter.cpp.o -o Reads_filter -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' [ 89%] Built target Reads_filter [ 93%] Linking CXX executable hinging cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout && /usr/bin/cmake -E cmake_link_script CMakeFiles/hinging.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hinge-A7WhLP/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hinging.dir/hinging.cpp.o -o hinging -lfmt ../lib/libLAInterface.a ../lib/libini.a /usr/lib/x86_64-linux-gnu/libboost_graph.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz /usr/lib/x86_64-linux-gnu/libboost_regex.a make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' [ 93%] Built target hinging [ 96%] Linking CXX executable get_maximal_reads cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal && /usr/bin/cmake -E cmake_link_script CMakeFiles/get_maximal_reads.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hinge-A7WhLP/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -o get_maximal_reads -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' [ 96%] Built target get_maximal_reads [100%] Linking CXX executable draft_assembly cd /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus && /usr/bin/cmake -E cmake_link_script CMakeFiles/draft_assembly.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hinge-A7WhLP/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/draft_assembly.dir/draft.cpp.o -o draft_assembly -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libfalcon.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz ../lib/libkmer_lookup.a ../lib/libDW_banded.a make[3]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' [100%] Built target draft_assembly make[2]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' dh: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/hinge/ -a cd obj-x86_64-linux-gnu && make -j10 install DESTDIR=/build/hinge-A7WhLP/hinge-0.5.0/debian/hinge AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/hinge-A7WhLP/hinge-0.5.0 -B/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph_nogt.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/download_NCTC_pipeline.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly_not_perfect.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_region.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_w_repeat.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw_pileup_region.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw_pileup_region_find_bridges.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/fasta_to_fastq.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_NCTC_json.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_consensus_gfa.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_annotation.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path_norevcomp.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_single_strand.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/interface_utils.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/longest_path.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/merge_hinges.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw.sh -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw_large.sh -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_alignment.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_qv.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_read.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/pileup.ipynb -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus_norevcomp.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_nctc.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping_nanopore.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/random_condensation.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/repeat_annotate_reads.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping2.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping3.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_alignment.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_read.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/split_las.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/unitig.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/Visualise_graph.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth_json.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/clip_ends.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/compute_n50_from_draft.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_and_annotate.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_annotate_clip_ends.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_create_gfa_compute_n50.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_with_gt.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/connected.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/correct_head.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_bandage_file.py -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/share/man/man1/hinge.1 -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/bin/hinge -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/Reads_filter -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_maximal_reads -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/consensus -- Installing: /build/hinge-A7WhLP/hinge-0.5.0/debian/hinge/usr/lib/hinge/hinging make[1]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0/obj-x86_64-linux-gnu' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installexamples make[1]: Entering directory '/build/hinge-A7WhLP/hinge-0.5.0' dh_installexamples # only install nominal.ini from the utils/ directory, but preserve # the directory structure (since demo scripts expect it) mkdir -p debian/hinge/usr/share/doc/hinge/examples/utils \ && cp utils/nominal.ini debian/hinge/usr/share/doc/hinge/examples/utils make[1]: Leaving directory '/build/hinge-A7WhLP/hinge-0.5.0' dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'hinge-dbgsym' in '../hinge-dbgsym_0.5.0-7_amd64.deb'. dpkg-deb: building package 'hinge' in '../hinge_0.5.0-7_amd64.deb'. dpkg-genbuildinfo --build=any -O../hinge_0.5.0-7_amd64.buildinfo dpkg-genchanges --build=any -O../hinge_0.5.0-7_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/hinge-A7WhLP /tmp/hinge-0.5.0-7ko_w6_66 I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.hH1snu3RNG... I: success in 5022.7588 seconds md5: hinge-dbgsym_0.5.0-7_amd64.deb: OK md5: hinge_0.5.0-7_amd64.deb: OK sha1: hinge-dbgsym_0.5.0-7_amd64.deb: OK sha1: hinge_0.5.0-7_amd64.deb: OK sha256: hinge-dbgsym_0.5.0-7_amd64.deb: OK sha256: hinge_0.5.0-7_amd64.deb: OK Checksums: OK