Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/d/discosnp/discosnp_4.4.4-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/discosnp-4.4.4-1srlzqnk1/discosnp_4.4.4-1_amd64.buildinfo Get source package info: discosnp=4.4.4-1 Source URL: http://snapshot.notset.fr/mr/package/discosnp/4.4.4-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.2-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.47 bash=5.0-7 binutils=2.35.1-1 binutils-common=2.35.1-1 binutils-x86-64-linux-gnu=2.35.1-1 bsdextrautils=2.36-3+b1 bsdutils=1:2.36-3+b1 build-essential=12.8 bzip2=1.0.8-4 cmake=3.18.2-1 cmake-data=3.18.2-1 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.0-13 dash=0.5.10.2-7 debconf=1.5.74 debhelper=13.2.1 debianutils=4.11.2 dh-autoreconf=19 dh-python=4.20200925 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 file=1:5.38-5 findutils=4.7.0-1 g++=4:10.2.0-1 g++-10=10.2.0-13 gcc=4:10.2.0-1 gcc-10=10.2.0-13 gcc-10-base=10.2.0-13 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.4-1 groff-base=1.22.4-5 gzip=1.10-2 hdf5-helpers=1.10.6+repack-2 hostname=3.23 init-system-helpers=1.58 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libaec-dev=1.0.4-1 libaec0=1.0.4-1 libarchive-zip-perl=1.68-1 libarchive13=3.4.3-2 libasan6=10.2.0-13 libatomic1=10.2.0-13 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3 libaudit1=1:2.8.5-3+b1 libbinutils=2.35.1-1 libblkid1=2.36-3+b1 libboost-dev=1.71.0.3 libboost1.71-dev=1.71.0-6+b2 libbrotli1=1.0.9-2 libbz2-1.0=1.0.8-4 libc-bin=2.31-3 libc-dev-bin=2.31-3 libc6=2.31-3 libc6-dev=2.31-3 libcap-ng0=0.7.9-2.2 libcc1-0=10.2.0-13 libcom-err2=1.45.6-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-1 libctf0=2.35.1-1 libcurl4=7.72.0-1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.254 libdebhelper-perl=13.2.1 libdpkg-perl=1.20.5 libelf1=0.181-1 libexpat1=2.2.9-1 libffi7=3.3-4 libfile-stripnondeterminism-perl=1.9.0-1 libgatbcore-dev=1.4.2+dfsg-5 libgatbcore3=1.4.2+dfsg-5 libgcc-10-dev=10.2.0-13 libgcc-s1=10.2.0-13 libgcrypt20=1.8.6-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libgfortran5=10.2.0-13 libglib2.0-0=2.66.0-2 libgmp10=2:6.2.0+dfsg-6 libgnutls30=3.6.15-4 libgomp1=10.2.0-13 libgpg-error0=1.38-2 libgssapi-krb5-2=1.17-10 libhdf5-103-1=1.10.6+repack-2 libhdf5-cpp-103-1=1.10.6+repack-2 libhdf5-dev=1.10.6+repack-2 libhdf5-fortran-102=1.10.6+repack-2 libhdf5-hl-100=1.10.6+repack-2 libhdf5-hl-cpp-100=1.10.6+repack-2 libhdf5-hl-fortran-100=1.10.6+repack-2 libhogweed6=3.6-2 libicu67=67.1-4 libidn2-0=2.3.0-1 libisl22=0.22.1-1 libitm1=10.2.0-13 libjpeg-dev=1:2.0.5-1.1 libjpeg62-turbo=1:2.0.5-1.1 libjpeg62-turbo-dev=1:2.0.5-1.1 libjsoncpp1=1.7.4-3.1 libk5crypto3=1.17-10 libkeyutils1=1.6.1-2 libkrb5-3=1.17-10 libkrb5support0=1.17-10 libldap-2.4-2=2.4.53+dfsg-1 liblsan0=10.2.0-13 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-5 libmagic1=1:5.38-5 libmount1=2.36-3+b1 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncurses6=6.2+20200918-1 libncursesw6=6.2+20200918-1 libnettle8=3.6-2 libnghttp2-14=1.41.0-3 libp11-kit0=0.23.21-2 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.34-7 libpcre3=2:8.39-13 libperl5.30=5.30.3-4 libpipeline1=1.5.3-1 libprocps8=2:3.3.16-5 libpsl5=0.21.0-1.1 libpython3-stdlib=3.8.2-3 libpython3.8-minimal=3.8.6-1 libpython3.8-stdlib=3.8.6-1 libquadmath0=10.2.0-13 libreadline8=8.0-4 librhash0=1.4.0-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.4.4-1 libselinux1=3.1-2 libsigsegv2=2.12-2 libsmartcols1=2.36-3+b1 libsqlite3-0=3.33.0-1 libssh2-1=1.8.0-2.1 libssl1.1=1.1.1g-1 libstdc++-10-dev=10.2.0-13 libstdc++6=10.2.0-13 libsub-override-perl=0.09-2 libsystemd0=246.6-1 libsz2=1.0.4-1 libtasn1-6=4.16.0-2 libtinfo6=6.2+20200918-1 libtool=2.4.6-14 libtsan0=10.2.0-13 libubsan1=10.2.0-13 libuchardet0=0.0.7-1 libudev1=246.6-1 libunistring2=0.9.10-4 libuuid1=2.36-3+b1 libuv1=1.39.0-1 libxml2=2.9.10+dfsg-6 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.8.10-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 mime-support=3.64 ncurses-base=6.2+20200918-1 ncurses-bin=6.2+20200918-1 patch=2.7.6-6 perl=5.30.3-4 perl-base=5.30.3-4 perl-modules-5.30=5.30.3-4 po-debconf=1.0.21 procps=2:3.3.16-5 python3=3.8.2-3 python3-distutils=3.8.5-1 python3-lib2to3=3.8.5-1 python3-minimal=3.8.2-3 python3.8=3.8.6-1 python3.8-minimal=3.8.6-1 readline-common=8.0-4 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tar=1.30+dfsg-7 util-linux=2.36-3+b1 xz-utils=5.2.4-1+b1 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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201004T083822Z/ 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 discosnp=4.4.4-1 && mkdir -p /build/discosnp-DVg9OR && dpkg-source --no-check -x /*.dsc /build/discosnp-DVg9OR/discosnp-4.4.4 && chown -R builduser:builduser /build/discosnp-DVg9OR" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/discosnp-DVg9OR/discosnp-4.4.4 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1601556852" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/discosnp-DVg9OR /tmp/discosnp-4.4.4-1srlzqnk1 bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201004T083822Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.MkTwWDsY3q 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.MkTwWDsY3q Reading package lists... Building dependency tree... util-linux is already the newest version (2.36-3+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 134 kB of archives. After this operation, 395 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20201004T083822Z unstable/main amd64 libfakeroot amd64 1.25.2-1 [46.9 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201004T083822Z unstable/main amd64 fakeroot amd64 1.25.2-1 [86.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (840 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 ... 4582 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.2-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.2-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.2-1_amd64.deb ... Unpacking fakeroot (1.25.2-1) ... Setting up libfakeroot:amd64 (1.25.2-1) ... Setting up fakeroot (1.25.2-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-3) ... 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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201004T083822Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.MkTwWDsY3q Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20201004T083822Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 20s (1119 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.MkTwWDsY3q I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d discosnp=4.4.4-1 && mkdir -p /build/discosnp-DVg9OR && dpkg-source --no-check -x /*.dsc /build/discosnp-DVg9OR/discosnp-4.4.4 && chown -R builduser:builduser /build/discosnp-DVg9OR"' exec /tmp/mmdebstrap.MkTwWDsY3q Reading package lists... NOTICE: 'discosnp' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/discosnp.git Please use: git clone https://salsa.debian.org/med-team/discosnp.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1132 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main discosnp 4.4.4-1 (dsc) [2114 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main discosnp 4.4.4-1 (tar) [1107 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main discosnp 4.4.4-1 (diff) [23.1 kB] Fetched 1132 kB in 1s (1310 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'discosnp_4.4.4-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting discosnp in /build/discosnp-DVg9OR/discosnp-4.4.4 dpkg-source: info: unpacking discosnp_4.4.4.orig.tar.gz dpkg-source: info: unpacking discosnp_4.4.4-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_gatb-core.patch dpkg-source: info: applying no_install_to_wrong_dir.patch dpkg-source: info: applying path_to_readme_file_names.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying adapt_test_scripts.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying shell_syntax.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/discosnp-DVg9OR/discosnp-4.4.4 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1601556852" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.MkTwWDsY3q dpkg-buildpackage: info: source package discosnp dpkg-buildpackage: info: source version 4.4.4-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 dh_clean debian/rules binary-arch dh binary-arch --with python3 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_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 10.2.0 -- The CXX compiler identification is GNU 10.2.0 -- 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 -- gatb-core is here '/build/discosnp-DVg9OR/discosnp-4.4.4/thirdparty/gatb-core' CMake Warning (dev) at /usr/lib/x86_64-linux-gnu/cmake/GatbCore.cmake:39 (add_subdirectory): The source directory /build/discosnp-DVg9OR/discosnp-4.4.4/thirdparty/gatb-core does not contain a CMakeLists.txt file. CMake does not support this case but it used to work accidentally and is being allowed for compatibility. Policy CMP0014 is not set: Input directories must have CMakeLists.txt. Run "cmake --help-policy CMP0014" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:47 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY -- Build files have been written to: /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu dh_auto_build -a cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/discosnp-DVg9OR/discosnp-4.4.4 -B/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/CMakeFiles /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' make -f tools/kissnp2/CMakeFiles/kissnp2.dir/build.make tools/kissnp2/CMakeFiles/kissnp2.dir/depend make -f tools/kissreads2/CMakeFiles/kissreads2.dir/build.make tools/kissreads2/CMakeFiles/kissreads2.dir/depend make -f tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/build.make tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/depend make -f tools/read_file_names/CMakeFiles/read_file_names.dir/build.make tools/read_file_names/CMakeFiles/read_file_names.dir/depend make[3]: Entering directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-DVg9OR/discosnp-4.4.4 /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissnp2 /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissnp2 /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissnp2/CMakeFiles/kissnp2.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-DVg9OR/discosnp-4.4.4 /build/discosnp-DVg9OR/discosnp-4.4.4/tools/read_file_names /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/read_file_names /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/read_file_names/CMakeFiles/read_file_names.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-DVg9OR/discosnp-4.4.4 /build/discosnp-DVg9OR/discosnp-4.4.4/tools/QHC /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/QHC /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-DVg9OR/discosnp-4.4.4 /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2 /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissreads2 /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissreads2/CMakeFiles/kissreads2.dir/DependInfo.cmake --color= Scanning dependencies of target read_file_names make[3]: Leaving directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' make -f tools/read_file_names/CMakeFiles/read_file_names.dir/build.make tools/read_file_names/CMakeFiles/read_file_names.dir/build Scanning dependencies of target kissnp2 make[3]: Entering directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' make -f tools/kissnp2/CMakeFiles/kissnp2.dir/build.make tools/kissnp2/CMakeFiles/kissnp2.dir/build Scanning dependencies of target quick_hierarchical_clustering make[3]: Entering directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' make -f tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/build.make tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/build make[3]: Entering directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' Scanning dependencies of target kissreads2 make[3]: Leaving directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' make -f tools/kissreads2/CMakeFiles/kissreads2.dir/build.make tools/kissreads2/CMakeFiles/kissreads2.dir/build make[3]: Entering directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' [ 4%] Building CXX object tools/read_file_names/CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/read_file_names && /usr/bin/c++ -I/build/discosnp-DVg9OR/discosnp-4.4.4/tools/read_file_names/src -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -c /build/discosnp-DVg9OR/discosnp-4.4.4/tools/read_file_names/src/get_read_file_names.cpp [ 8%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Bubble.cpp.o cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissnp2/src -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissnp2.dir/src/Bubble.cpp.o -c /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissnp2/src/Bubble.cpp [ 13%] Building CXX object tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o [ 17%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o -c /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/Kissreads2.cpp cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/QHC && /usr/bin/c++ -I/build/discosnp-DVg9OR/discosnp-4.4.4/tools/QHC/src -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o -c /build/discosnp-DVg9OR/discosnp-4.4.4/tools/QHC/src/quick_hierarchical_clustering.cpp [ 21%] Linking CXX executable ../../bin/quick_hierarchical_clustering cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/QHC && /usr/bin/cmake -E cmake_link_script CMakeFiles/quick_hierarchical_clustering.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o -o ../../bin/quick_hierarchical_clustering -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' [ 21%] Built target quick_hierarchical_clustering make -f tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build.make tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/depend make[3]: Entering directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-DVg9OR/discosnp-4.4.4 /build/discosnp-DVg9OR/discosnp-4.4.4/tools/create_coverage_h5_file /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/create_coverage_h5_file /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/DependInfo.cmake --color= Scanning dependencies of target create_coverage_h5_file make[3]: Leaving directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' make -f tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build.make tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build make[3]: Entering directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' [ 26%] Building CXX object tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/create_coverage_h5_file && /usr/bin/c++ -I/build/discosnp-DVg9OR/discosnp-4.4.4/tools/create_coverage_h5_file/src -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o -c /build/discosnp-DVg9OR/discosnp-4.4.4/tools/create_coverage_h5_file/src/create_coverage_h5_file.cpp [ 30%] Linking CXX executable ../../bin/read_file_names cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/read_file_names && /usr/bin/cmake -E cmake_link_script CMakeFiles/read_file_names.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -o ../../bin/read_file_names -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' [ 30%] Built target read_file_names [ 34%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/commons.cpp.o cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/commons.cpp.o -c /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/commons.cpp [ 39%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Filter.cpp.o cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissnp2/src -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissnp2.dir/src/Filter.cpp.o -c /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissnp2/src/Filter.cpp [ 43%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/couple.cpp.o cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/couple.cpp.o -c /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/couple.cpp [ 47%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/extension_algorithm.cpp.o cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/extension_algorithm.cpp.o -c /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/extension_algorithm.cpp [ 52%] Linking CXX executable ../../bin/create_coverage_h5_file cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/create_coverage_h5_file && /usr/bin/cmake -E cmake_link_script CMakeFiles/create_coverage_h5_file.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o -o ../../bin/create_coverage_h5_file -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' [ 52%] Built target create_coverage_h5_file [ 56%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o -c /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/fragment_index.cpp [ 60%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissnp2/src -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o -c /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissnp2/src/Kissnp2.cpp [ 65%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment_info.cpp.o cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/fragment_info.cpp.o -c /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/fragment_info.cpp [ 69%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/interface_libchash.cpp.o cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/interface_libchash.cpp.o -c /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/interface_libchash.cpp [ 73%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/libchash.cpp.o cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/libchash.cpp.o -c /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp: In function ‘HTItem* HashFind(HashTable*, u_long)’: /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:215:7: note: in expansion of macro ‘READ_UL’ 215 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1216:4: note: in expansion of macro ‘LOAD_AND_RETURN’ 1216 | LOAD_AND_RETURN(ht, Find(ht, KEY_TRUNC(ht, key), NULL)); | ^~~~~~~~~~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp: In function ‘HTItem* HashFindLast(HashTable*)’: /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:215:7: note: in expansion of macro ‘READ_UL’ 215 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1221:4: note: in expansion of macro ‘LOAD_AND_RETURN’ 1221 | LOAD_AND_RETURN(ht, ht->posLastFind); | ^~~~~~~~~~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp: In function ‘HTItem* HashFirstBucket(HashTable*)’: /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:215:7: note: in expansion of macro ‘READ_UL’ 215 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1285:7: note: in expansion of macro ‘LOAD_AND_RETURN’ 1285 | { LOAD_AND_RETURN(ht, retval);} | ^~~~~~~~~~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp: In function ‘HTItem* HashNextBucket(HashTable*)’: /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:215:7: note: in expansion of macro ‘READ_UL’ 215 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1295:8: note: in expansion of macro ‘LOAD_AND_RETURN’ 1295 | {LOAD_AND_RETURN(ht, retval);} | ^~~~~~~~~~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp: In function ‘HashTable* HashDoLoad(FILE*, char* (*)(FILE*, int), HashTable*)’: /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1402:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1402 | fread(szMagicKey, 1, 4, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1411:4: note: in expansion of macro ‘READ_UL’ 1411 | READ_UL(fp, ht->cchKey); | ^~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1412:4: note: in expansion of macro ‘READ_UL’ 1412 | READ_UL(fp, ht->cItems); | ^~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1413:4: note: in expansion of macro ‘READ_UL’ 1413 | READ_UL(fp, ht->cDeletedItems); | ^~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1416:4: note: in expansion of macro ‘READ_UL’ 1416 | READ_UL(fp, cchKey); | ^~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1418:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1418 | fread(rgchKeys, 1, cchKey, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1423:7: note: in expansion of macro ‘READ_UL’ 1423 | READ_UL(fp, bck->data); /* all we need if dataRead is NULL */ | ^~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp: In function ‘u_long SparseRead(FILE*, SparseBin**)’: /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:617:4: note: in expansion of macro ‘READ_UL’ 617 | READ_UL(fp, cBuckets); /* actually, cBuckets is stored */ | ^~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:622:3: note: in expansion of macro ‘READ_UL’ 622 | READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]); | ^~~~~~~ [ 78%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/list.cpp.o cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/list.cpp.o -c /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/list.cpp [ 82%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/main.cpp.o cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/main.cpp.o -c /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/main.cpp [ 86%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/outputs.cpp.o cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/outputs.cpp.o -c /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissreads2/src/outputs.cpp [ 91%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/main.cpp.o cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissnp2/src -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissnp2.dir/src/main.cpp.o -c /build/discosnp-DVg9OR/discosnp-4.4.4/tools/kissnp2/src/main.cpp [ 95%] Linking CXX executable ../../bin/kissreads2 cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/kissreads2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o CMakeFiles/kissreads2.dir/src/commons.cpp.o CMakeFiles/kissreads2.dir/src/couple.cpp.o CMakeFiles/kissreads2.dir/src/extension_algorithm.cpp.o CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o CMakeFiles/kissreads2.dir/src/fragment_info.cpp.o CMakeFiles/kissreads2.dir/src/interface_libchash.cpp.o CMakeFiles/kissreads2.dir/src/libchash.cpp.o CMakeFiles/kissreads2.dir/src/list.cpp.o CMakeFiles/kissreads2.dir/src/main.cpp.o CMakeFiles/kissreads2.dir/src/outputs.cpp.o -o ../../bin/kissreads2 -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' [ 95%] Built target kissreads2 [100%] Linking CXX executable ../../bin/kissnp2 cd /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/kissnp2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-DVg9OR/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/kissnp2.dir/src/Bubble.cpp.o CMakeFiles/kissnp2.dir/src/Filter.cpp.o CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o CMakeFiles/kissnp2.dir/src/main.cpp.o -o ../../bin/kissnp2 -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' [100%] Built target kissnp2 make[2]: Leaving directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' dh_auto_test -a create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a dh_auto_install -a cd obj-x86_64-linux-gnu && make -j4 install DESTDIR=/build/discosnp-DVg9OR/discosnp-4.4.4/debian/discosnp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/discosnp-DVg9OR/discosnp-4.4.4 -B/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/discosnp-DVg9OR/discosnp-4.4.4/debian/discosnp/usr/bin/kissnp2 -- Set runtime path of "/build/discosnp-DVg9OR/discosnp-4.4.4/debian/discosnp/usr/bin/kissnp2" to "" -- Installing: /build/discosnp-DVg9OR/discosnp-4.4.4/debian/discosnp/usr/bin/kissreads2 -- Set runtime path of "/build/discosnp-DVg9OR/discosnp-4.4.4/debian/discosnp/usr/bin/kissreads2" to "" -- Installing: /build/discosnp-DVg9OR/discosnp-4.4.4/debian/discosnp/usr/bin/quick_hierarchical_clustering -- Set runtime path of "/build/discosnp-DVg9OR/discosnp-4.4.4/debian/discosnp/usr/bin/quick_hierarchical_clustering" to "" -- Installing: /build/discosnp-DVg9OR/discosnp-4.4.4/debian/discosnp/usr/bin/read_file_names -- Set runtime path of "/build/discosnp-DVg9OR/discosnp-4.4.4/debian/discosnp/usr/bin/read_file_names" to "" -- Installing: /build/discosnp-DVg9OR/discosnp-4.4.4/debian/discosnp/usr/bin/create_coverage_h5_file -- Set runtime path of "/build/discosnp-DVg9OR/discosnp-4.4.4/debian/discosnp/usr/bin/create_coverage_h5_file" to "" make[1]: Leaving directory '/build/discosnp-DVg9OR/discosnp-4.4.4/obj-x86_64-linux-gnu' debian/rules override_dh_install make[1]: Entering directory '/build/discosnp-DVg9OR/discosnp-4.4.4' dh_install mkdir -p debian/discosnp/usr/lib/discosnp/bin mv debian/discosnp/usr/bin/read_file_names debian/discosnp/usr/lib/discosnp/bin mv debian/discosnp/usr/bin/quick_hierarchical_clustering debian/discosnp/usr/lib/discosnp/bin rm -rf debian/discosnp/usr/share/discosnp/scripts/jenkins make[1]: Leaving directory '/build/discosnp-DVg9OR/discosnp-4.4.4' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman make[1]: Entering directory '/build/discosnp-DVg9OR/discosnp-4.4.4' dh_installman # dh_installman interprets .sh as language - just copy manpages manually cp -a debian/mans/*.sh.1 debian/discosnp/usr/share/man/man1 make[1]: Leaving directory '/build/discosnp-DVg9OR/discosnp-4.4.4' dh_python3 -a I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/discoSnpRAD/clustering_scripts/fasta_and_cluster_to_filtered_vcf.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/create_filtered_vcf.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/vcf_formatting_functions.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_common.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_compacted_int_to_fa.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_compacted_paths_to_fa.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_msr_to_gfa.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_node_ids_to_node_sequences.py dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a -a dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'discosnp-dbgsym' in '../discosnp-dbgsym_4.4.4-1_amd64.deb'. dpkg-deb: building package 'discosnp' in '../discosnp_4.4.4-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../discosnp_4.4.4-1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/discosnp-DVg9OR /tmp/discosnp-4.4.4-1srlzqnk1 I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.MkTwWDsY3q... I: success in 619.9793 seconds md5: discosnp-dbgsym_4.4.4-1_amd64.deb: OK md5: discosnp_4.4.4-1_amd64.deb: OK sha1: discosnp-dbgsym_4.4.4-1_amd64.deb: OK sha1: discosnp_4.4.4-1_amd64.deb: OK sha256: discosnp-dbgsym_4.4.4-1_amd64.deb: OK sha256: discosnp_4.4.4-1_amd64.deb: OK Checksums: OK