Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/d/discosnp/discosnp_2.6.1-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/discosnp-2.6.1-110_72_wy/discosnp_2.6.1-1_amd64.buildinfo Get source package info: discosnp=1:2.6.1-1 Source URL: http://snapshot.notset.fr/mr/package/discosnp/1:2.6.1-1/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 binutils=2.37-10 binutils-common=2.37-10 binutils-x86-64-linux-gnu=2.37-10 bsdextrautils=2.37.2-4 bsdutils=1:2.37.2-4 build-essential=12.9 bzip2=1.0.8-4 cmake=3.22.0-1 cmake-data=3.22.0-1 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-12 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.5.2 debianutils=5.5-1 dh-autoreconf=20 dh-elpa-helper=2.0.9 dh-python=5.20211114 dh-strip-nondeterminism=1.12.1-1 diffutils=1:3.7-5 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 emacsen-common=3.0.4 file=1:5.41-2 findutils=4.8.0-1 g++=4:11.2.0-2 g++-11=11.2.0-12 gcc=4:11.2.0-2 gcc-11=11.2.0-12 gcc-11-base=11.2.0-12 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 init-system-helpers=1.60 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=11.2.0-12 libatomic1=11.2.0-12 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1+b1 libbinutils=2.37-10 libblkid1=2.37.2-4 libboost-dev=1.74.0.3 libboost1.74-dev=1.74.0-13 libbrotli1=1.0.9-2+b3 libbz2-1.0=1.0.8-4 libc-bin=2.32-4 libc-dev-bin=2.32-4 libc6=2.32-4 libc6-dev=2.32-4 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-12 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.26-1 libcrypt1=1:4.4.26-1 libctf-nobfd0=2.37-10 libctf0=2.37-10 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=13.5.2 libdpkg-perl=1.20.9 libelf1=0.186-1 libexpat1=2.4.1-3 libffi8=3.4.2-3 libfile-stripnondeterminism-perl=1.12.1-1 libgatbcore-dev=1.4.2+dfsg-7 libgatbcore3=1.4.2+dfsg-7 libgcc-11-dev=11.2.0-12 libgcc-s1=11.2.0-12 libgcrypt20=1.9.4-4 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgfortran5=11.2.0-12 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.2-2 libgomp1=11.2.0-12 libgpg-error0=1.42-3 libgssapi-krb5-2=1.18.3-7 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 libicu67=67.1-7 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=11.2.0-12 libjpeg-dev=1:2.1.2-1 libjpeg62-turbo=1:2.1.2-1 libjpeg62-turbo-dev=1:2.1.2-1 libjsoncpp24=1.9.4-5 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 libldap-2.4-2=2.4.59+dfsg-1 liblsan0=11.2.0-12 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 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 libp11-kit0=0.24.0-5 libpam-modules=1.4.0-10 libpam-modules-bin=1.4.0-10 libpam-runtime=1.4.0-10 libpam0g=1.4.0-10 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.4-1 libprocps8=2:3.3.17-5 libpsl5=0.21.0-1.2 libpython3-stdlib=3.9.8-1 libpython3.9-minimal=3.9.9-1 libpython3.9-stdlib=3.9.9-1 libquadmath0=11.2.0-12 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 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=11.2.0-12 libstdc++6=11.2.0-12 libsub-override-perl=0.09-2 libsystemd0=249.7-1 libsz2=1.0.6-1 libtasn1-6=4.18.0-4 libtinfo6=6.3-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-12 libubsan1=11.2.0-12 libuchardet0=0.0.7-1 libudev1=249.7-1 libunistring2=0.9.10-6 libuuid1=2.37.2-4 libuv1=1.42.0-1 libxml2=2.9.12+dfsg-5+b1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.15.5-1 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 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 python3=3.9.8-1 python3-distutils=3.9.9-2 python3-lib2to3=3.9.9-2 python3-minimal=3.9.8-1 python3.9=3.9.9-1 python3.9-minimal=3.9.9-1 readline-common=8.1-2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.00-1 tar=1.34+dfsg-1 tzdata=2021e-1 util-linux=2.37.2-4 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/20211218T215256Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211218T215256Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211203T090951Z/ 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=1:2.6.1-1 && mkdir -p /build/discosnp-cl0Z2e && dpkg-source --no-check -x /*.dsc /build/discosnp-cl0Z2e/discosnp-2.6.1 && chown -R builduser:builduser /build/discosnp-cl0Z2e" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/discosnp-cl0Z2e/discosnp-2.6.1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1638718445" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/discosnp-cl0Z2e /tmp/discosnp-2.6.1-110_72_wy bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211203T090951Z 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.Bb7BVcqtB6 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.Bb7BVcqtB6 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/20211203T090951Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211203T090951Z 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 (1045 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 ... 4673 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.32-4) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211218T215256Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211218T215256Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211203T090951Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.Bb7BVcqtB6 Get:1 http://snapshot.notset.fr/archive/debian/20211218T215256Z bookworm InRelease [129 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20211203T090951Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20211218T215256Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211218T215256Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211218T215256Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211218T215256Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211218T215256Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211218T215256Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20211218T215256Z bookworm/main Sources [11.8 MB] Get:4 http://snapshot.notset.fr/archive/debian/20211218T215256Z bookworm/main amd64 Packages [11.2 MB] Fetched 23.1 MB in 20s (1175 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.Bb7BVcqtB6 I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d discosnp=1:2.6.1-1 && mkdir -p /build/discosnp-cl0Z2e && dpkg-source --no-check -x /*.dsc /build/discosnp-cl0Z2e/discosnp-2.6.1 && chown -R builduser:builduser /build/discosnp-cl0Z2e"' exec /tmp/mmdebstrap.Bb7BVcqtB6 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 1415 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211218T215256Z bookworm/main discosnp 1:2.6.1-1 (dsc) [2116 B] Get:2 http://snapshot.notset.fr/archive/debian/20211218T215256Z bookworm/main discosnp 1:2.6.1-1 (tar) [1390 kB] Get:3 http://snapshot.notset.fr/archive/debian/20211218T215256Z bookworm/main discosnp 1:2.6.1-1 (diff) [22.1 kB] Fetched 1415 kB in 1s (1184 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'discosnp_2.6.1-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting discosnp in /build/discosnp-cl0Z2e/discosnp-2.6.1 dpkg-source: info: unpacking discosnp_2.6.1.orig.tar.gz dpkg-source: info: unpacking discosnp_2.6.1-1.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-cl0Z2e/discosnp-2.6.1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1638718445" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.Bb7BVcqtB6 dpkg-buildpackage: info: source package discosnp dpkg-buildpackage: info: source version 1:2.6.1-1 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_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 CMake Deprecation Warning at CMakeLists.txt:3 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- gatb-core is here '/build/discosnp-cl0Z2e/discosnp-2.6.1/thirdparty/gatb-core' CMake Warning (dev) at /usr/lib/x86_64-linux-gnu/cmake/GatbCore.cmake:39 (add_subdirectory): The source directory /build/discosnp-cl0Z2e/discosnp-2.6.1/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 CMAKE_FIND_USE_PACKAGE_REGISTRY -- Build files have been written to: /build/discosnp-cl0Z2e/discosnp-2.6.1/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/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/discosnp-cl0Z2e/discosnp-2.6.1 -B/build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/CMakeFiles /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/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 -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-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' cd /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-cl0Z2e/discosnp-2.6.1 /build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissnp2 /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/kissnp2 /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/kissnp2/CMakeFiles/kissnp2.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' cd /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-cl0Z2e/discosnp-2.6.1 /build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissreads2 /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/kissreads2 /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/kissreads2/CMakeFiles/kissreads2.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' cd /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-cl0Z2e/discosnp-2.6.1 /build/discosnp-cl0Z2e/discosnp-2.6.1/tools/QHC /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/QHC /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' cd /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-cl0Z2e/discosnp-2.6.1 /build/discosnp-cl0Z2e/discosnp-2.6.1/tools/read_file_names /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/read_file_names /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/read_file_names/CMakeFiles/read_file_names.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' cd /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-cl0Z2e/discosnp-2.6.1 /build/discosnp-cl0Z2e/discosnp-2.6.1/tools/create_coverage_h5_file /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/create_coverage_h5_file /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' make -f tools/kissnp2/CMakeFiles/kissnp2.dir/build.make tools/kissnp2/CMakeFiles/kissnp2.dir/build make[3]: Leaving directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' make -f tools/kissreads2/CMakeFiles/kissreads2.dir/build.make tools/kissreads2/CMakeFiles/kissreads2.dir/build make[3]: Leaving directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/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 -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-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/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 make[3]: Entering directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' [ 5%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Bubble.cpp.o [ 10%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o [ 15%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Filter.cpp.o cd /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissnp2/src -g -O2 -ffile-prefix-map=/build/discosnp-cl0Z2e/discosnp-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissnp2/CMakeFiles/kissnp2.dir/src/Bubble.cpp.o -MF CMakeFiles/kissnp2.dir/src/Bubble.cpp.o.d -o CMakeFiles/kissnp2.dir/src/Bubble.cpp.o -c /build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissnp2/src/Bubble.cpp [ 20%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o [ 25%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/commons.cpp.o cd /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissnp2/src -g -O2 -ffile-prefix-map=/build/discosnp-cl0Z2e/discosnp-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissnp2/CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o -MF CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o.d -o CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o -c /build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissnp2/src/Kissnp2.cpp [ 35%] Building CXX object tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o [ 40%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/main.cpp.o cd /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissnp2/src -g -O2 -ffile-prefix-map=/build/discosnp-cl0Z2e/discosnp-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissnp2/CMakeFiles/kissnp2.dir/src/Filter.cpp.o -MF CMakeFiles/kissnp2.dir/src/Filter.cpp.o.d -o CMakeFiles/kissnp2.dir/src/Filter.cpp.o -c /build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissnp2/src/Filter.cpp [ 40%] Building CXX object tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o cd /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissreads2/src -g -O2 -ffile-prefix-map=/build/discosnp-cl0Z2e/discosnp-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o -MF CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o.d -o CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o -c /build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissreads2/src/Kissreads2.cpp cd /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissreads2/src -g -O2 -ffile-prefix-map=/build/discosnp-cl0Z2e/discosnp-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/commons.cpp.o -MF CMakeFiles/kissreads2.dir/src/commons.cpp.o.d -o CMakeFiles/kissreads2.dir/src/commons.cpp.o -c /build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissreads2/src/commons.cpp [ 45%] Building CXX object tools/read_file_names/CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o cd /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/create_coverage_h5_file && /usr/bin/c++ -I/build/discosnp-cl0Z2e/discosnp-2.6.1/tools/create_coverage_h5_file/src -g -O2 -ffile-prefix-map=/build/discosnp-cl0Z2e/discosnp-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o -MF CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o.d -o CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o -c /build/discosnp-cl0Z2e/discosnp-2.6.1/tools/create_coverage_h5_file/src/create_coverage_h5_file.cpp cd /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/QHC && /usr/bin/c++ -I/build/discosnp-cl0Z2e/discosnp-2.6.1/tools/QHC/src -g -O2 -ffile-prefix-map=/build/discosnp-cl0Z2e/discosnp-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o -MF CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o.d -o CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o -c /build/discosnp-cl0Z2e/discosnp-2.6.1/tools/QHC/src/quick_hierarchical_clustering.cpp cd /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissnp2/src -g -O2 -ffile-prefix-map=/build/discosnp-cl0Z2e/discosnp-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissnp2/CMakeFiles/kissnp2.dir/src/main.cpp.o -MF CMakeFiles/kissnp2.dir/src/main.cpp.o.d -o CMakeFiles/kissnp2.dir/src/main.cpp.o -c /build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissnp2/src/main.cpp cd /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/read_file_names && /usr/bin/c++ -I/build/discosnp-cl0Z2e/discosnp-2.6.1/tools/read_file_names/src -g -O2 -ffile-prefix-map=/build/discosnp-cl0Z2e/discosnp-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/read_file_names/CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -MF CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o.d -o CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -c /build/discosnp-cl0Z2e/discosnp-2.6.1/tools/read_file_names/src/get_read_file_names.cpp [ 50%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment.cpp.o cd /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissreads2/src -g -O2 -ffile-prefix-map=/build/discosnp-cl0Z2e/discosnp-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment.cpp.o -MF CMakeFiles/kissreads2.dir/src/fragment.cpp.o.d -o CMakeFiles/kissreads2.dir/src/fragment.cpp.o -c /build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissreads2/src/fragment.cpp [ 55%] Linking CXX executable ../../bin/quick_hierarchical_clustering cd /build/discosnp-cl0Z2e/discosnp-2.6.1/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 -ffile-prefix-map=/build/discosnp-cl0Z2e/discosnp-2.6.1=. -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-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' [ 55%] Built target quick_hierarchical_clustering [ 60%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o cd /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissreads2/src -g -O2 -ffile-prefix-map=/build/discosnp-cl0Z2e/discosnp-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o -MF CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o.d -o CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o -c /build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissreads2/src/fragment_index.cpp [ 65%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/interface_xhash.cpp.o cd /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissreads2/src -g -O2 -ffile-prefix-map=/build/discosnp-cl0Z2e/discosnp-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/interface_xhash.cpp.o -MF CMakeFiles/kissreads2.dir/src/interface_xhash.cpp.o.d -o CMakeFiles/kissreads2.dir/src/interface_xhash.cpp.o -c /build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissreads2/src/interface_xhash.cpp [ 70%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/main.cpp.o cd /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissreads2/src -g -O2 -ffile-prefix-map=/build/discosnp-cl0Z2e/discosnp-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/main.cpp.o -MF CMakeFiles/kissreads2.dir/src/main.cpp.o.d -o CMakeFiles/kissreads2.dir/src/main.cpp.o -c /build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissreads2/src/main.cpp [ 75%] Linking CXX executable ../../bin/read_file_names cd /build/discosnp-cl0Z2e/discosnp-2.6.1/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 -ffile-prefix-map=/build/discosnp-cl0Z2e/discosnp-2.6.1=. -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-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' [ 80%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/outputs.cpp.o cd /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissreads2/src -g -O2 -ffile-prefix-map=/build/discosnp-cl0Z2e/discosnp-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/outputs.cpp.o -MF CMakeFiles/kissreads2.dir/src/outputs.cpp.o.d -o CMakeFiles/kissreads2.dir/src/outputs.cpp.o -c /build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissreads2/src/outputs.cpp [ 80%] Built target read_file_names [ 85%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/read_mapper.cpp.o cd /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissreads2/src -g -O2 -ffile-prefix-map=/build/discosnp-cl0Z2e/discosnp-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/read_mapper.cpp.o -MF CMakeFiles/kissreads2.dir/src/read_mapper.cpp.o.d -o CMakeFiles/kissreads2.dir/src/read_mapper.cpp.o -c /build/discosnp-cl0Z2e/discosnp-2.6.1/tools/kissreads2/src/read_mapper.cpp [ 90%] Linking CXX executable ../../bin/kissnp2 cd /build/discosnp-cl0Z2e/discosnp-2.6.1/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 -ffile-prefix-map=/build/discosnp-cl0Z2e/discosnp-2.6.1=. -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-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' [ 95%] Linking CXX executable ../../bin/create_coverage_h5_file cd /build/discosnp-cl0Z2e/discosnp-2.6.1/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 -ffile-prefix-map=/build/discosnp-cl0Z2e/discosnp-2.6.1=. -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 [ 95%] Built target kissnp2 make[3]: Leaving directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' [ 95%] Built target create_coverage_h5_file [100%] Linking CXX executable ../../bin/kissreads2 cd /build/discosnp-cl0Z2e/discosnp-2.6.1/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 -ffile-prefix-map=/build/discosnp-cl0Z2e/discosnp-2.6.1=. -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/fragment.cpp.o CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o CMakeFiles/kissreads2.dir/src/interface_xhash.cpp.o CMakeFiles/kissreads2.dir/src/main.cpp.o CMakeFiles/kissreads2.dir/src/outputs.cpp.o CMakeFiles/kissreads2.dir/src/read_mapper.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-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' [100%] Built target kissreads2 make[2]: Leaving directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/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/discosnp/ -a cd obj-x86_64-linux-gnu && make -j10 install DESTDIR=/build/discosnp-cl0Z2e/discosnp-2.6.1/debian/discosnp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/discosnp-cl0Z2e/discosnp-2.6.1 -B/build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/discosnp-cl0Z2e/discosnp-2.6.1/debian/discosnp/usr/bin/kissnp2 -- Set runtime path of "/build/discosnp-cl0Z2e/discosnp-2.6.1/debian/discosnp/usr/bin/kissnp2" to "" -- Installing: /build/discosnp-cl0Z2e/discosnp-2.6.1/debian/discosnp/usr/bin/kissreads2 -- Set runtime path of "/build/discosnp-cl0Z2e/discosnp-2.6.1/debian/discosnp/usr/bin/kissreads2" to "" -- Installing: /build/discosnp-cl0Z2e/discosnp-2.6.1/debian/discosnp/usr/bin/quick_hierarchical_clustering -- Set runtime path of "/build/discosnp-cl0Z2e/discosnp-2.6.1/debian/discosnp/usr/bin/quick_hierarchical_clustering" to "" -- Installing: /build/discosnp-cl0Z2e/discosnp-2.6.1/debian/discosnp/usr/bin/read_file_names -- Set runtime path of "/build/discosnp-cl0Z2e/discosnp-2.6.1/debian/discosnp/usr/bin/read_file_names" to "" -- Installing: /build/discosnp-cl0Z2e/discosnp-2.6.1/debian/discosnp/usr/bin/create_coverage_h5_file -- Set runtime path of "/build/discosnp-cl0Z2e/discosnp-2.6.1/debian/discosnp/usr/bin/create_coverage_h5_file" to "" make[1]: Leaving directory '/build/discosnp-cl0Z2e/discosnp-2.6.1/obj-x86_64-linux-gnu' debian/rules override_dh_install make[1]: Entering directory '/build/discosnp-cl0Z2e/discosnp-2.6.1' 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-cl0Z2e/discosnp-2.6.1' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman make[1]: Entering directory '/build/discosnp-cl0Z2e/discosnp-2.6.1' 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-cl0Z2e/discosnp-2.6.1' 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_facts_to_gfa.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_filter_badly_overlapping_variants.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_node_ids_to_node_sequences.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_paths_to_fa.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_phased_paths_to_fa.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 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 'discosnp' in '../discosnp_2.6.1-1_amd64.deb'. dpkg-deb: building package 'discosnp-dbgsym' in '../discosnp-dbgsym_2.6.1-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../discosnp_2.6.1-1_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-cl0Z2e /tmp/discosnp-2.6.1-110_72_wy I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.Bb7BVcqtB6... I: success in 1672.5702 seconds md5: discosnp-dbgsym_2.6.1-1_amd64.deb: OK md5: discosnp_2.6.1-1_amd64.deb: OK sha1: discosnp-dbgsym_2.6.1-1_amd64.deb: OK sha1: discosnp_2.6.1-1_amd64.deb: OK sha256: discosnp-dbgsym_2.6.1-1_amd64.deb: OK sha256: discosnp_2.6.1-1_amd64.deb: OK Checksums: OK