Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/s/seer/seer_1.1.4-6_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/seer-1.1.4-6vfu1mkq9/seer_1.1.4-6_amd64.buildinfo Get source package info: seer=1.1.4-6 Source URL: http://snapshot.notset.fr/mr/package/seer/1.1.4-6/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.4-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-3+b2 binutils=2.37-7 binutils-common=2.37-7 binutils-x86-64-linux-gnu=2.37-7 bsdextrautils=2.37.2-3 bsdutils=1:2.37.2-3 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:11.2.0-2 cpp-11=11.2.0-9 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.77 debhelper=13.5.2 debianutils=5.5-1 dh-autoreconf=20 dh-strip-nondeterminism=1.12.0-1 diffutils=1:3.7-5 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.39-3 findutils=4.8.0-1 g++=4:11.2.0-2 g++-11=11.2.0-9 gcc=4:11.2.0-2 gcc-10-base=10.3.0-11 gcc-11=11.2.0-9 gcc-11-base=11.2.0-9 gettext=0.21-4 gettext-base=0.21-4 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 libarmadillo-dev=1:10.6.2+dfsg-1+b1 libarmadillo10=1:10.6.2+dfsg-1+b1 libarpack2=3.8.0-1 libarpack2-dev=3.8.0-1 libasan6=11.2.0-9 libatomic1=11.2.0-9 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1 libbinutils=2.37-7 libblas-dev=3.10.0-1 libblas3=3.10.0-1 libblkid1=2.37.2-3 libboost-dev=1.74.0.3 libboost-program-options-dev=1.74.0.3 libboost-program-options1.74-dev=1.74.0-11 libboost-program-options1.74.0=1.74.0-11 libboost1.74-dev=1.74.0-11 libbrotli1=1.0.9-2+b2 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=11.2.0-9 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.25-2 libcrypt1=1:4.4.25-2 libctf-nobfd0=2.37-7 libctf0=2.37-7 libcurl4=7.74.0-1.3+b1 libcurl4-openssl-dev=7.74.0-1.3+b1 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.260 libdebhelper-perl=13.5.2 libdlib-data=19.10-3.1 libdlib-dev=19.10-3.1 libdlib19=19.10-3.1 libdpkg-perl=1.20.9 libelf1=0.185-2 libffi8=3.4.2-2 libfile-stripnondeterminism-perl=1.12.0-1 libgcc-10-dev=10.3.0-11 libgcc-11-dev=11.2.0-9 libgcc-s1=11.2.0-9 libgcrypt20=1.9.4-3+b1 libgdbm-compat4=1.21-1 libgdbm6=1.21-1 libgfortran5=11.2.0-9 libgmp10=2:6.2.1+dfsg-2 libgnutls30=3.7.2-2 libgomp1=11.2.0-9 libgpg-error0=1.42-3 libgssapi-krb5-2=1.18.3-7 libgzstream-dev=1.5+git20171107.9a20658-1+b1 libgzstream0=1.5+git20171107.9a20658-1+b1 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=0.23-1 libitm1=11.2.0-9 libjpeg-dev=1:2.0.6-4 libjpeg62-turbo=1:2.0.6-4 libjpeg62-turbo-dev=1:2.0.6-4 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblapack-dev=3.10.0-1 liblapack3=3.10.0-1 libldap-2.4-2=2.4.59+dfsg-1 liblsan0=11.2.0-9 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.37.2-3 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 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=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.3-1 libpng16-16=1.6.37-3 libpsl5=0.21.0-1.2 libquadmath0=11.2.0-9 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2.1 libsasl2-modules-db=2.1.27+dfsg-2.1 libseccomp2=2.5.2-2 libselinux1=3.1-3 libsigsegv2=2.13-1 libsmartcols1=2.37.2-3 libssh2-1=1.10.0-2 libssl-dev=1.1.1l-1 libssl1.1=1.1.1l-1 libstdc++-10-dev=10.3.0-11 libstdc++-11-dev=11.2.0-9 libstdc++6=11.2.0-9 libsub-override-perl=0.09-2 libsuperlu-dev=5.2.2+dfsg1-2 libsuperlu5=5.2.2+dfsg1-2 libsystemd0=247.9-4 libsz2=1.0.6-1 libtasn1-6=4.17.0-2 libtinfo6=6.2+20210905-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-9 libubsan1=11.2.0-9 libuchardet0=0.0.7-1 libudev1=247.9-4 libunistring2=0.9.10-6 libuuid1=2.37.2-3 libxml2=2.9.12+dfsg-5 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.14.9-2 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20210905-1 ncurses-bin=6.2+20210905-1 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 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 util-linux=2.37.2-3 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/20211016T025026Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211016T025026Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220402T210321Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211011T150038Z/ 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 seer=1.1.4-6 && mkdir -p /build/seer-6d9xWJ && dpkg-source --no-check -x /*.dsc /build/seer-6d9xWJ/seer-1.1.4 && chown -R builduser:builduser /build/seer-6d9xWJ" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/seer-6d9xWJ/seer-1.1.4 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1634155845" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/seer-6d9xWJ /tmp/seer-1.1.4-6vfu1mkq9 bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211011T150038Z 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.j_tgxHzK_9 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.j_tgxHzK_9 Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-3). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20211011T150038Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211011T150038Z 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 (742 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 ... 4667 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/20211016T025026Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211016T025026Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220402T210321Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211011T150038Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.j_tgxHzK_9 Get:1 http://snapshot.notset.fr/archive/debian/20211016T025026Z bookworm InRelease [128 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220402T210321Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20211011T150038Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20211016T025026Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211016T025026Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211016T025026Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211016T025026Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211016T025026Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211016T025026Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20211016T025026Z bookworm/main Sources [11.7 MB] Get:5 http://snapshot.notset.fr/archive/debian/20211016T025026Z bookworm/main amd64 Packages [11.2 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20220402T210321Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20220402T210321Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20220402T210321Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20220402T210321Z unstable/main amd64 Packages [12.4 MB] Fetched 35.6 MB in 30s (1205 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.j_tgxHzK_9 I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d seer=1.1.4-6 && mkdir -p /build/seer-6d9xWJ && dpkg-source --no-check -x /*.dsc /build/seer-6d9xWJ/seer-1.1.4 && chown -R builduser:builduser /build/seer-6d9xWJ"' exec /tmp/mmdebstrap.j_tgxHzK_9 Reading package lists... NOTICE: 'seer' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/seer.git Please use: git clone https://salsa.debian.org/med-team/seer.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 983 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211016T025026Z bookworm/main seer 1.1.4-6 (dsc) [2022 B] Get:2 http://snapshot.notset.fr/archive/debian/20211016T025026Z bookworm/main seer 1.1.4-6 (tar) [972 kB] Get:3 http://snapshot.notset.fr/archive/debian/20211016T025026Z bookworm/main seer 1.1.4-6 (diff) [8532 B] Fetched 983 kB in 1s (1257 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'seer_1.1.4-6.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting seer in /build/seer-6d9xWJ/seer-1.1.4 dpkg-source: info: unpacking seer_1.1.4.orig.tar.gz dpkg-source: info: unpacking seer_1.1.4-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_lib_location.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying gcc11.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/seer-6d9xWJ/seer-1.1.4 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1634155845" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.j_tgxHzK_9 dpkg-buildpackage: info: source package seer dpkg-buildpackage: info: source version 1.1.4-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j10 clean make[1]: Entering directory '/build/seer-6d9xWJ/seer-1.1.4' cd src && make clean make[2]: Entering directory '/build/seer-6d9xWJ/seer-1.1.4/src' rm -f *.o ~* seer kmds map_back combineKmers filter_seer make[2]: Leaving directory '/build/seer-6d9xWJ/seer-1.1.4/src' cd test && make clean make[2]: Entering directory '/build/seer-6d9xWJ/seer-1.1.4/test' rm -f *.o ~* tests_passed make[2]: Leaving directory '/build/seer-6d9xWJ/seer-1.1.4/test' make[1]: Leaving directory '/build/seer-6d9xWJ/seer-1.1.4' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/build/seer-6d9xWJ/seer-1.1.4' dh_auto_build -- LDFLAGS+=-L/usr/lib/x86_64-linux-gnu/hdf5/serial make -j10 "INSTALL=install --strip-program=true" LDFLAGS\+=-L/usr/lib/x86_64-linux-gnu/hdf5/serial make[2]: Entering directory '/build/seer-6d9xWJ/seer-1.1.4' cd src && make all make[3]: Entering directory '/build/seer-6d9xWJ/seer-1.1.4/src' g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o sample.o sample.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o significant_kmer.o significant_kmer.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmer.o kmer.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o covar.o covar.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerCommon.o seerCommon.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerErr.o seerErr.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerIO.o seerIO.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerBasicFilter.o seerBasicFilter.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerMain.o seerMain.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerCmdLine.o seerCmdLine.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerStats.o seerStats.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerContinuousAssoc.o seerContinuousAssoc.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerBinaryAssoc.o seerBinaryAssoc.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o logitFunction.o logitFunction.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o linearFunction.o linearFunction.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmdsMain.o kmdsMain.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmdsStruct.o kmdsStruct.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmdsCmdLine.o kmdsCmdLine.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o fasta.o fasta.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o mapMain.o mapMain.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o mapCmdLine.o mapCmdLine.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o combineInit.o combineInit.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o combineCmdLine.o combineCmdLine.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o combineKmers.o combineKmers.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o filter_seer.o filter_seer.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o filterCmdLine.o filterCmdLine.cpp g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial combineInit.o combineCmdLine.o combineKmers.o -lgzstream -lz -lboost_program_options -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial -o combineKmers g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial significant_kmer.o filter_seer.o filterCmdLine.o -lboost_program_options -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial -o filter_seer g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial fasta.o significant_kmer.o mapMain.o mapCmdLine.o -lboost_program_options -lpthread -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial -o map_back g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial sample.o significant_kmer.o kmer.o covar.o seerCommon.o seerErr.o seerIO.o seerBasicFilter.o seerMain.o seerCmdLine.o seerStats.o seerContinuousAssoc.o seerBinaryAssoc.o logitFunction.o linearFunction.o -lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas -lpthread -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial -o seer g++ -g -O2 -ffile-prefix-map=/build/seer-6d9xWJ/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial sample.o significant_kmer.o kmer.o covar.o seerCommon.o seerErr.o seerIO.o seerBasicFilter.o kmdsMain.o kmdsStruct.o kmdsCmdLine.o -lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas -lpthread -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial -o kmds make[3]: Leaving directory '/build/seer-6d9xWJ/seer-1.1.4/src' make[2]: Leaving directory '/build/seer-6d9xWJ/seer-1.1.4' make[1]: Leaving directory '/build/seer-6d9xWJ/seer-1.1.4' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/seer-6d9xWJ/seer-1.1.4' dh_auto_install -- PREFIX=/build/seer-6d9xWJ/seer-1.1.4/debian/seer/usr make -j10 install DESTDIR=/build/seer-6d9xWJ/seer-1.1.4/debian/seer AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=/build/seer-6d9xWJ/seer-1.1.4/debian/seer/usr make[2]: Entering directory '/build/seer-6d9xWJ/seer-1.1.4' cd src && make all make[3]: Entering directory '/build/seer-6d9xWJ/seer-1.1.4/src' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/seer-6d9xWJ/seer-1.1.4/src' cd src && make install make[3]: Entering directory '/build/seer-6d9xWJ/seer-1.1.4/src' install -d /build/seer-6d9xWJ/seer-1.1.4/debian/seer/usr/bin install seer kmds map_back combineKmers filter_seer /build/seer-6d9xWJ/seer-1.1.4/debian/seer/usr/bin make[3]: Leaving directory '/build/seer-6d9xWJ/seer-1.1.4/src' make[2]: Leaving directory '/build/seer-6d9xWJ/seer-1.1.4' for pl in scripts/*.pl ; do \ plbase=`basename ${pl} .pl` ; \ sed "s+Usage: ./${plbase}.pl+Usage: ${plbase}+" ${pl} > /build/seer-6d9xWJ/seer-1.1.4/debian/seer/usr/bin/${plbase} ; \ done # Fix broken usage hint: sed -i "s+Usage: ./hits_to_matrix.pl+Usage: reformat_output+" /build/seer-6d9xWJ/seer-1.1.4/debian/seer/usr/bin/reformat_output make[1]: Leaving directory '/build/seer-6d9xWJ/seer-1.1.4' dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a debian/rules override_dh_fixperms make[1]: Entering directory '/build/seer-6d9xWJ/seer-1.1.4' dh_fixperms find debian -name Makefile -exec chmod -x \{\} \; find debian -name "*.fa" -exec chmod -x \{\} \; make[1]: Leaving directory '/build/seer-6d9xWJ/seer-1.1.4' dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/seer/usr/bin/combineKmers was not linked against libz.so.1 (it uses none of the library's symbols) dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'seer' in '../seer_1.1.4-6_amd64.deb'. dpkg-deb: building package 'seer-dbgsym' in '../seer-dbgsym_1.1.4-6_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../seer_1.1.4-6_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/seer-6d9xWJ /tmp/seer-1.1.4-6vfu1mkq9 I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.j_tgxHzK_9... I: success in 618.9918 seconds md5: seer-dbgsym_1.1.4-6_amd64.deb: OK md5: Value of 'md5' differs for seer_1.1.4-6_amd64.deb md5: Size differs for seer_1.1.4-6_amd64.deb sha1: seer-dbgsym_1.1.4-6_amd64.deb: OK sha1: Value of 'sha1' differs for seer_1.1.4-6_amd64.deb sha1: Size differs for seer_1.1.4-6_amd64.deb sha256: seer-dbgsym_1.1.4-6_amd64.deb: OK sha256: Value of 'sha256' differs for seer_1.1.4-6_amd64.deb sha256: Size differs for seer_1.1.4-6_amd64.deb Checksums: FAIL Cannot generate diffoscope for seer_1.1.4-6_amd64.deb: RetryError[]