Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/b/bowtie2/bowtie2_2.4.5-1_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/bowtie2-2.4.5-11d9dry3l/bowtie2_2.4.5-1_all.buildinfo Get source package info: bowtie2=2.4.5-1 Source URL: http://snapshot.notset.fr/mr/package/bowtie2/2.4.5-1/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=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6 binutils=2.38-1 binutils-common=2.38-1 binutils-x86-64-linux-gnu=2.38-1 bsdextrautils=2.37.3-1+b1 bsdutils=1:2.37.3-1+b1 build-essential=12.9 bzip2=1.0.8-5 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-16 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.6 debianutils=5.7-0.1 dh-autoreconf=20 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dpkg=1.21.1 dpkg-dev=1.21.1 dwz=0.14-1 file=1:5.41-2 findutils=4.8.0-1 g++=4:11.2.0-2 g++-11=11.2.0-16 gcc=4:11.2.0-2 gcc-11=11.2.0-16 gcc-11-base=11.2.0-16 gettext=0.21-4 gettext-base=0.21-4 grep=3.7-1 groff-base=1.22.4-8 gzip=1.10-4 help2man=1.49.1 hostname=3.23 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-16 libatomic1=11.2.0-16 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1 libbinutils=2.38-1 libblkid1=2.37.3-1+b1 libbz2-1.0=1.0.8-5 libc-bin=2.33-6 libc-dev-bin=2.33-6 libc6=2.33-6 libc6-dev=2.33-6 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-16 libclone-perl=0.45-1+b2 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-1 libctf0=2.38-1 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.6 libdpkg-perl=1.21.1 libelf1=0.186-1 libexpat1=2.4.4-1 libffi8=3.4.2-4 libfile-stripnondeterminism-perl=1.13.0-1 libfile-which-perl=1.23-1 libgcc-11-dev=11.2.0-16 libgcc-s1=11.2.0-16 libgcrypt20=1.9.4-5 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgmp10=2:6.2.1+dfsg-3 libgomp1=11.2.0-16 libgpg-error0=1.43-3 libgssapi-krb5-2=1.18.3-7 libicu67=67.1-7 libisl23=0.24-2 libitm1=11.2.0-16 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblocal-lib-perl=2.000028-1 liblocale-gettext-perl=1.07-4+b2 liblsan0=11.2.0-16 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 libmodule-build-perl=0.423100-1 libmount1=2.37.3-1+b1 libmpc3=1.2.1-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncursesw6=6.3-2 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-11 libpam-modules-bin=1.4.0-11 libpam-runtime=1.4.0-11 libpam0g=1.4.0-11 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libperl5.34=5.34.0-3 libpipeline1=1.5.5-1 libpython3-stdlib=3.9.8-1 libpython3.9-minimal=3.9.10-1 libpython3.9-stdlib=3.9.10-1 libquadmath0=11.2.0-16 libreadline8=8.1.2-1 libseccomp2=2.5.3-2 libselinux1=3.3-1+b1 libsigsegv2=2.14-1 libsimde-dev=0.7.2-6 libsmartcols1=2.37.3-1+b1 libsqlite3-0=3.37.2-2 libssl1.1=1.1.1m-1 libstdc++-11-dev=11.2.0-16 libstdc++6=11.2.0-16 libsub-override-perl=0.09-2 libsystemd0=250.3-2 libtbb-dev=2020.3-1 libtbb2=2020.3-1 libtest-deep-perl=1.130-1 libtinfo6=6.3-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-16 libubsan1=11.2.0-16 libuchardet0=0.0.7-1 libudev1=250.3-2 libunistring2=1.0-1 libuuid1=2.37.3-1+b1 libxml2=2.9.12+dfsg-5+b1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.16.7-2 login=1:4.11.1+dfsg1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.1-1 mawk=1.3.4.20200120-3+b1 media-types=5.0.0 ncurses-base=6.3-2 ncurses-bin=6.3-2 patch=2.7.6-7 perl=5.34.0-3 perl-base=5.34.0-3 perl-modules-5.34=5.34.0-3 po-debconf=1.0.21+nmu1 python3=3.9.8-1 python3-minimal=3.9.8-1 python3.9=3.9.10-1 python3.9-minimal=3.9.10-1 readline-common=8.1.2-1 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.01-1 tar=1.34+dfsg-1 tzdata=2021e-1 util-linux=2.37.3-1+b1 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/20220315T214517Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220315T214517Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220218T095549Z/ 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 bowtie2=2.4.5-1 && mkdir -p /build/bowtie2-pmC30H && dpkg-source --no-check -x /*.dsc /build/bowtie2-pmC30H/bowtie2-2.4.5 && chown -R builduser:builduser /build/bowtie2-pmC30H" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bowtie2-pmC30H/bowtie2-2.4.5 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1645112818" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/bowtie2-pmC30H /tmp/bowtie2-2.4.5-11d9dry3l bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220218T095549Z 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._ckdPSfDcT 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._ckdPSfDcT Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.3-1+b1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 136 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220218T095549Z unstable/main amd64 libfakeroot amd64 1.27-1 [48.5 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220218T095549Z unstable/main amd64 fakeroot amd64 1.27-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 136 kB in 0s (1035 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 ... 4696 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.27-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.27-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.27-1_amd64.deb ... Unpacking fakeroot (1.27-1) ... Setting up libfakeroot:amd64 (1.27-1) ... Setting up fakeroot (1.27-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-6) ... 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/20220315T214517Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220315T214517Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220218T095549Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap._ckdPSfDcT Get:1 http://snapshot.notset.fr/archive/debian/20220315T214517Z bookworm InRelease [130 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20220218T095549Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20220315T214517Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220315T214517Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220315T214517Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220315T214517Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220315T214517Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220315T214517Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20220315T214517Z bookworm/main Sources [11.9 MB] Get:4 http://snapshot.notset.fr/archive/debian/20220315T214517Z bookworm/main amd64 Packages [11.3 MB] Fetched 23.4 MB in 20s (1176 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._ckdPSfDcT I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d bowtie2=2.4.5-1 && mkdir -p /build/bowtie2-pmC30H && dpkg-source --no-check -x /*.dsc /build/bowtie2-pmC30H/bowtie2-2.4.5 && chown -R builduser:builduser /build/bowtie2-pmC30H"' exec /tmp/mmdebstrap._ckdPSfDcT Reading package lists... NOTICE: 'bowtie2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/bowtie2.git Please use: git clone https://salsa.debian.org/med-team/bowtie2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 10.6 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220315T214517Z bookworm/main bowtie2 2.4.5-1 (dsc) [2350 B] Get:2 http://snapshot.notset.fr/archive/debian/20220315T214517Z bookworm/main bowtie2 2.4.5-1 (tar) [10.6 MB] Get:3 http://snapshot.notset.fr/archive/debian/20220315T214517Z bookworm/main bowtie2 2.4.5-1 (diff) [17.6 kB] Fetched 10.6 MB in 8s (1265 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'bowtie2_2.4.5-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting bowtie2 in /build/bowtie2-pmC30H/bowtie2-2.4.5 dpkg-source: info: unpacking bowtie2_2.4.5.orig.tar.gz dpkg-source: info: unpacking bowtie2_2.4.5-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying drop-not-needed-js-from-manual.patch dpkg-source: info: applying wrong-interpreter-path.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying skip_test_requiring_non-free_libmath-random-perl.patch dpkg-source: info: applying do-not-rebuild-during-test.patch dpkg-source: info: applying simde dpkg-source: info: applying correct_64bit_test dpkg-source: info: applying no_sanity dpkg-source: info: applying use-source-date-epoch-in-Makefile.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bowtie2-pmC30H/bowtie2-2.4.5 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1645112818" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap._ckdPSfDcT dpkg-buildpackage: info: source package bowtie2 dpkg-buildpackage: info: source version 2.4.5-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . debian/rules clean dh clean dh_auto_clean make -j10 clean make[1]: Entering directory '/build/bowtie2-pmC30H/bowtie2-2.4.5' rm -f bowtie2-build-s bowtie2-build-l bowtie2-align-s bowtie2-align-l bowtie2-inspect-s bowtie2-inspect-l bowtie2-build-s-debug bowtie2-build-l-debug bowtie2-align-s-debug bowtie2-align-l-debug bowtie2-inspect-s-debug bowtie2-inspect-l-debug \ bowtie2-build-s.exe bowtie2-build-l.exe bowtie2-align-s.exe bowtie2-align-l.exe bowtie2-inspect-s.exe bowtie2-inspect-l.exe bowtie2-build-s-debug.exe bowtie2-build-l-debug.exe bowtie2-align-s-debug.exe bowtie2-align-l-debug.exe bowtie2-inspect-s-debug.exe bowtie2-inspect-l-debug.exe \ bowtie2-*.zip rm -f core.* .tmp.head rm -rf *.dSYM rm -rf .tmp make[1]: Leaving directory '/build/bowtie2-pmC30H/bowtie2-2.4.5' dh_clean debian/rules binary-indep dh binary-indep dh_update_autotools_config -i dh_autoreconf -i dh_auto_configure -i debian/rules override_dh_auto_build make[1]: Entering directory '/build/bowtie2-pmC30H/bowtie2-2.4.5' LD_PRELOAD= dh_auto_build -- EXTRA_FLAGS="-std=c++98 -Wl,-z,relro -Wl,-z,now" POPCNT_CAPABILITY=1 HOSTNAME=reproducible-hostname make -j10 "INSTALL=install --strip-program=true" "EXTRA_FLAGS=-std=c++98 -Wl,-z,relro -Wl,-z,now" POPCNT_CAPABILITY=1 HOSTNAME=reproducible-hostname make[2]: Entering directory '/build/bowtie2-pmC30H/bowtie2-2.4.5' g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++11 -fopenmp-simd -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -g -O2 -ffile-prefix-map=/build/bowtie2-pmC30H/bowtie2-2.4.5=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++11 -fopenmp-simd -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`LC_ALL=C date -u -d@1645112818`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -Wdate-time -D_FORTIFY_SOURCE=2 -Ithird_party -I third_party -g -O2 -ffile-prefix-map=/build/bowtie2-pmC30H/bowtie2-2.4.5=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DBOWTIE2 -DNDEBUG -Wall \ -Wdate-time -D_FORTIFY_SOURCE=2 -Ithird_party -I third_party \ -o bowtie2-build-s bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \ -Wl,-z,relro -Wl,-z,now -lpthread -lz g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++11 -fopenmp-simd -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -g -O2 -ffile-prefix-map=/build/bowtie2-pmC30H/bowtie2-2.4.5=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++11 -fopenmp-simd -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`LC_ALL=C date -u -d@1645112818`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -Wdate-time -D_FORTIFY_SOURCE=2 -Ithird_party -I third_party -g -O2 -ffile-prefix-map=/build/bowtie2-pmC30H/bowtie2-2.4.5=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -Wdate-time -D_FORTIFY_SOURCE=2 -Ithird_party -I third_party \ -o bowtie2-build-l bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \ -Wl,-z,relro -Wl,-z,now -lpthread -lz g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++11 -fopenmp-simd -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -g -O2 -ffile-prefix-map=/build/bowtie2-pmC30H/bowtie2-2.4.5=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++11 -fopenmp-simd -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`LC_ALL=C date -u -d@1645112818`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -Wdate-time -D_FORTIFY_SOURCE=2 -Ithird_party -I third_party -g -O2 -ffile-prefix-map=/build/bowtie2-pmC30H/bowtie2-2.4.5=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DBOWTIE2 -DNDEBUG -Wall \ -Wdate-time -D_FORTIFY_SOURCE=2 -Ithird_party -I third_party \ -o bowtie2-align-s bt2_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \ -Wl,-z,relro -Wl,-z,now -lpthread -lz g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++11 -fopenmp-simd -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -g -O2 -ffile-prefix-map=/build/bowtie2-pmC30H/bowtie2-2.4.5=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++11 -fopenmp-simd -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`LC_ALL=C date -u -d@1645112818`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -Wdate-time -D_FORTIFY_SOURCE=2 -Ithird_party -I third_party -g -O2 -ffile-prefix-map=/build/bowtie2-pmC30H/bowtie2-2.4.5=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -Wdate-time -D_FORTIFY_SOURCE=2 -Ithird_party -I third_party \ -o bowtie2-align-l bt2_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \ -Wl,-z,relro -Wl,-z,now -lpthread -lz g++ -O3 -funroll-loops -g3 \ -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++11 -fopenmp-simd -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -g -O2 -ffile-prefix-map=/build/bowtie2-pmC30H/bowtie2-2.4.5=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++11 -fopenmp-simd -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`LC_ALL=C date -u -d@1645112818`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -Wdate-time -D_FORTIFY_SOURCE=2 -Ithird_party -I third_party -g -O2 -ffile-prefix-map=/build/bowtie2-pmC30H/bowtie2-2.4.5=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \ -Wdate-time -D_FORTIFY_SOURCE=2 -Ithird_party -I third_party \ -o bowtie2-inspect-s bt2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp \ -Wl,-z,relro -Wl,-z,now -lpthread -lz g++ -O3 -funroll-loops -g3 \ -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++11 -fopenmp-simd -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -g -O2 -ffile-prefix-map=/build/bowtie2-pmC30H/bowtie2-2.4.5=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++11 -fopenmp-simd -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`LC_ALL=C date -u -d@1645112818`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -Wdate-time -D_FORTIFY_SOURCE=2 -Ithird_party -I third_party -g -O2 -ffile-prefix-map=/build/bowtie2-pmC30H/bowtie2-2.4.5=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -DBOWTIE_64BIT_INDEX -Wall \ -Wdate-time -D_FORTIFY_SOURCE=2 -Ithird_party -I third_party \ -o bowtie2-inspect-l bt2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp \ -Wl,-z,relro -Wl,-z,now -lpthread -lz aligner_seed2.cpp: In member function ‘size_t Descent::recalcOutgoing(const Read&, const Scoring&, TAlScore, TAlScore, DescentRedundancyChecker&, EFactory&, const EList&, const EList&, PerReadMetrics&)’: aligner_seed2.cpp:585:21: warning: ‘edge.DescentEdge::nex’ may be used uninitialized [-Wmaybe-uninitialized] 585 | DescentEdge edge; | ^~~~ make[2]: Leaving directory '/build/bowtie2-pmC30H/bowtie2-2.4.5' make[1]: Leaving directory '/build/bowtie2-pmC30H/bowtie2-2.4.5' create-stamp debian/debhelper-build-stamp dh_prep -i dh_auto_install -i make -j10 install DESTDIR=/build/bowtie2-pmC30H/bowtie2-2.4.5/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bowtie2-pmC30H/bowtie2-2.4.5' mkdir -p /build/bowtie2-pmC30H/bowtie2-2.4.5/debian/tmp/usr/local/bin for file in bowtie2-build-s bowtie2-build-l bowtie2-align-s bowtie2-align-l bowtie2-inspect-s bowtie2-inspect-l bowtie2-inspect bowtie2-build bowtie2 ; do \ cp -f $file /build/bowtie2-pmC30H/bowtie2-2.4.5/debian/tmp/usr/local/bin ; \ done make[1]: Leaving directory '/build/bowtie2-pmC30H/bowtie2-2.4.5' debian/rules override_dh_install make[1]: Entering directory '/build/bowtie2-pmC30H/bowtie2-2.4.5' dh_install -X.gitignore make[1]: Leaving directory '/build/bowtie2-pmC30H/bowtie2-2.4.5' dh_installdocs -i debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/bowtie2-pmC30H/bowtie2-2.4.5' dh_installchangelogs NEWS make[1]: Leaving directory '/build/bowtie2-pmC30H/bowtie2-2.4.5' debian/rules override_dh_installman make[1]: Entering directory '/build/bowtie2-pmC30H/bowtie2-2.4.5' mkdir -p /build/bowtie2-pmC30H/bowtie2-2.4.5/debian/bowtie2/usr/share/man/man1/ debian/help2man-wrapper bowtie2 "wrapper for bowtie2-align-*" debian/help2man-wrapper bowtie2-build "wrapper for bowtie2-build-*" debian/help2man-wrapper bowtie2-build-l "building a colorspace index for bowtie2" debian/help2man-wrapper bowtie2-build-s "building a colorspace index for bowtie2" debian/help2man-wrapper bowtie2-inspect "wrapper for bowtie2-inspect-* index" debian/help2man-wrapper bowtie2-inspect-l "extracts information from a bowtie2 index" debian/help2man-wrapper bowtie2-inspect-s "extracts information from a bowtie2 index" debian/help2man-wrapper bowtie2-align-l "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences" debian/help2man-wrapper bowtie2-align-s "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences" rm -f /build/bowtie2-pmC30H/bowtie2-2.4.5/debian/bowtie2/usr/bin/bowtie2-buildc make[1]: Leaving directory '/build/bowtie2-pmC30H/bowtie2-2.4.5' dh_perl -i dh_link -i dh_strip_nondeterminism -i dh_compress -i dh_fixperms -i dh_missing -i dh_installdeb -i debian/rules override_dh_gencontrol make[1]: Entering directory '/build/bowtie2-pmC30H/bowtie2-2.4.5' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.2-6), " make[1]: Leaving directory '/build/bowtie2-pmC30H/bowtie2-2.4.5' dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'bowtie2-examples' in '../bowtie2-examples_2.4.5-1_all.deb'. dpkg-genbuildinfo --build=all -O../bowtie2_2.4.5-1_all.buildinfo dpkg-genchanges --build=all -O../bowtie2_2.4.5-1_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/bowtie2-pmC30H /tmp/bowtie2-2.4.5-11d9dry3l I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap._ckdPSfDcT... I: success in 432.1557 seconds md5: bowtie2-examples_2.4.5-1_all.deb: OK sha1: bowtie2-examples_2.4.5-1_all.deb: OK sha256: bowtie2-examples_2.4.5-1_all.deb: OK Checksums: OK