Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/b/bitseq/bitseq_0.7.5+dfsg-6_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/bitseq-0.7.5+dfsg-6b1a9abd7/bitseq_0.7.5+dfsg-6_amd64.buildinfo Get source package info: bitseq=0.7.5+dfsg-6 Source URL: http://snapshot.notset.fr/mr/package/bitseq/0.7.5+dfsg-6/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.4-1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.51 bash=5.1-3+b1 binutils=2.37-5 binutils-common=2.37-5 binutils-x86-64-linux-gnu=2.37-5 bsdextrautils=2.37.2-1 bsdutils=1:2.37.2-1 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.3.0-8 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.77 debhelper=13.5.1 debianutils=5.4-3 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++=4:10.2.1-1 g++-10=10.3.0-8 gcc=4:10.2.1-1 gcc-10=10.3.0-8 gcc-10-base=10.3.0-8 gcc-11-base=11.2.0-3 gettext=0.21-4 gettext-base=0.21-4 grep=3.7-1 groff-base=1.22.4-6 gzip=1.10-4 help2man=1.48.5 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-3 libatomic1=11.2.0-3 libattr1=1:2.5.1-1 libaudit-common=1:3.0.5-1 libaudit1=1:3.0.5-1 libbam-dev=0.1.19+dfsg-2 libbinutils=2.37-5 libblas3=3.10.0-1 libblkid1=2.37.2-1 libboost-dev=1.74.0.3 libboost1.74-dev=1.74.0-9 libbz2-1.0=1.0.8-4 libc-bin=2.31-17 libc-dev-bin=2.31-17 libc6=2.31-17 libc6-dev=2.31-17 libcap-ng0=0.7.9-2.2+b1 libcc1-0=11.2.0-3 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.25-1 libcrypt1=1:4.4.25-1 libctf-nobfd0=2.37-5 libctf0=2.37-5 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.260 libdebhelper-perl=13.5.1 libdpkg-perl=1.20.9 libelf1=0.185-2 libexpat1=2.2.10-2 libffi7=3.3-6 libfile-stripnondeterminism-perl=1.12.0-1 libgcc-10-dev=10.3.0-8 libgcc-s1=11.2.0-3 libgcrypt20=1.8.7-6 libgdbm-compat4=1.20-1 libgdbm6=1.20-1 libgfortran5=11.2.0-3 libgmp10=2:6.2.1+dfsg-1 libgomp1=11.2.0-3 libgpg-error0=1.42-3 libgssapi-krb5-2=1.18.3-7 libicu67=67.1-7 libisl23=0.23-1 libitm1=11.2.0-3 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblapack3=3.10.0-1 liblocale-gettext-perl=1.07-4+b1 liblsan0=11.2.0-3 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.37.2-1 libmpc3=1.2.0-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncursesw6=6.2+20201114-4 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 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=5.32.1-5 libpipeline1=1.5.3-1 libpython3-stdlib=3.9.2-3 libpython3.9-minimal=3.9.7-1 libpython3.9-stdlib=3.9.7-1 libquadmath0=11.2.0-3 libreadline8=8.1-2 libseccomp2=2.5.1-1 libselinux1=3.1-3 libsigsegv2=2.13-1 libsmartcols1=2.37.2-1 libsqlite3-0=3.36.0-2 libssl1.1=1.1.1l-1 libstdc++-10-dev=10.3.0-8 libstdc++6=11.2.0-3 libsub-override-perl=0.09-2 libsystemd0=247.9-1 libtinfo6=6.2+20201114-4 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-3 libubsan1=11.2.0-3 libuchardet0=0.0.7-1 libudev1=247.9-1 libunistring2=0.9.10-6 libuuid1=2.37.2-1 libxml2=2.9.12+dfsg-3 libzstd1=1.4.8+dfsg-2.1 linux-libc-dev=5.10.46-4 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 media-types=4.0.0 ncurses-base=6.2+20201114-4 ncurses-bin=6.2+20201114-4 patch=2.7.6-7 perl=5.32.1-5 perl-base=5.32.1-5 perl-modules-5.32=5.32.1-5 po-debconf=1.0.21+nmu1 python3=3.9.2-3 python3-minimal=3.9.2-3 python3-numpy=1:1.19.5-1 python3-pkg-resources=52.0.0-4 python3.9=3.9.7-1 python3.9-minimal=3.9.7-1 readline-common=8.1-2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=2.96-7 tar=1.34+dfsg-1 tzdata=2021a-1 util-linux=2.37.2-1 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/20210907T024355Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210907T024355Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210902T205533Z/ 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 bitseq=0.7.5+dfsg-6 && mkdir -p /build/bitseq-gyKD9D && dpkg-source --no-check -x /*.dsc /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg && chown -R builduser:builduser /build/bitseq-gyKD9D" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1630558579" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/bitseq-gyKD9D /tmp/bitseq-0.7.5+dfsg-6b1a9abd7 bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20210902T205533Z 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.bsEogezx0R 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.bsEogezx0R Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-1). 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/20210902T205533Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210902T205533Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1033 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 ... 4670 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-17) ... 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/20210907T024355Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210907T024355Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210902T205533Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.bsEogezx0R Get:1 http://snapshot.notset.fr/archive/debian/20210907T024355Z bookworm InRelease [112 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20210902T205533Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210907T024355Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210907T024355Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210907T024355Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210907T024355Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210907T024355Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210907T024355Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210907T024355Z bookworm/main Sources [11.6 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210907T024355Z bookworm/main amd64 Packages [11.3 MB] Fetched 23.0 MB in 19s (1187 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.bsEogezx0R I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d bitseq=0.7.5+dfsg-6 && mkdir -p /build/bitseq-gyKD9D && dpkg-source --no-check -x /*.dsc /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg && chown -R builduser:builduser /build/bitseq-gyKD9D"' exec /tmp/mmdebstrap.bsEogezx0R Reading package lists... NOTICE: 'bitseq' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/bitseq.git Please use: git clone https://salsa.debian.org/med-team/bitseq.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 88.9 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210907T024355Z bookworm/main bitseq 0.7.5+dfsg-6 (dsc) [2046 B] Get:2 http://snapshot.notset.fr/archive/debian/20210907T024355Z bookworm/main bitseq 0.7.5+dfsg-6 (tar) [79.1 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210907T024355Z bookworm/main bitseq 0.7.5+dfsg-6 (diff) [7760 B] Fetched 88.9 kB in 0s (1118 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'bitseq_0.7.5+dfsg-6.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting bitseq in /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg dpkg-source: info: unpacking bitseq_0.7.5+dfsg.orig.tar.xz dpkg-source: info: unpacking bitseq_0.7.5+dfsg-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying link_against_system_samtools.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying fix_clean_target.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying fix_build_options.patch dpkg-source: info: applying 2to3.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1630558579" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.bsEogezx0R dpkg-buildpackage: info: source package bitseq dpkg-buildpackage: info: source version 0.7.5+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j10 clean make[1]: Entering directory '/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg' rm -f *.o convertSamples estimateDE estimateExpression estimateHyperPar estimateVBExpression extractSamples getFoldChange getGeneExpression getPPLR getVariance getWithinGeneExpression parseAlignment transposeLargeFile make[1]: Leaving directory '/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j10 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg' g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c ArgumentParser.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o common.o common.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -ffunction-sections -fdata-sections -c FileHeader.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c misc.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c MyTimer.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TranscriptInfo.o TranscriptInfo.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c PosteriorSamples.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -c CollapsedSampler.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o GibbsParameters.o GibbsParameters.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -c GibbsSampler.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -c Sampler.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TagAlignments.o TagAlignments.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o transposeFiles.o transposeFiles.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lowess.o lowess.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TranscriptExpression.o TranscriptExpression.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -fopenmp -DSUPPORT_OPENMP -c SimpleSparse.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -c VariationalBayes.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -fopenmp -DSUPPORT_OPENMP -c ReadDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TranscriptSequence.o TranscriptSequence.cpp ReadDistribution.cpp: In member function ‘bool ReadDistribution::observed(ns_rD::fragmentP)’: ReadDistribution.cpp:265:9: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses] 265 | (! frag->second->core.flag & BAM_FREVERSE))){ | ^~~~~~~~~~~~~~~~~~~~~~~~~ ReadDistribution.cpp: In member function ‘bool ReadDistribution::getP(ns_rD::fragmentP, double&, double&)’: ReadDistribution.cpp:687:14: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses] 687 | (! frag->second->core.flag & BAM_FREVERSE))){ | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections convertSamples.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o TranscriptInfo.o -o convertSamples g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateDE.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o estimateDE g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o CollapsedSampler.o GibbsParameters.o GibbsSampler.o Sampler.o TagAlignments.o TranscriptInfo.o transposeFiles.o -o estimateExpression g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateHyperPar.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o lowess.o PosteriorSamples.o TranscriptExpression.o -o estimateHyperPar g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateVBExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o SimpleSparse.o TagAlignments.o TranscriptInfo.o transposeFiles.o VariationalBayes.o -o estimateVBExpression g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections extractSamples.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o extractSamples g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getFoldChange.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getFoldChange g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getGeneExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o TranscriptInfo.o -o getGeneExpression g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getPPLR.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getPPLR g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getVariance.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getVariance g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getWithinGeneExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o TranscriptInfo.o -o getWithinGeneExpression g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -fopenmp -DSUPPORT_OPENMP -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections -pthread parseAlignment.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o ReadDistribution.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o -lbam -lz -o parseAlignment g++ -g -O2 -ffile-prefix-map=/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections transposeLargeFile.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o transposeFiles.o -o transposeLargeFile make[1]: Leaving directory '/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg' 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 debian/rules override_dh_auto_install make[1]: Entering directory '/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg' find -maxdepth 1 -type f -perm /111 -exec dh_install '{}' /usr/bin ';' # Provide scripts with extensions in Debian Med dir and without extension in /usr/bin mkdir -p /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq//usr/lib/debian-med/bin rm -f debian/bitseq/usr/bin/releaseDo.sh # internal BitSeq file, not intended for users mv debian/bitseq/usr/bin/*.py debian/bitseq/usr/bin/*.sh /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq//usr/lib/debian-med/bin # parseAlignment.py suggests itself not to be used so do not expose this for script in /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq//usr/lib/debian-med/bin/* ; do \ bscript=`basename ${script}` ; \ if [ "${bscript}" = "parseAlignment.py" ] ; then continue ; fi ; \ ln -s /usr/lib/debian-med/bin/${bscript} /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//`echo ${bscript} | sed -e 's/\.py$//' -e 's/\.sh$//'` ; \ done make[1]: Leaving directory '/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman make[1]: Entering directory '/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg' # try to create man pages whereever possible mkdir -p /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1/ help2man --no-info --name='convert or normalize MCMC expression samples' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//convertSamples > /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//convertSamples.1 help2man --no-info --name='this bitseq module estimates differential expression from data sets' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//estimateDE > /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//estimateDE.1 help2man --no-info --name='estimate expression given precomputed probabilities of (observed) reads'' alignments' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//estimateExpression > /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//estimateExpression.1 help2man --no-info --name='estimate expression dependent hyperparameters for bitseq' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//estimateHyperPar > /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//estimateHyperPar.1 help2man --no-info --name='estimate expression given precomputed probabilities of (observed) reads'' alignments' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//estimateVBExpression > /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//estimateVBExpression.1 help2man --no-info --name='extract MCMC samples of selected transcripts' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//extractSamples > /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//extractSamples.1 help2man --no-info --name='computes log_2 Fold Change from MCMC expression samples' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//getFoldChange > /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//getFoldChange.1 help2man --no-info --name='compute expression of whole genes' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//getGeneExpression > /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//getGeneExpression.1 help2man --no-info --name='compute PPLR from MCMC expression samples' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//getPPLR > /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//getPPLR.1 help2man --no-info --name='estimates variance of MCMC samples' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//getVariance > /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//getVariance.1 help2man --no-info --name='compute relative expression of transcripts within genes' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//getWithinGeneExpression > /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//getWithinGeneExpression.1 help2man --no-info --name='pre\-compute probabilities of (observed) reads'' alignments' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//parseAlignment > /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//parseAlignment.1 help2man --no-info --name='helper for bitseq to transpose files lines and columns' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//transposeLargeFile > /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//transposeLargeFile.1 help2man --no-info --name='extracts information about transcripts from reference Fasta file' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq//usr/lib/debian-med/bin/extractTranscriptInfo.py > /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//extractTranscriptInfo.1 help2man --no-info --name='generate read counts for each input file' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq//usr/lib/debian-med/bin/getCounts.py > /build/bitseq-gyKD9D/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//getCounts.1 make[1]: Leaving directory '/build/bitseq-gyKD9D/bitseq-0.7.5+dfsg' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a -a dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'bitseq' in '../bitseq_0.7.5+dfsg-6_amd64.deb'. dpkg-deb: building package 'bitseq-dbgsym' in '../bitseq-dbgsym_0.7.5+dfsg-6_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../bitseq_0.7.5+dfsg-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/bitseq-gyKD9D /tmp/bitseq-0.7.5+dfsg-6b1a9abd7 I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.bsEogezx0R... I: success in 2290.2373 seconds md5: bitseq-dbgsym_0.7.5+dfsg-6_amd64.deb: OK md5: bitseq_0.7.5+dfsg-6_amd64.deb: OK sha1: bitseq-dbgsym_0.7.5+dfsg-6_amd64.deb: OK sha1: bitseq_0.7.5+dfsg-6_amd64.deb: OK sha256: bitseq-dbgsym_0.7.5+dfsg-6_amd64.deb: OK sha256: bitseq_0.7.5+dfsg-6_amd64.deb: OK Checksums: OK