Thu May 2 02:07:01 UTC 2024 I: starting to build bitseq/trixie/amd64 on jenkins on '2024-05-02 02:06' Thu May 2 02:07:01 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_33/10119/console.log Thu May 2 02:07:01 UTC 2024 I: Downloading source for trixie/bitseq=0.7.5+dfsg-6 --2024-05-02 02:07:01-- http://deb.debian.org/debian/pool/main/b/bitseq/bitseq_0.7.5%2bdfsg-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2046 (2.0K) [text/prs.lines.tag] Saving to: ‘bitseq_0.7.5+dfsg-6.dsc’ 0K . 100% 235M=0s 2024-05-02 02:07:01 (235 MB/s) - ‘bitseq_0.7.5+dfsg-6.dsc’ saved [2046/2046] Thu May 2 02:07:01 UTC 2024 I: bitseq_0.7.5+dfsg-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bitseq Binary: bitseq Architecture: any Version: 0.7.5+dfsg-6 Maintainer: Debian Med Packaging Team Uploaders: Tim Booth , Andreas Tille Homepage: https://github.com/BitSeq/BitSeq Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/bitseq Vcs-Git: https://salsa.debian.org/med-team/bitseq.git Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libboost-dev, help2man, python3, python3-numpy Package-List: bitseq deb science optional arch=any Checksums-Sha1: a93fba144039e99acc006846921cb02b61febb47 79132 bitseq_0.7.5+dfsg.orig.tar.xz 2299b7e009150f9ef78b6b4fc86a2c81b3137ce9 7760 bitseq_0.7.5+dfsg-6.debian.tar.xz Checksums-Sha256: bd48fd14f9687aa4813d5e4f0a8b206616dc7fd9b1060969803f391c9534c04c 79132 bitseq_0.7.5+dfsg.orig.tar.xz 8850552c11a44fc0242f1c9196de5f127d8e9427bb13a5d4416da97d06cdc9ee 7760 bitseq_0.7.5+dfsg-6.debian.tar.xz Files: dbb476c736ab9e1384d55a41dd267336 79132 bitseq_0.7.5+dfsg.orig.tar.xz 987a1943cef4326c0d63da7f82412fe8 7760 bitseq_0.7.5+dfsg-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmEwWfsRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHrmBAAkfACeArrg9q6JQc4I40aJVfFebC8eHXI f1/5MhBY9e6HwrS6NU2iT3XUvBBJ1bFimJuTaF24qYnNQSknHhR47wqId+D9FRdf TCp83oBlu22YlEJ8rSD8bSvfr+FDdrBXapmK98n6f1+CLcbulSqjItiJxN5UlPvg PFHgJvFDKhhp4s4iNTv0zBL96IaBg6kaA9ncLpItmys7OLZU6qSwg9PbZFyQ4K4W 0cF2OQoFCIwsIRMVreweAzn5H1N0HqTADHVZlz506NyayaXlvUnMZ4HAnD2WdOhY Yomn9KJb0VPe6WFwMq3xR13HHg67o41McM6AcJgVbUbXqyGUciROhRY0oTzTapNy RIRLTcBI+0YLbNvVNwemvYmXzlEizyoUI5Q+WHOJBmLd5O6RwSg3UuekPVZWUmIX fabVIRRRPK0JGOsaNoUUe2wMmioD89GhmDs3lSAJuufDoaqyL/rglic75UL42r7C UFOCxWqyIIFuFF4lZU+r6szF3gR7bKysucRtyECZa7XEuWSw38SVGA1GBPtlRqMq UKUZ6AkcOAgnM+Hj4uWaPkAFYJSv2ZINygcAj3UtJEdklv7OLN+kSsNWjfXEw/O3 wCVbapB8zN8UoWhoyEmfO71w63cNn/YJrmMcb4NCcdSQGRU/ZenuKcHhqfIVyRft DzgjwZm8uUQ= =4wxB -----END PGP SIGNATURE----- Thu May 2 02:07:01 UTC 2024 I: Checking whether the package is not for us Thu May 2 02:07:01 UTC 2024 I: Starting 1st build on remote node infom01-amd64.debian.net. Thu May 2 02:07:01 UTC 2024 I: Preparing to do remote build '1' on infom01-amd64.debian.net. Thu May 2 02:10:36 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed May 1 14:07:03 -12 2024 I: pbuilder-time-stamp: 1714615623 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bitseq_0.7.5+dfsg-6.dsc] I: copying [./bitseq_0.7.5+dfsg.orig.tar.xz] I: copying [./bitseq_0.7.5+dfsg-6.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Sep 2 04:58:35 2021 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bitseq_0.7.5+dfsg-6.dsc: no acceptable signature found dpkg-source: info: extracting bitseq in 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: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/735879/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='48529eff8b8a457383ab5952b8310f5e' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='735879' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.hH0rpAHD/pbuilderrc_CPCt --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hH0rpAHD/b1 --logfile b1/build.log bitseq_0.7.5+dfsg-6.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom01-amd64 6.1.0-20-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 23 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/735879/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libboost-dev, help2man, python3, python3-numpy dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19875 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbam-dev{a} libboost-dev{a} libboost1.83-dev{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 36 newly installed, 0 to remove and 0 not upgraded. Need to get 30.9 MB of archives. After unpacking 237 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: python3 but it is not installable Depends: python3-numpy but it is not installable The following actions will resolve these dependencies: Remove the following packages: 1) libdb5.3 [5.3.28+dfsg2-4+b1 (now)] 2) libssl3 [3.1.5-1 (now)] Install the following packages: 3) libblis4-serial [0.9.0-1+b2 (testing)] 4) libdb5.3t64 [5.3.28+dfsg2-7 (testing)] 5) libexpat1 [2.6.2-1 (testing)] 6) libgfortran5 [14-20240330-1 (testing)] 7) liblapack3 [3.12.0-3 (testing)] 8) libpython3-stdlib [3.11.8-1 (testing)] 9) libpython3.11-minimal [3.11.9-1 (testing)] 10) libpython3.11-stdlib [3.11.9-1 (testing)] 11) libpython3.12-minimal [3.12.3-1 (testing)] 12) libpython3.12-stdlib [3.12.3-1 (testing)] 13) libreadline8t64 [8.2-4 (testing)] 14) libssl3t64 [3.2.1-3 (testing)] 15) media-types [10.1.0 (testing)] 16) netbase [6.4 (testing)] 17) python3 [3.11.8-1 (testing)] 18) python3-minimal [3.11.8-1 (testing)] 19) python3-numpy [1:1.24.2-2 (testing)] 20) python3-pkg-resources [68.1.2-2 (testing)] 21) python3.11 [3.11.9-1 (testing)] 22) python3.11-minimal [3.11.9-1 (testing)] 23) python3.12 [3.12.3-1 (testing)] 24) python3.12-minimal [3.12.3-1 (testing)] 25) readline-common [8.2-4 (testing)] 26) tzdata [2024a-3 (testing)] The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbam-dev{a} libblis4-serial{a} libboost-dev{a} libboost1.83-dev{a} libdb5.3t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} liblapack3{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} libssl3t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3-numpy{a} python3-pkg-resources{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages will be REMOVED: libdb5.3{a} libssl3{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 60 newly installed, 2 to remove and 0 not upgraded. Need to get 60.2 MB of archives. After unpacking 366 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-7 [697 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libssl3t64 amd64 3.2.1-3 [2244 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 liblocale-gettext-perl amd64 1.07-6+b1 [15.2 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-3 [255 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 16 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.3-1 [809 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.3-1 [2139 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-3+b1 [1180 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.0-3 [1401 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 41 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libbam-dev amd64 0.1.19+dfsg-6 [118 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libblis4-serial amd64 0.9.0-1+b2 [5282 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-2+b2 [10.6 MB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 55 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.3-1 [1951 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.3-1 [659 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.24.2-2 [6299 kB] Fetched 60.2 MB in 3s (18.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: libperl5.38:amd64 depends on libdb5.3. libpam-modules:amd64 depends on libdb5.3. (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 ... 19875 files and directories currently installed.) Removing libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Selecting previously unselected package libdb5.3t64:amd64. (Reading database ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up libblis4-serial:amd64 (0.9.0-1+b2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blis-serial/libblis.so.4 to provide /usr/lib/x86_64-linux-gnu/libblis.so.4 (libblis.so.4-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/blis-serial/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' Local time is now: Thu May 2 02:09:10 UTC 2024. Universal Time is now: Thu May 2 02:09:10 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up libgfortran5:amd64 (14-20240330-1) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up readline-common (8.2-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up liblocale-gettext-perl (1.07-6+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.12-minimal (3.12.3-1) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up libbam-dev (0.1.19+dfsg-6) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up libpython3.12-stdlib:amd64 (3.12.3-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-numpy (1:1.24.2-2) ... Processing triggers for libc-bin (2.37-18) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/bitseq-0.7.5+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bitseq_0.7.5+dfsg-6_source.changes 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 -j12 clean make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/bitseq-0.7.5+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/bitseq-0.7.5+dfsg' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c ArgumentParser.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -ffunction-sections -fdata-sections -c FileHeader.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c misc.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c MyTimer.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c PosteriorSamples.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -c CollapsedSampler.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -c GibbsSampler.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -c Sampler.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -fopenmp -DSUPPORT_OPENMP -c SimpleSparse.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -c VariationalBayes.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -fopenmp -DSUPPORT_OPENMP -c ReadDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 make[1]: Leaving directory '/build/reproducible-path/bitseq-0.7.5+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//`echo ${bscript} | sed -e 's/\.py$//' -e 's/\.sh$//'` ; \ done make[1]: Leaving directory '/build/reproducible-path/bitseq-0.7.5+dfsg' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/bitseq-0.7.5+dfsg' # try to create man pages whereever possible mkdir -p /build/reproducible-path/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/reproducible-path/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//convertSamples > /build/reproducible-path/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/reproducible-path/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//estimateDE > /build/reproducible-path/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/reproducible-path/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//estimateExpression > /build/reproducible-path/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/reproducible-path/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//estimateHyperPar > /build/reproducible-path/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/reproducible-path/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//estimateVBExpression > /build/reproducible-path/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/reproducible-path/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//extractSamples > /build/reproducible-path/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/reproducible-path/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//getFoldChange > /build/reproducible-path/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/reproducible-path/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//getGeneExpression > /build/reproducible-path/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/reproducible-path/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//getPPLR > /build/reproducible-path/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/reproducible-path/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//getVariance > /build/reproducible-path/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/reproducible-path/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//getWithinGeneExpression > /build/reproducible-path/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/reproducible-path/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//parseAlignment > /build/reproducible-path/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/reproducible-path/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//transposeLargeFile > /build/reproducible-path/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/reproducible-path/bitseq-0.7.5+dfsg/debian/bitseq//usr/lib/debian-med/bin/extractTranscriptInfo.py > /build/reproducible-path/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/reproducible-path/bitseq-0.7.5+dfsg/debian/bitseq//usr/lib/debian-med/bin/getCounts.py > /build/reproducible-path/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//getCounts.1 make[1]: Leaving directory '/build/reproducible-path/bitseq-0.7.5+dfsg' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb 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=binary -O../bitseq_0.7.5+dfsg-6_amd64.buildinfo dpkg-genchanges --build=binary -O../bitseq_0.7.5+dfsg-6_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/735879 and its subdirectories I: Current time: Wed May 1 14:10:35 -12 2024 I: pbuilder-time-stamp: 1714615835 Thu May 2 02:10:36 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom02-amd64.debian.net. Thu May 2 02:10:36 UTC 2024 I: Preparing to do remote build '2' on infom02-amd64.debian.net. Thu May 2 02:14:18 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. Thu May 2 02:14:19 UTC 2024 I: bitseq_0.7.5+dfsg-6_amd64.changes: Format: 1.8 Date: Thu, 02 Sep 2021 06:56:19 +0200 Source: bitseq Binary: bitseq bitseq-dbgsym Architecture: amd64 Version: 0.7.5+dfsg-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: bitseq - Bayesian Inference of Transcripts from Sequencing Data Changes: bitseq (0.7.5+dfsg-6) unstable; urgency=medium . * Fix watchfile to detect new versions on github (routine-update) * Standards-Version: 4.6.0 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. Checksums-Sha1: f83f8e8cb44f5fbd91e0bfd689b58f6edd24c026 9716720 bitseq-dbgsym_0.7.5+dfsg-6_amd64.deb 8bcf55772c15536a0cd9ad5435b7145b85f8e25e 6097 bitseq_0.7.5+dfsg-6_amd64.buildinfo 91cab53f6f01d0b9ac6d841b5c5f2ee0d073d53a 350336 bitseq_0.7.5+dfsg-6_amd64.deb Checksums-Sha256: 971f0531213c6c88628a8b9eb8b9079f1076319723d4599efdc04f74dfcdd8b8 9716720 bitseq-dbgsym_0.7.5+dfsg-6_amd64.deb 50ebadb47180e73fc1349d59f6e962d24b9e39ea070d2d36bf3849caeac95b02 6097 bitseq_0.7.5+dfsg-6_amd64.buildinfo ba2d01ecb75bfd7aa07617c43d3eaf1355e9caf3eec8d5d554a1d75fdca2b40c 350336 bitseq_0.7.5+dfsg-6_amd64.deb Files: 47c189c360b8b68d6916552ec1ecaa74 9716720 debug optional bitseq-dbgsym_0.7.5+dfsg-6_amd64.deb 19e94cf80515af322c2483bb5dddd8ac 6097 science optional bitseq_0.7.5+dfsg-6_amd64.buildinfo af5f13fdc190a990da0d021d6d002cde 350336 science optional bitseq_0.7.5+dfsg-6_amd64.deb Thu May 2 02:14:20 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_33-10119.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.hH0rpAHD/bitseq_0.7.5+dfsg-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.hH0rpAHD/bitseq_0.7.5+dfsg-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.hH0rpAHD/bitseq_0.7.5+dfsg-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.hH0rpAHD/b1/bitseq_0.7.5+dfsg-6_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.hH0rpAHD/b2/bitseq_0.7.5+dfsg-6_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.502s) 0.502s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.125s) 0.125s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 853ms CPU time consumed: 851ms Thu May 2 02:14:21 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Thu May 2 02:14:21 UTC 2024 I: bitseq from trixie built successfully and reproducibly on amd64. Thu May 2 02:14:23 UTC 2024 I: Submitting .buildinfo files to external archives: Thu May 2 02:14:23 UTC 2024 I: Submitting 8.0K b1/bitseq_0.7.5+dfsg-6_amd64.buildinfo.asc Thu May 2 02:14:23 UTC 2024 I: Submitting 8.0K b2/bitseq_0.7.5+dfsg-6_amd64.buildinfo.asc Thu May 2 02:14:24 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu May 2 02:14:24 UTC 2024 I: Done submitting .buildinfo files. Thu May 2 02:14:24 UTC 2024 I: Removing signed bitseq_0.7.5+dfsg-6_amd64.buildinfo.asc files: removed './b1/bitseq_0.7.5+dfsg-6_amd64.buildinfo.asc' removed './b2/bitseq_0.7.5+dfsg-6_amd64.buildinfo.asc'