Thu May 9 20:03:12 UTC 2024 I: starting to build genometester/trixie/amd64 on jenkins on '2024-05-09 20:03' Thu May 9 20:03:12 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_24/20169/console.log Thu May 9 20:03:12 UTC 2024 I: Downloading source for trixie/genometester=4.0+git20200511.91cecb5+dfsg-1 --2024-05-09 20:03:12-- http://deb.debian.org/debian/pool/main/g/genometester/genometester_4.0%2bgit20200511.91cecb5%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2224 (2.2K) [text/prs.lines.tag] Saving to: ‘genometester_4.0+git20200511.91cecb5+dfsg-1.dsc’ 0K .. 100% 210M=0s 2024-05-09 20:03:12 (210 MB/s) - ‘genometester_4.0+git20200511.91cecb5+dfsg-1.dsc’ saved [2224/2224] Thu May 9 20:03:12 UTC 2024 I: genometester_4.0+git20200511.91cecb5+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: genometester Binary: genometester Architecture: any Version: 4.0+git20200511.91cecb5+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Liubov Chuprikova , Andreas Tille Homepage: https://github.com/bioinfo-ut/GenomeTester4 Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/genometester Vcs-Git: https://salsa.debian.org/med-team/genometester.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12) Package-List: genometester deb science optional arch=any Checksums-Sha1: 9bb2833f18dd955907cb4eb34c60f5a161714b12 87872 genometester_4.0+git20200511.91cecb5+dfsg.orig.tar.xz f06ad509d6ccab4724444478241842469a855ce8 232860 genometester_4.0+git20200511.91cecb5+dfsg-1.debian.tar.xz Checksums-Sha256: 4b1360ab90dd0469945d7c88e1e361804849e27e15594e132882ffb84ae25808 87872 genometester_4.0+git20200511.91cecb5+dfsg.orig.tar.xz 1dd432ab7e6eb091554876f38d27a72d6cdb6fa511ab310ad2df7ebb4c59763d 232860 genometester_4.0+git20200511.91cecb5+dfsg-1.debian.tar.xz Files: 25bdcb96a8dd105d0944c144b53c606b 87872 genometester_4.0+git20200511.91cecb5+dfsg.orig.tar.xz 396b72e53338bd3173402c3baa7403ce 232860 genometester_4.0+git20200511.91cecb5+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJHBAEBCAAxFiEEhMGXeonn7+0+XKYuL9i+2sAg7tEFAl7BfoQTHG1vZWxsZXJA ZGViaWFuLm9yZwAKCRAv2L7awCDu0XMGD/4rxUZ5IVCoR2dnaBQrNUfkA/RVigUs +dBKucXGFw1g2981A10lsoyVhAgqglFcilBNg5VDrgnZqBBmujWytSB9D4xsHMaK 9y4gXOAU9PeGMTSDM844kIuuv66I6y4HtXbZ2/f7QnTgZ8xU/E6I1SpXeteO9wqj g02O4XF5Z6g6W29JJ80s+2vEACoB18lzfrJMCeXBwCWAKxnLjLPbHlwsZzEKJUI7 pfIWvQX4+Zm2xS1cI6W8rqaEUuvDhGBbck/PULdqPIOz6/QhyyR0cG2ZTlLUOFXt ARGzPKEYtd09N8RzQAK4pVHQQxCkXl8lrh0vWwRTho1yxgJ3Qd8SrUj3IeOMjeaX +/B0ySZAylKGBKSM4BkiwvYa/1458BJv/L1rrtU2YGGIBfAkYtxfbCNitNRomtAQ WXAOke8+0UKPSwNe18XR9Y2uiOyfryVco6clMPQfFiYAdVdCnkNMED+r1PZ4eOZ1 R7QKpeIo3Kk1QCd3iWN7mkDO63aQY9FqA/WYzCQvWOXaf6XgQ0RL9yWMDot22iGE FzLwRzdK7WPw8pDYToUSeB3a4iGSVpKIHE0cwafcfrmvZwKUvE5F6Q3DdMmlezNE EIsnV1+zI6nN0/SMC1K1vt8gadHMjJtLlI7uL37c/T4q/r8zuT53U5DWimJsjwUt 4lvNRgibXH45jw== =eWXy -----END PGP SIGNATURE----- Thu May 9 20:03:12 UTC 2024 I: Checking whether the package is not for us Thu May 9 20:03:12 UTC 2024 I: Starting 1st build on remote node ionos15-amd64.debian.net. Thu May 9 20:03:12 UTC 2024 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Thu May 9 20:03:56 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Jun 11 14:26:15 -12 2025 I: pbuilder-time-stamp: 1749695175 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 [genometester_4.0+git20200511.91cecb5+dfsg-1.dsc] I: copying [./genometester_4.0+git20200511.91cecb5+dfsg.orig.tar.xz] I: copying [./genometester_4.0+git20200511.91cecb5+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun May 17 18:12:20 2020 gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./genometester_4.0+git20200511.91cecb5+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting genometester in genometester-4.0+git20200511.91cecb5+dfsg dpkg-source: info: unpacking genometester_4.0+git20200511.91cecb5+dfsg.orig.tar.xz dpkg-source: info: unpacking genometester_4.0+git20200511.91cecb5+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add_debug_symbols.patch dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2604832/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=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='94632291ad674c3493c1d859124f93c1' 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='2604832' 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.dJGIOOpM/pbuilderrc_ff5g --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.dJGIOOpM/b1 --logfile b1/build.log genometester_4.0+git20200511.91cecb5+dfsg-1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 11 17:46 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2604832/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 (= 12) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19699 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 (= 12); however: Package debhelper-compat 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} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{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} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 19.0 MB of archives. After unpacking 73.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Fetched 19.0 MB in 0s (134 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19699 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_amd64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../22-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_amd64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... 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 libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... 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 gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.38-7) ... 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/genometester-4.0+git20200511.91cecb5+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 > ../genometester_4.0+git20200511.91cecb5+dfsg-1_source.changes dpkg-buildpackage: info: source package genometester dpkg-buildpackage: info: source version 4.0+git20200511.91cecb5+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Moeller dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/genometester-4.0+git20200511.91cecb5+dfsg' dh_auto_clean cd src && make -j42 clean make[2]: Entering directory '/build/reproducible-path/genometester-4.0+git20200511.91cecb5+dfsg/src' rm -f *.o glistmaker glistquery glistcompare make[2]: Leaving directory '/build/reproducible-path/genometester-4.0+git20200511.91cecb5+dfsg/src' rm -f src/gdistribution src/gmer_caller src/gmer_counter make[1]: Leaving directory '/build/reproducible-path/genometester-4.0+git20200511.91cecb5+dfsg' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/genometester-4.0+git20200511.91cecb5+dfsg' dh_auto_build cd src && make -j42 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/genometester-4.0+git20200511.91cecb5+dfsg/src' gcc glistmaker.c common.c common.h fasta.c fasta.h wordtable.c wordtable.h wordmap.c wordmap.h buffer.c buffer.h sequence.c sequence.h sequence-file.c sequence-file.h queue.c queue.h utils.c utils.h -o glistmaker -lm -lpthread -lrt -g -O2 -ffile-prefix-map=/build/reproducible-path/genometester-4.0+git20200511.91cecb5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -O3 -g -Wall -Wl,-z,relro -Wl,-z,now gcc glistquery.c wordtable.c wordtable.h wordmap.c wordmap.h fasta.c fasta.h buffer.c buffer.h sequence.c sequence.h sequence-file.c sequence-file.h common.c common.h queue.c queue.h utils.c utils.h -o glistquery -lm -lpthread -lrt -g -O2 -ffile-prefix-map=/build/reproducible-path/genometester-4.0+git20200511.91cecb5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -O3 -g -Wall -Wl,-z,relro -Wl,-z,now gcc glistcompare.c wordtable.c wordmap.c fasta.c buffer.c sequence.c sequence-file.c sequence-file.h common.c queue.c queue.h utils.c -o glistcompare -lm -lpthread -lrt -g -O2 -ffile-prefix-map=/build/reproducible-path/genometester-4.0+git20200511.91cecb5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -O3 -g -Wall -Wl,-z,relro -Wl,-z,now glistmaker.c: In function ‘process’: glistmaker.c:380:33: warning: ‘t’ may be used uninitialized [-Wmaybe-uninitialized] 380 | wordtable_build_filename (t[0], c, 1024, outputname); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ glistmaker.c:373:44: note: ‘t’ declared here 373 | wordtable *t[MAX_MERGED_TABLES]; | ^ make[2]: Leaving directory '/build/reproducible-path/genometester-4.0+git20200511.91cecb5+dfsg/src' dh_auto_build -- gmer_counter cd src && make -j42 "INSTALL=install --strip-program=true" gmer_counter make[2]: Entering directory '/build/reproducible-path/genometester-4.0+git20200511.91cecb5+dfsg/src' gcc gmer_counter.c index.c index.h trie.c trie.h wordmap.c wordmap.h sequence.c sequence.h sequence-file.c sequence-file.h wordtable.c wordtable.h fasta.c fasta.h thread-pool.c thread-pool.h queue.c queue.h utils.c utils.h database.c database.h -o gmer_counter -lm -lpthread -lrt -g -O2 -ffile-prefix-map=/build/reproducible-path/genometester-4.0+git20200511.91cecb5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -O3 -g -Wall -Wl,-z,relro -Wl,-z,now -Wall make[2]: Leaving directory '/build/reproducible-path/genometester-4.0+git20200511.91cecb5+dfsg/src' dh_auto_build -- gmer_caller cd src && make -j42 "INSTALL=install --strip-program=true" gmer_caller make[2]: Entering directory '/build/reproducible-path/genometester-4.0+git20200511.91cecb5+dfsg/src' gcc binomial.c binomial.h genotypes.c genotypes.h simplex.c simplex.h thread-pool.c thread-pool.h utils.c utils.h gmer_caller.c -o gmer_caller -lm -lpthread -lrt -g -O2 -ffile-prefix-map=/build/reproducible-path/genometester-4.0+git20200511.91cecb5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -O3 -g -Wall -Wl,-z,relro -Wl,-z,now -Wall gmer_caller.c: In function ‘main’: gmer_caller.c:495:16: warning: variable ‘coverage_specified’ set but not used [-Wunused-but-set-variable] 495 | unsigned int coverage_specified = 0; | ^~~~~~~~~~~~~~~~~~ gmer_caller.c: At top level: gmer_caller.c:903:1: warning: ‘logL2’ defined but not used [-Wunused-function] 903 | logL2 (const float arg[], unsigned int count, unsigned int tulem2[], unsigned int katvus2[]) | ^~~~~ gmer_caller.c: In function ‘parse_calls’: gmer_caller.c:167:24: warning: ‘best_a’ may be used uninitialized [-Wmaybe-uninitialized] 167 | calls[i].counts[0] = best_a; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ gmer_caller.c:150:9: note: ‘best_a’ was declared here 150 | int best_a, best_b, best_delta; | ^~~~~~ gmer_caller.c:168:24: warning: ‘best_b’ may be used uninitialized [-Wmaybe-uninitialized] 168 | calls[i].counts[1] = best_b; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ gmer_caller.c:150:17: note: ‘best_b’ was declared here 150 | int best_a, best_b, best_delta; | ^~~~~~ gmer_caller.c: In function ‘main’: gmer_caller.c:785:9: warning: ‘calls_x’ may be used uninitialized [-Wmaybe-uninitialized] 785 | print_genotypes (lines, calls_x, nx, params, pB, (non_canonical) ? 0 : 2, prob_cutoff, alternatives, nthreads); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gmer_caller.c:509:22: note: ‘calls_x’ was declared here 509 | SNPCall *calls_a, *calls_x, *calls_y; | ^~~~~~~ make[2]: Leaving directory '/build/reproducible-path/genometester-4.0+git20200511.91cecb5+dfsg/src' dh_auto_build -- gdistribution cd src && make -j42 "INSTALL=install --strip-program=true" gdistribution make[2]: Entering directory '/build/reproducible-path/genometester-4.0+git20200511.91cecb5+dfsg/src' gcc gdistribution.c wordtable.c wordmap.c fasta.c buffer.c sequence.c sequence-file.c sequence-file.h common.c queue.c queue.h utils.c -o gdistribution -lm -lpthread -lrt -g -O2 -ffile-prefix-map=/build/reproducible-path/genometester-4.0+git20200511.91cecb5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -O3 -g -Wall -Wl,-z,relro -Wl,-z,now gdistribution.c: In function ‘main’: gdistribution.c:55:9: warning: unused variable ‘freqs’ [-Wunused-variable] 55 | Freq *freqs; | ^~~~~ make[2]: Leaving directory '/build/reproducible-path/genometester-4.0+git20200511.91cecb5+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/genometester-4.0+git20200511.91cecb5+dfsg' dh_auto_test -O--sourcedirectory=src create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_auto_install --destdir=debian/genometester/ -O--sourcedirectory=src dh_install -O--sourcedirectory=src dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src dh_installman -O--sourcedirectory=src dh_installinit -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -O--sourcedirectory=src dh_strip -O--sourcedirectory=src dh_makeshlibs -O--sourcedirectory=src dh_shlibdeps -O--sourcedirectory=src dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'genometester' in '../genometester_4.0+git20200511.91cecb5+dfsg-1_amd64.deb'. dpkg-deb: building package 'genometester-dbgsym' in '../genometester-dbgsym_4.0+git20200511.91cecb5+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../genometester_4.0+git20200511.91cecb5+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../genometester_4.0+git20200511.91cecb5+dfsg-1_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: including full 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/2604832 and its subdirectories I: Current time: Wed Jun 11 14:26:56 -12 2025 I: pbuilder-time-stamp: 1749695216 Thu May 9 20:03:57 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Thu May 9 20:03:57 UTC 2024 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Thu May 9 20:05:34 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Thu May 9 20:05:35 UTC 2024 I: genometester_4.0+git20200511.91cecb5+dfsg-1_amd64.changes: Format: 1.8 Date: Sun, 17 May 2020 20:06:55 +0200 Source: genometester Binary: genometester genometester-dbgsym Architecture: amd64 Version: 4.0+git20200511.91cecb5+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Steffen Moeller Description: genometester - toolkit for performing set operations on k-mer lists Changes: genometester (4.0+git20200511.91cecb5+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 12 (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. (routine-update) * Added d/TODO to indicate missing man page (also a lintian warning) * Improved clean. Checksums-Sha1: 04ce94150e93b5940d94b0ab6bf28a0959872a3a 281056 genometester-dbgsym_4.0+git20200511.91cecb5+dfsg-1_amd64.deb 4f8524ddc7a0a532fac309672aaeb33a1bc35668 5359 genometester_4.0+git20200511.91cecb5+dfsg-1_amd64.buildinfo 82c177eb68e8760c2331c1976afdc86b998c10a4 309200 genometester_4.0+git20200511.91cecb5+dfsg-1_amd64.deb Checksums-Sha256: 00086b29b950f7b462748ca6927878bcb725d259de090dbc3c76bd1582567e72 281056 genometester-dbgsym_4.0+git20200511.91cecb5+dfsg-1_amd64.deb b5b00851c31761dd22ba303c5e2c392f67dad5129257ac622f31a10359d154ae 5359 genometester_4.0+git20200511.91cecb5+dfsg-1_amd64.buildinfo be028e8efeac0f6fbfb3035eda0259c7302583cf2f53b9c17cc6bfa8e689ec09 309200 genometester_4.0+git20200511.91cecb5+dfsg-1_amd64.deb Files: 7134d7b5915908aeb0c1d04e349cf893 281056 debug optional genometester-dbgsym_4.0+git20200511.91cecb5+dfsg-1_amd64.deb c90c0a7c744af15b2a3564b8999ebfc5 5359 science optional genometester_4.0+git20200511.91cecb5+dfsg-1_amd64.buildinfo 4b2483d49a443bd1c9f31d1b415fcd2a 309200 science optional genometester_4.0+git20200511.91cecb5+dfsg-1_amd64.deb Thu May 9 20:05:36 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_24-20169.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.dJGIOOpM/genometester_4.0+git20200511.91cecb5+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.dJGIOOpM/genometester_4.0+git20200511.91cecb5+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.dJGIOOpM/genometester_4.0+git20200511.91cecb5+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.dJGIOOpM/b1/genometester_4.0+git20200511.91cecb5+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.dJGIOOpM/b2/genometester_4.0+git20200511.91cecb5+dfsg-1_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: 0.384s) 0.384s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.024s) 0.024s 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: 731ms CPU time consumed: 729ms Thu May 9 20:05:37 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Thu May 9 20:05:37 UTC 2024 I: genometester from trixie built successfully and reproducibly on amd64. Thu May 9 20:05:38 UTC 2024 I: Submitting .buildinfo files to external archives: Thu May 9 20:05:38 UTC 2024 I: Submitting 8.0K b1/genometester_4.0+git20200511.91cecb5+dfsg-1_amd64.buildinfo.asc Thu May 9 20:05:39 UTC 2024 I: Submitting 8.0K b2/genometester_4.0+git20200511.91cecb5+dfsg-1_amd64.buildinfo.asc Thu May 9 20:05:40 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu May 9 20:05:40 UTC 2024 I: Done submitting .buildinfo files. Thu May 9 20:05:40 UTC 2024 I: Removing signed genometester_4.0+git20200511.91cecb5+dfsg-1_amd64.buildinfo.asc files: removed './b1/genometester_4.0+git20200511.91cecb5+dfsg-1_amd64.buildinfo.asc' removed './b2/genometester_4.0+git20200511.91cecb5+dfsg-1_amd64.buildinfo.asc'