Running as unit: rb-build-amd64_29-21277.service ==================================================================================== Sat Sep 28 10:37:27 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_29) on jenkins, called using "ionos1-amd64 ionos15-amd64" as arguments. Sat Sep 28 10:37:27 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-8j03ZDpH" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Sep 28 10:37:27 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Sat Sep 28 10:37:27 UTC 2024 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-h5Cqcm' Sat Sep 28 10:37:28 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Sat Sep 28 10:37:28 UTC 2024 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-0Kix0i' ok, let's check if amap-align is building anywhere yet… ok, amap-align is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of amap-align in unstable on amd64 on jenkins now. 1st build will be done on ionos1-amd64.debian.net. 2nd build will be done on ionos15-amd64.debian.net. ============================================================================= Sat Sep 28 10:37:41 UTC 2024 I: starting to build amap-align/unstable/amd64 on jenkins on '2024-09-28 10:37' Sat Sep 28 10:37:41 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_29/21277/console.log 1727519861 amd64 unstable amap-align Sat Sep 28 10:37:41 UTC 2024 I: Downloading source for unstable/amap-align=2.2+git20080214.600fc29+dfsg-2 --2024-09-28 10:37:41-- http://deb.debian.org/debian/pool/main/a/amap-align/amap-align_2.2%2bgit20080214.600fc29%2bdfsg-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2176 (2.1K) [text/prs.lines.tag] Saving to: ‘amap-align_2.2+git20080214.600fc29+dfsg-2.dsc’ 0K .. 100% 315M=0s 2024-09-28 10:37:41 (315 MB/s) - ‘amap-align_2.2+git20080214.600fc29+dfsg-2.dsc’ saved [2176/2176] --2024-09-28 10:37:41-- http://deb.debian.org/debian/pool/main/a/amap-align/amap-align_2.2%2bgit20080214.600fc29%2bdfsg-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2176 (2.1K) [text/prs.lines.tag] Saving to: ‘amap-align_2.2+git20080214.600fc29+dfsg-2.dsc’ 0K .. 100% 315M=0s 2024-09-28 10:37:41 (315 MB/s) - ‘amap-align_2.2+git20080214.600fc29+dfsg-2.dsc’ saved [2176/2176] Sat Sep 28 10:37:41 UTC 2024 I: amap-align_2.2+git20080214.600fc29+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: amap-align Binary: amap-align Architecture: any Version: 2.2+git20080214.600fc29+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: https://github.com/mes5k/amap-align Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/amap-align Vcs-Git: https://salsa.debian.org/med-team/amap-align.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: amap-align deb science optional arch=any Checksums-Sha1: 685963f5b938e285cc938d8ab6a4a8084e18458a 65472 amap-align_2.2+git20080214.600fc29+dfsg.orig.tar.xz 72ab5ac9cd5ae3ef8cb19b370e9f84ec1735dd13 8816 amap-align_2.2+git20080214.600fc29+dfsg-2.debian.tar.xz Checksums-Sha256: d879efc7da2ecd1fdd9d22a1615601a301d8bc13f2e67802a481a1c5a9912786 65472 amap-align_2.2+git20080214.600fc29+dfsg.orig.tar.xz 9f5380e7c54c7b776345b0e36ba45f2fe17a77b369d502292e23d603c9aa4def 8816 amap-align_2.2+git20080214.600fc29+dfsg-2.debian.tar.xz Files: 09d47fa8f11b57de3e186e8ed389ac28 65472 amap-align_2.2+git20080214.600fc29+dfsg.orig.tar.xz 05350276dd770ce7d041eb917eb80241 8816 amap-align_2.2+git20080214.600fc29+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl+yQzwRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtG/BQ/+NHdPLI04EHEQ/tyO54GjJtTFC4/e3mPl pdx8FSkw2U5LLNn7yNkVBmwerml3PHT8y0YiwvL/Q6UbedvXf2kHzBrtwTfKrTmi LPIBPqFMmDoMlhmIMT70Dq6UwCfw+IicmUpYEjeVSjDd1L4eTBqO8BEHeYvmPH0s 6FFUpKlQYeSMWGAxS7fgrL6x/dctkhLrfdcFVoIZpeIcuPspFP3i0+JPNUGQyK+Q IZNVr+nWyjn3ddVt+CyWeXFWVM0t0ABBuRWtNP1Hrqku2UWmc9HSY82UZSkmqRfZ zeCDduoYDQOBSlYCIDwV/N0JIggnudq/I7W9Z3heYp+RIyDJZmqWbrdi4swJE7cO 8aF1EQveNTSm8rIUkQbIfXgxxpNv4Grc2Jlv5kI8AXqxFHSm1STqdXlY4WP0lKel nOkFPsyvSbfGW2T0rZIVkD6SbAzDXsAaINozI/GgIJKl7UNCirll0o2LW9Jn2Cg6 8ckIpMNEaM6GMM952coA3D19tWnK/I2mUcsTFbTwJH1HDCjgNsle5orYLjZjwj9V fRMNSXMHrZtp1fI9SeWXYmX9fP1MN5JcaYSjXzHfH4DpuEaTJGKWhzgh3P42nZzH TFousDLOqsenif9b7W83GellbxPzfsGS16BAuYjJN1n1p/kfYIoJNwTd/6/b4sPR sHLy9TEVE3k= =i9LX -----END PGP SIGNATURE----- Sat Sep 28 10:37:41 UTC 2024 I: Checking whether the package is not for us Sat Sep 28 10:37:41 UTC 2024 I: Starting 1st build on remote node ionos1-amd64.debian.net. Sat Sep 28 10:37:41 UTC 2024 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Sat Sep 28 10:37:41 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Sat Sep 28 10:37:41 UTC 2024 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-QTHfI6' ==================================================================================== Sat Sep 28 10:37:46 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "1 amap-align unstable /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD 2.2+git20080214.600fc29+dfsg-2" as arguments. Sat Sep 28 10:37:46 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-Oo7z6GrV" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Sep 28 10:37:46 UTC 2024 I: Downloading source for unstable/amap-align=2.2+git20080214.600fc29+dfsg-2 Reading package lists... NOTICE: 'amap-align' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/amap-align.git Please use: git clone https://salsa.debian.org/med-team/amap-align.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 76.5 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main amap-align 2.2+git20080214.600fc29+dfsg-2 (dsc) [2176 B] Get:2 http://deb.debian.org/debian unstable/main amap-align 2.2+git20080214.600fc29+dfsg-2 (tar) [65.5 kB] Get:3 http://deb.debian.org/debian unstable/main amap-align 2.2+git20080214.600fc29+dfsg-2 (diff) [8816 B] Fetched 76.5 kB in 0s (1829 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'amap-align' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/amap-align.git Please use: git clone https://salsa.debian.org/med-team/amap-align.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 76.5 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main amap-align 2.2+git20080214.600fc29+dfsg-2 (dsc) [2176 B] Get:2 http://deb.debian.org/debian unstable/main amap-align 2.2+git20080214.600fc29+dfsg-2 (tar) [65.5 kB] Get:3 http://deb.debian.org/debian unstable/main amap-align 2.2+git20080214.600fc29+dfsg-2 (diff) [8816 B] Fetched 76.5 kB in 0s (1829 kB/s) Download complete and in download only mode ============================================================================= Building amap-align in unstable on amd64 on ionos1-amd64 now. Date: Sat Sep 28 10:37:46 UTC 2024 Date UTC: Sat Sep 28 10:37:46 UTC 2024 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Sep 27 22:37:47 -12 2024 I: pbuilder-time-stamp: 1727519867 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [amap-align_2.2+git20080214.600fc29+dfsg-2.dsc] I: copying [./amap-align_2.2+git20080214.600fc29+dfsg.orig.tar.xz] I: copying [./amap-align_2.2+git20080214.600fc29+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Nov 16 09:15:40 2020 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 ./amap-align_2.2+git20080214.600fc29+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting amap-align in amap-align-2.2+git20080214.600fc29+dfsg dpkg-source: info: unpacking amap-align_2.2+git20080214.600fc29+dfsg.orig.tar.xz dpkg-source: info: unpacking amap-align_2.2+git20080214.600fc29+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-gcc-4.3.diff dpkg-source: info: applying fix-gcc-4.6.diff dpkg-source: info: applying hardening.patch dpkg-source: info: applying mayhem.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3746134/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=20 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='b75782d9c172470385d70f6d430ef547' 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='3746134' 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.sR4KIppD/pbuilderrc_O82S --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/b1 --logfile b1/build.log amap-align_2.2+git20080214.600fc29+dfsg-2.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.106-3 (2024-08-26) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3746134/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) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19787 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. 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} 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, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 19.8 MB of archives. After unpacking 75.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-8 [97.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Fetched 19.8 MB in 4s (4433 kB/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 ... 19787 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... 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_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... 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_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-8_amd64.deb ... Unpacking bsdextrautils (2.40.2-8) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... 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_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... 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_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... 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 libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.191-2_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../23-libicu72_72.1-5_amd64.deb ... Unpacking libicu72:amd64 (72.1-5) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-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 .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libicu72:amd64 (72.1-5) ... Setting up bsdextrautils (2.40.2-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... 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 (1.14.0-1) ... Setting up gettext (0.22.5-2) ... 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 (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... 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/amap-align-2.2+git20080214.600fc29+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 > ../amap-align_2.2+git20080214.600fc29+dfsg-2_source.changes dpkg-buildpackage: info: source package amap-align dpkg-buildpackage: info: source version 2.2+git20080214.600fc29+dfsg-2 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 --sourcedirectory=align dh_auto_clean -O--sourcedirectory=align cd align && make -j20 clean make[1]: Entering directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg/align' rm -f amap make[1]: Leaving directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg/align' dh_autoreconf_clean -O--sourcedirectory=align dh_clean -O--sourcedirectory=align debian/rules binary dh binary --sourcedirectory=align dh_update_autotools_config -O--sourcedirectory=align dh_autoreconf -O--sourcedirectory=align dh_auto_configure -O--sourcedirectory=align debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg' dh_auto_build cd align && make -j20 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg/align' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=1 -DVERSION='"AMAP.2.2"' -funroll-loops -lm -o amap Amap.cc -Wl,-z,relro -Wl,-z,now In file included from MultiSequence.h:18, from Amap.cc:8: Sequence.h: In member function 'Sequence* Sequence::Clone() const': Sequence.h:293:21: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] 293 | *(ret->data) = *data; | ^~~~ In file included from Amap.cc:7: SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = char]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ In file included from Amap.cc:9: MultiSequenceDag.h: At global scope: MultiSequenceDag.h:329:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 329 | class greater_index : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from SafeVector.h:12: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ MultiSequenceDag.h:341:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 341 | class smaller_index : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ MultiSequenceDag.h:353:24: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 353 | class smaller_weight : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ MultiSequenceDag.h: In member function 'std::string MultiSequenceDag::GetSequences()': MultiSequenceDag.h:749:99: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 749 | else if (pepGroup[(int) oldPtrs[j][colPos[j]] - 'A'] == consensus || consensus >= 'A' && pepSim[(int) consensus - 'A'][(int) oldPtrs[j][colPos[j]] - 'A']) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MultiSequenceDag.h: In member function 'MultiSequence* MultiSequenceDag::AlignDag(const SafeVector >&, float, bool, bool, bool, float)': MultiSequenceDag.h:849:74: warning: operation on 'guiFrame' may be undefined [-Wsequence-point] 849 | if (outputForGUI && guiStartWeight >= edge->weight && !(guiFrame = ++guiFrame % guiStepSize)) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MultiSequenceDag.h:849:74: warning: operation on 'guiFrame' may be undefined [-Wsequence-point] In file included from Amap.cc:12: ProbabilisticModel.h: In member function 'void ProbabilisticModel::ComputeNewParameters(Sequence*, Sequence*, const VF&, const VF&, VF&, VF&, VF&, VVF&, VF&, bool) const': ProbabilisticModel.h:504:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 504 | if (enableTrainEmissions && i != 1 || j != 1){ | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ Amap.cc: In function 'void PrintParameters(const char*, const VF&, const VF&, const VF&, const VVF&, const VF&, const char*)': Amap.cc:323:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 323 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); | ^~~ Amap.cc:323:88: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 323 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); | ^~~~~~~ Amap.cc:324:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 324 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); | ^~~ Amap.cc:324:87: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 324 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); | ^~~~~~~ Amap.cc:325:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 325 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); | ^~~ Amap.cc:325:89: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 325 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); | ^~~~~~~ Amap.cc: In function 'MultiSequence* DoAlign(MultiSequence*, const ProbabilisticModel&, VF&, VF&, VF&, VVF&, VF&)': Amap.cc:482:24: warning: implicitly-declared 'SafeVector >& SafeVector >::operator=(const SafeVector >&)' is deprecated [-Wdeprecated-copy] 482 | sparseMatrices = originalSparseMatrices; | ^~~~~~~~~~~~~~~~~~~~~~ SafeVector.h:29:3: note: because 'SafeVector >' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = SafeVector]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ Amap.cc: In function 'void ReadParameters()': Amap.cc:1081:40: warning: implicitly-declared 'SafeVector >& SafeVector >::operator=(const SafeVector >&)' is deprecated [-Wdeprecated-copy] 1081 | emitPairs = VVF (256, VF (256, 1e-10)); | ^ SafeVector.h:29:3: note: because 'SafeVector >' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = SafeVector]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ Amap.cc:1082:29: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] 1082 | emitSingle = VF (256, 1e-5); | ^ SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = float]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ make[2]: Leaving directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg/align' #### This is how the *.jar can be recreated # cd display && mkdir -p lib && ant jar #### Unfortunately the command suggested in readme ## java -jar display/AmapDisplay.jar examples/BB12020.tfa.out #### segfaults. So currently this display function is not supported make[1]: Leaving directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg' dh_auto_test -O--sourcedirectory=align create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=align dh_prep -O--sourcedirectory=align dh_auto_install --destdir=debian/amap-align/ -O--sourcedirectory=align dh_install -O--sourcedirectory=align dh_installdocs -O--sourcedirectory=align dh_installchangelogs -O--sourcedirectory=align debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg' dh_installexamples chmod 644 debian/amap-align/usr/share/doc/amap-align/examples/BB12020.tfa make[1]: Leaving directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg' dh_installman -O--sourcedirectory=align dh_installsystemduser -O--sourcedirectory=align dh_perl -O--sourcedirectory=align dh_link -O--sourcedirectory=align dh_strip_nondeterminism -O--sourcedirectory=align dh_compress -O--sourcedirectory=align dh_fixperms -O--sourcedirectory=align dh_missing -O--sourcedirectory=align dh_dwz -a -O--sourcedirectory=align dh_strip -a -O--sourcedirectory=align dh_makeshlibs -a -O--sourcedirectory=align dh_shlibdeps -a -O--sourcedirectory=align dh_installdeb -O--sourcedirectory=align dh_gencontrol -O--sourcedirectory=align dh_md5sums -O--sourcedirectory=align dh_builddeb -O--sourcedirectory=align dpkg-deb: building package 'amap-align-dbgsym' in '../amap-align-dbgsym_2.2+git20080214.600fc29+dfsg-2_amd64.deb'. dpkg-deb: building package 'amap-align' in '../amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../amap-align_2.2+git20080214.600fc29+dfsg-2_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/3746134 and its subdirectories I: Current time: Fri Sep 27 22:40:33 -12 2024 I: pbuilder-time-stamp: 1727520033 Sat Sep 28 10:40:33 UTC 2024 I: Signing ./b1/amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo as amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo.asc Sat Sep 28 10:40:33 UTC 2024 I: Signed ./b1/amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo as ./b1/amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo.asc Sat Sep 28 10:40:33 UTC 2024 - build #1 for amap-align/unstable/amd64 on ionos1-amd64 done. Starting cleanup. All cleanup done. Sat Sep 28 10:40:33 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-Oo7z6GrV, removing. /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD: total 16 -rw-r--r-- 1 jenkins jenkins 2176 Nov 16 2020 amap-align_2.2+git20080214.600fc29+dfsg-2.dsc drwxr-xr-x 2 jenkins jenkins 4096 Sep 28 10:40 b1 drwxr-xr-x 2 jenkins jenkins 4096 Sep 28 10:37 b2 -rw------- 1 jenkins jenkins 3416 Sep 28 10:37 rbuildlog.ihywzRh /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/b1: total 1132 -rw-r--r-- 1 jenkins jenkins 940888 Sep 28 10:40 amap-align-dbgsym_2.2+git20080214.600fc29+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 8816 Sep 28 10:40 amap-align_2.2+git20080214.600fc29+dfsg-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2176 Sep 28 10:40 amap-align_2.2+git20080214.600fc29+dfsg-2.dsc -rw-r--r-- 1 jenkins jenkins 5096 Sep 28 10:40 amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 5978 Sep 28 10:40 amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1890 Sep 28 10:40 amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 146268 Sep 28 10:40 amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1741 Sep 28 10:40 amap-align_2.2+git20080214.600fc29+dfsg-2_source.changes -rw-r--r-- 1 jenkins jenkins 27678 Sep 28 10:40 build.log /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/b2: total 0 Sat Sep 28 10:40:38 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Sep 27 22:37:47 -12 2024 I: pbuilder-time-stamp: 1727519867 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [amap-align_2.2+git20080214.600fc29+dfsg-2.dsc] I: copying [./amap-align_2.2+git20080214.600fc29+dfsg.orig.tar.xz] I: copying [./amap-align_2.2+git20080214.600fc29+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Nov 16 09:15:40 2020 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 ./amap-align_2.2+git20080214.600fc29+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting amap-align in amap-align-2.2+git20080214.600fc29+dfsg dpkg-source: info: unpacking amap-align_2.2+git20080214.600fc29+dfsg.orig.tar.xz dpkg-source: info: unpacking amap-align_2.2+git20080214.600fc29+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-gcc-4.3.diff dpkg-source: info: applying fix-gcc-4.6.diff dpkg-source: info: applying hardening.patch dpkg-source: info: applying mayhem.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3746134/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=20 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='b75782d9c172470385d70f6d430ef547' 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='3746134' 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.sR4KIppD/pbuilderrc_O82S --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/b1 --logfile b1/build.log amap-align_2.2+git20080214.600fc29+dfsg-2.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.106-3 (2024-08-26) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3746134/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) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19787 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. 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} 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, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 19.8 MB of archives. After unpacking 75.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-8 [97.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Fetched 19.8 MB in 4s (4433 kB/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 ... 19787 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... 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 ... 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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 (1.14.0-1) ... Setting up gettext (0.22.5-2) ... 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 (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... 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/amap-align-2.2+git20080214.600fc29+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 > ../amap-align_2.2+git20080214.600fc29+dfsg-2_source.changes dpkg-buildpackage: info: source package amap-align dpkg-buildpackage: info: source version 2.2+git20080214.600fc29+dfsg-2 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 --sourcedirectory=align dh_auto_clean -O--sourcedirectory=align cd align && make -j20 clean make[1]: Entering directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg/align' rm -f amap make[1]: Leaving directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg/align' dh_autoreconf_clean -O--sourcedirectory=align dh_clean -O--sourcedirectory=align debian/rules binary dh binary --sourcedirectory=align dh_update_autotools_config -O--sourcedirectory=align dh_autoreconf -O--sourcedirectory=align dh_auto_configure -O--sourcedirectory=align debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg' dh_auto_build cd align && make -j20 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg/align' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=1 -DVERSION='"AMAP.2.2"' -funroll-loops -lm -o amap Amap.cc -Wl,-z,relro -Wl,-z,now In file included from MultiSequence.h:18, from Amap.cc:8: Sequence.h: In member function 'Sequence* Sequence::Clone() const': Sequence.h:293:21: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] 293 | *(ret->data) = *data; | ^~~~ In file included from Amap.cc:7: SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = char]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ In file included from Amap.cc:9: MultiSequenceDag.h: At global scope: MultiSequenceDag.h:329:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 329 | class greater_index : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from SafeVector.h:12: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ MultiSequenceDag.h:341:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 341 | class smaller_index : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ MultiSequenceDag.h:353:24: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 353 | class smaller_weight : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ MultiSequenceDag.h: In member function 'std::string MultiSequenceDag::GetSequences()': MultiSequenceDag.h:749:99: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 749 | else if (pepGroup[(int) oldPtrs[j][colPos[j]] - 'A'] == consensus || consensus >= 'A' && pepSim[(int) consensus - 'A'][(int) oldPtrs[j][colPos[j]] - 'A']) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MultiSequenceDag.h: In member function 'MultiSequence* MultiSequenceDag::AlignDag(const SafeVector >&, float, bool, bool, bool, float)': MultiSequenceDag.h:849:74: warning: operation on 'guiFrame' may be undefined [-Wsequence-point] 849 | if (outputForGUI && guiStartWeight >= edge->weight && !(guiFrame = ++guiFrame % guiStepSize)) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MultiSequenceDag.h:849:74: warning: operation on 'guiFrame' may be undefined [-Wsequence-point] In file included from Amap.cc:12: ProbabilisticModel.h: In member function 'void ProbabilisticModel::ComputeNewParameters(Sequence*, Sequence*, const VF&, const VF&, VF&, VF&, VF&, VVF&, VF&, bool) const': ProbabilisticModel.h:504:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 504 | if (enableTrainEmissions && i != 1 || j != 1){ | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ Amap.cc: In function 'void PrintParameters(const char*, const VF&, const VF&, const VF&, const VVF&, const VF&, const char*)': Amap.cc:323:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 323 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); | ^~~ Amap.cc:323:88: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 323 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); | ^~~~~~~ Amap.cc:324:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 324 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); | ^~~ Amap.cc:324:87: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 324 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); | ^~~~~~~ Amap.cc:325:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 325 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); | ^~~ Amap.cc:325:89: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 325 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); | ^~~~~~~ Amap.cc: In function 'MultiSequence* DoAlign(MultiSequence*, const ProbabilisticModel&, VF&, VF&, VF&, VVF&, VF&)': Amap.cc:482:24: warning: implicitly-declared 'SafeVector >& SafeVector >::operator=(const SafeVector >&)' is deprecated [-Wdeprecated-copy] 482 | sparseMatrices = originalSparseMatrices; | ^~~~~~~~~~~~~~~~~~~~~~ SafeVector.h:29:3: note: because 'SafeVector >' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = SafeVector]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ Amap.cc: In function 'void ReadParameters()': Amap.cc:1081:40: warning: implicitly-declared 'SafeVector >& SafeVector >::operator=(const SafeVector >&)' is deprecated [-Wdeprecated-copy] 1081 | emitPairs = VVF (256, VF (256, 1e-10)); | ^ SafeVector.h:29:3: note: because 'SafeVector >' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = SafeVector]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ Amap.cc:1082:29: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] 1082 | emitSingle = VF (256, 1e-5); | ^ SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = float]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ make[2]: Leaving directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg/align' #### This is how the *.jar can be recreated # cd display && mkdir -p lib && ant jar #### Unfortunately the command suggested in readme ## java -jar display/AmapDisplay.jar examples/BB12020.tfa.out #### segfaults. So currently this display function is not supported make[1]: Leaving directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg' dh_auto_test -O--sourcedirectory=align create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=align dh_prep -O--sourcedirectory=align dh_auto_install --destdir=debian/amap-align/ -O--sourcedirectory=align dh_install -O--sourcedirectory=align dh_installdocs -O--sourcedirectory=align dh_installchangelogs -O--sourcedirectory=align debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg' dh_installexamples chmod 644 debian/amap-align/usr/share/doc/amap-align/examples/BB12020.tfa make[1]: Leaving directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg' dh_installman -O--sourcedirectory=align dh_installsystemduser -O--sourcedirectory=align dh_perl -O--sourcedirectory=align dh_link -O--sourcedirectory=align dh_strip_nondeterminism -O--sourcedirectory=align dh_compress -O--sourcedirectory=align dh_fixperms -O--sourcedirectory=align dh_missing -O--sourcedirectory=align dh_dwz -a -O--sourcedirectory=align dh_strip -a -O--sourcedirectory=align dh_makeshlibs -a -O--sourcedirectory=align dh_shlibdeps -a -O--sourcedirectory=align dh_installdeb -O--sourcedirectory=align dh_gencontrol -O--sourcedirectory=align dh_md5sums -O--sourcedirectory=align dh_builddeb -O--sourcedirectory=align dpkg-deb: building package 'amap-align-dbgsym' in '../amap-align-dbgsym_2.2+git20080214.600fc29+dfsg-2_amd64.deb'. dpkg-deb: building package 'amap-align' in '../amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../amap-align_2.2+git20080214.600fc29+dfsg-2_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/3746134 and its subdirectories I: Current time: Fri Sep 27 22:40:33 -12 2024 I: pbuilder-time-stamp: 1727520033 Sat Sep 28 10:40:40 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Sat Sep 28 10:40:40 UTC 2024 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Sat Sep 28 10:40:40 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Sat Sep 28 10:40:40 UTC 2024 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-WPv7x5' ==================================================================================== Fri Oct 31 17:03:41 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "2 amap-align unstable /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD 2.2+git20080214.600fc29+dfsg-2" as arguments. Fri Oct 31 17:03:41 UTC 2025 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-g6fa9V3a" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Oct 31 17:03:41 UTC 2025 I: Downloading source for unstable/amap-align=2.2+git20080214.600fc29+dfsg-2 Reading package lists... NOTICE: 'amap-align' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/amap-align.git Please use: git clone https://salsa.debian.org/med-team/amap-align.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 76.5 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main amap-align 2.2+git20080214.600fc29+dfsg-2 (dsc) [2176 B] Get:2 http://deb.debian.org/debian unstable/main amap-align 2.2+git20080214.600fc29+dfsg-2 (tar) [65.5 kB] Get:3 http://deb.debian.org/debian unstable/main amap-align 2.2+git20080214.600fc29+dfsg-2 (diff) [8816 B] Fetched 76.5 kB in 0s (2490 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'amap-align' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/amap-align.git Please use: git clone https://salsa.debian.org/med-team/amap-align.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 76.5 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main amap-align 2.2+git20080214.600fc29+dfsg-2 (dsc) [2176 B] Get:2 http://deb.debian.org/debian unstable/main amap-align 2.2+git20080214.600fc29+dfsg-2 (tar) [65.5 kB] Get:3 http://deb.debian.org/debian unstable/main amap-align 2.2+git20080214.600fc29+dfsg-2 (diff) [8816 B] Fetched 76.5 kB in 0s (2490 kB/s) Download complete and in download only mode ============================================================================= Re-Building amap-align in unstable on amd64 on ionos15-amd64 now. Date: Fri Oct 31 17:03:41 UTC 2025 Date UTC: Fri Oct 31 17:03:41 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/pbuilderrc_eBT2 + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' amap-align = debian-installer -o amap-align = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' amap-align = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/pbuilderrc_eBT2 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/b2 --logfile b2/build.log amap-align_2.2+git20080214.600fc29+dfsg-2.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Sat Nov 1 07:03:42 +14 2025 I: pbuilder-time-stamp: 1761930222 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [amap-align_2.2+git20080214.600fc29+dfsg-2.dsc] I: copying [./amap-align_2.2+git20080214.600fc29+dfsg.orig.tar.xz] I: copying [./amap-align_2.2+git20080214.600fc29+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Nov 16 09:15:40 2020 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 ./amap-align_2.2+git20080214.600fc29+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting amap-align in amap-align-2.2+git20080214.600fc29+dfsg dpkg-source: info: unpacking amap-align_2.2+git20080214.600fc29+dfsg.orig.tar.xz dpkg-source: info: unpacking amap-align_2.2+git20080214.600fc29+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-gcc-4.3.diff dpkg-source: info: applying fix-gcc-4.6.diff dpkg-source: info: applying hardening.patch dpkg-source: info: applying mayhem.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3767107/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Oct 31 17:03 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3767107/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3767107/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=93093e2bed48494fbd48f575fff6405a LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3767107 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/pbuilderrc_eBT2 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/b2 --logfile b2/build.log amap-align_2.2+git20080214.600fc29+dfsg-2.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.10.6+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.6-1~bpo12+1 (2024-08-26) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3767107/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) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19787 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. 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} 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, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 19.8 MB of archives. After unpacking 75.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-8 [97.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Fetched 19.8 MB in 0s (84.2 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 ... 19787 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... 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_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... 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_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-8_amd64.deb ... Unpacking bsdextrautils (2.40.2-8) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... 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_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... 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_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... 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 libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.191-2_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../23-libicu72_72.1-5_amd64.deb ... Unpacking libicu72:amd64 (72.1-5) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-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 .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libicu72:amd64 (72.1-5) ... Setting up bsdextrautils (2.40.2-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... 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 (1.14.0-1) ... Setting up gettext (0.22.5-2) ... 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 (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... 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: user script /srv/workspace/pbuilder/3767107/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3767107/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../amap-align_2.2+git20080214.600fc29+dfsg-2_source.changes dpkg-buildpackage: info: source package amap-align dpkg-buildpackage: info: source version 2.2+git20080214.600fc29+dfsg-2 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 --sourcedirectory=align dh_auto_clean -O--sourcedirectory=align cd align && make -j42 clean make[1]: Entering directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg/align' rm -f amap make[1]: Leaving directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg/align' dh_autoreconf_clean -O--sourcedirectory=align dh_clean -O--sourcedirectory=align debian/rules binary dh binary --sourcedirectory=align dh_update_autotools_config -O--sourcedirectory=align dh_autoreconf -O--sourcedirectory=align dh_auto_configure -O--sourcedirectory=align debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg' dh_auto_build cd align && make -j42 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg/align' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=1 -DVERSION='"AMAP.2.2"' -funroll-loops -lm -o amap Amap.cc -Wl,-z,relro -Wl,-z,now In file included from MultiSequence.h:18, from Amap.cc:8: Sequence.h: In member function 'Sequence* Sequence::Clone() const': Sequence.h:293:21: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] 293 | *(ret->data) = *data; | ^~~~ In file included from Amap.cc:7: SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = char]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ In file included from Amap.cc:9: MultiSequenceDag.h: At global scope: MultiSequenceDag.h:329:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 329 | class greater_index : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from SafeVector.h:12: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ MultiSequenceDag.h:341:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 341 | class smaller_index : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ MultiSequenceDag.h:353:24: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 353 | class smaller_weight : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ MultiSequenceDag.h: In member function 'std::string MultiSequenceDag::GetSequences()': MultiSequenceDag.h:749:99: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 749 | else if (pepGroup[(int) oldPtrs[j][colPos[j]] - 'A'] == consensus || consensus >= 'A' && pepSim[(int) consensus - 'A'][(int) oldPtrs[j][colPos[j]] - 'A']) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MultiSequenceDag.h: In member function 'MultiSequence* MultiSequenceDag::AlignDag(const SafeVector >&, float, bool, bool, bool, float)': MultiSequenceDag.h:849:74: warning: operation on 'guiFrame' may be undefined [-Wsequence-point] 849 | if (outputForGUI && guiStartWeight >= edge->weight && !(guiFrame = ++guiFrame % guiStepSize)) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MultiSequenceDag.h:849:74: warning: operation on 'guiFrame' may be undefined [-Wsequence-point] In file included from Amap.cc:12: ProbabilisticModel.h: In member function 'void ProbabilisticModel::ComputeNewParameters(Sequence*, Sequence*, const VF&, const VF&, VF&, VF&, VF&, VVF&, VF&, bool) const': ProbabilisticModel.h:504:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 504 | if (enableTrainEmissions && i != 1 || j != 1){ | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ Amap.cc: In function 'void PrintParameters(const char*, const VF&, const VF&, const VF&, const VVF&, const VF&, const char*)': Amap.cc:323:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 323 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); | ^~~ Amap.cc:323:88: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 323 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); | ^~~~~~~ Amap.cc:324:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 324 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); | ^~~ Amap.cc:324:87: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 324 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); | ^~~~~~~ Amap.cc:325:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 325 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); | ^~~ Amap.cc:325:89: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 325 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); | ^~~~~~~ Amap.cc: In function 'MultiSequence* DoAlign(MultiSequence*, const ProbabilisticModel&, VF&, VF&, VF&, VVF&, VF&)': Amap.cc:482:24: warning: implicitly-declared 'SafeVector >& SafeVector >::operator=(const SafeVector >&)' is deprecated [-Wdeprecated-copy] 482 | sparseMatrices = originalSparseMatrices; | ^~~~~~~~~~~~~~~~~~~~~~ SafeVector.h:29:3: note: because 'SafeVector >' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = SafeVector]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ Amap.cc: In function 'void ReadParameters()': Amap.cc:1081:40: warning: implicitly-declared 'SafeVector >& SafeVector >::operator=(const SafeVector >&)' is deprecated [-Wdeprecated-copy] 1081 | emitPairs = VVF (256, VF (256, 1e-10)); | ^ SafeVector.h:29:3: note: because 'SafeVector >' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = SafeVector]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ Amap.cc:1082:29: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] 1082 | emitSingle = VF (256, 1e-5); | ^ SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = float]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ make[2]: Leaving directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg/align' #### This is how the *.jar can be recreated # cd display && mkdir -p lib && ant jar #### Unfortunately the command suggested in readme ## java -jar display/AmapDisplay.jar examples/BB12020.tfa.out #### segfaults. So currently this display function is not supported make[1]: Leaving directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg' dh_auto_test -O--sourcedirectory=align create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=align dh_prep -O--sourcedirectory=align dh_auto_install --destdir=debian/amap-align/ -O--sourcedirectory=align dh_install -O--sourcedirectory=align dh_installdocs -O--sourcedirectory=align dh_installchangelogs -O--sourcedirectory=align debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg' dh_installexamples chmod 644 debian/amap-align/usr/share/doc/amap-align/examples/BB12020.tfa make[1]: Leaving directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg' dh_installman -O--sourcedirectory=align dh_installsystemduser -O--sourcedirectory=align dh_perl -O--sourcedirectory=align dh_link -O--sourcedirectory=align dh_strip_nondeterminism -O--sourcedirectory=align dh_compress -O--sourcedirectory=align dh_fixperms -O--sourcedirectory=align dh_missing -O--sourcedirectory=align dh_dwz -a -O--sourcedirectory=align dh_strip -a -O--sourcedirectory=align dh_makeshlibs -a -O--sourcedirectory=align dh_shlibdeps -a -O--sourcedirectory=align dh_installdeb -O--sourcedirectory=align dh_gencontrol -O--sourcedirectory=align dh_md5sums -O--sourcedirectory=align dh_builddeb -O--sourcedirectory=align dpkg-deb: building package 'amap-align' in '../amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.deb'. dpkg-deb: building package 'amap-align-dbgsym' in '../amap-align-dbgsym_2.2+git20080214.600fc29+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../amap-align_2.2+git20080214.600fc29+dfsg-2_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: user script /srv/workspace/pbuilder/3767107/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3767107/tmp/hooks/B01_cleanup finished 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/3767107 and its subdirectories I: Current time: Sat Nov 1 07:04:35 +14 2025 I: pbuilder-time-stamp: 1761930275 + false + set +x Fri Oct 31 17:04:35 UTC 2025 I: Signing ./b2/amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo as amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo.asc Fri Oct 31 17:04:35 UTC 2025 I: Signed ./b2/amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo as ./b2/amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo.asc Fri Oct 31 17:04:35 UTC 2025 - build #2 for amap-align/unstable/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Fri Oct 31 17:04:35 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-g6fa9V3a, removing. /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD: total 44 -rw-r--r-- 1 jenkins jenkins 2176 Nov 16 2020 amap-align_2.2+git20080214.600fc29+dfsg-2.dsc drwxr-xr-x 2 jenkins jenkins 4096 Sep 28 10:40 b1 drwxr-xr-x 2 jenkins jenkins 4096 Sep 28 10:41 b2 -rw------- 1 jenkins jenkins 31382 Sep 28 10:40 rbuildlog.ihywzRh /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/b1: total 1140 -rw-r--r-- 1 jenkins jenkins 940888 Sep 28 10:40 amap-align-dbgsym_2.2+git20080214.600fc29+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 8816 Sep 28 10:40 amap-align_2.2+git20080214.600fc29+dfsg-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2176 Sep 28 10:40 amap-align_2.2+git20080214.600fc29+dfsg-2.dsc -rw-r--r-- 1 jenkins jenkins 5096 Sep 28 10:40 amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 5978 Sep 28 10:40 amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1890 Sep 28 10:40 amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 146268 Sep 28 10:40 amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1741 Sep 28 10:40 amap-align_2.2+git20080214.600fc29+dfsg-2_source.changes -rw-r--r-- 1 jenkins jenkins 27678 Sep 28 10:40 build.log /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/b2: total 1136 -rw-r--r-- 1 jenkins jenkins 940888 Sep 28 10:41 amap-align-dbgsym_2.2+git20080214.600fc29+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 8816 Sep 28 10:41 amap-align_2.2+git20080214.600fc29+dfsg-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2176 Sep 28 10:41 amap-align_2.2+git20080214.600fc29+dfsg-2.dsc -rw-r--r-- 1 jenkins jenkins 5105 Sep 28 10:41 amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 5987 Sep 28 10:41 amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1890 Sep 28 10:41 amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 146268 Sep 28 10:41 amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1741 Sep 28 10:41 amap-align_2.2+git20080214.600fc29+dfsg-2_source.changes -rw-r--r-- 1 jenkins jenkins 29622 Sep 28 10:41 build.log Sat Sep 28 10:41:36 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Sat Sep 28 10:41:37 UTC 2024 I: amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.changes: Format: 1.8 Date: Mon, 16 Nov 2020 09:45:41 +0100 Source: amap-align Binary: amap-align amap-align-dbgsym Architecture: amd64 Version: 2.2+git20080214.600fc29+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: amap-align - Protein multiple alignment by sequence annealing Changes: amap-align (2.2+git20080214.600fc29+dfsg-2) unstable; urgency=medium . * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Trim trailing whitespace. * Set upstream metadata fields: Bug-Database, Bug-Submit. * Refer to specific version of license GPL-2+. Checksums-Sha1: cc6af463e3467a7a96b8e3fe95ee2f55b278859c 940888 amap-align-dbgsym_2.2+git20080214.600fc29+dfsg-2_amd64.deb a8c0ae5d91799a0aa35f7d8de11a85262f567a6a 5096 amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo 5f0eb73aefd316ba5e7e6e197a997deed5ca2c2a 146268 amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.deb Checksums-Sha256: 9bc3d2cc59c8d10c5b68b1c69589abdf942666dad46b2bb2b27d7ecbf15fdfab 940888 amap-align-dbgsym_2.2+git20080214.600fc29+dfsg-2_amd64.deb 30fca65f211a7b05fdcb6a1767ee250125200c46ea4c009f12e1c3f575f9cdfc 5096 amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo 56bfa89beeaef27e195f09bbd76e6f3806af08fc497e8f4573fa521edc83a2fe 146268 amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.deb Files: 6d19fa610954fa98dc143cf2dfa61c12 940888 debug optional amap-align-dbgsym_2.2+git20080214.600fc29+dfsg-2_amd64.deb 680f476ae479a9e4363d8dce96a04100 5096 science optional amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo 86e5b337e869924d234407c7508f2111 146268 science optional amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/amap-align_2.2+git20080214.600fc29+dfsg-2.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/amap-align_2.2+git20080214.600fc29+dfsg-2.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/amap-align_2.2+git20080214.600fc29+dfsg-2.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/amap-align_2.2+git20080214.600fc29+dfsg-2.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/amap-align_2.2+git20080214.600fc29+dfsg-2.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-09-28 10:40:38.687309464 +0000 +++ b2/build.log 2024-09-28 10:41:36.520849851 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Sep 27 22:37:47 -12 2024 -I: pbuilder-time-stamp: 1727519867 +I: Current time: Sat Nov 1 07:03:42 +14 2025 +I: pbuilder-time-stamp: 1761930222 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying mayhem.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3746134/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3767107/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 31 17:03 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3767107/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3767107/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=20 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='b75782d9c172470385d70f6d430ef547' - 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='3746134' - PS1='# ' - PS2='> ' + INVOCATION_ID=93093e2bed48494fbd48f575fff6405a + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3767107 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.sR4KIppD/pbuilderrc_O82S --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/b1 --logfile b1/build.log amap-align_2.2+git20080214.600fc29+dfsg-2.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/pbuilderrc_eBT2 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/b2 --logfile b2/build.log amap-align_2.2+git20080214.600fc29+dfsg-2.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.106-3 (2024-08-26) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.10.6+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.6-1~bpo12+1 (2024-08-26) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3746134/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3767107/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -141,7 +173,7 @@ Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] -Fetched 19.8 MB in 4s (4433 kB/s) +Fetched 19.8 MB in 0s (84.2 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 ... 19787 files and directories currently installed.) @@ -272,7 +304,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/amap-align-2.2+git20080214.600fc29+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 > ../amap-align_2.2+git20080214.600fc29+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/3767107/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3767107/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../amap-align_2.2+git20080214.600fc29+dfsg-2_source.changes dpkg-buildpackage: info: source package amap-align dpkg-buildpackage: info: source version 2.2+git20080214.600fc29+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -282,7 +318,7 @@ debian/rules clean dh clean --sourcedirectory=align dh_auto_clean -O--sourcedirectory=align - cd align && make -j20 clean + cd align && make -j42 clean make[1]: Entering directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg/align' rm -f amap make[1]: Leaving directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg/align' @@ -296,7 +332,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg' dh_auto_build - cd align && make -j20 "INSTALL=install --strip-program=true" + cd align && make -j42 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg/align' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/amap-align-2.2+git20080214.600fc29+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=1 -DVERSION='"AMAP.2.2"' -funroll-loops -lm -o amap Amap.cc -Wl,-z,relro -Wl,-z,now In file included from MultiSequence.h:18, @@ -421,8 +457,8 @@ dh_gencontrol -O--sourcedirectory=align dh_md5sums -O--sourcedirectory=align dh_builddeb -O--sourcedirectory=align -dpkg-deb: building package 'amap-align-dbgsym' in '../amap-align-dbgsym_2.2+git20080214.600fc29+dfsg-2_amd64.deb'. dpkg-deb: building package 'amap-align' in '../amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.deb'. +dpkg-deb: building package 'amap-align-dbgsym' in '../amap-align-dbgsym_2.2+git20080214.600fc29+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -430,12 +466,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3767107/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3767107/tmp/hooks/B01_cleanup finished 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/3746134 and its subdirectories -I: Current time: Fri Sep 27 22:40:33 -12 2024 -I: pbuilder-time-stamp: 1727520033 +I: removing directory /srv/workspace/pbuilder/3767107 and its subdirectories +I: Current time: Sat Nov 1 07:04:35 +14 2025 +I: pbuilder-time-stamp: 1761930275 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/amap-align_2.2+git20080214.600fc29+dfsg-2.diff: 68.2% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/amap-align_2.2+git20080214.600fc29+dfsg-2.diff.gz b2/build.log: 75.5% -- replaced with stdout Compressing the 1st log... b1/build.log: 76.3% -- replaced with stdout Sat Sep 28 10:41:38 UTC 2024 I: diffoscope 278 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_amap-align_unstable_amd64_1727520098 + touch /var/log/reproducible-builds/diffoscope_stamp_amap-align_unstable_amd64_1727520098 + RESULT=0 + systemd-run '--description=diffoscope on amap-align/2.2+git20080214.600fc29+dfsg-2 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_29-21277 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD --run-session -c jenkins-reproducible-unstable-diffoscope-930b71bc-3bac-4865-9992-8d8c471a80e8 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/dbd-tmp-9zE700W ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/amap-align_2.2+git20080214.600fc29+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/amap-align_2.2+git20080214.600fc29+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/amap-align_2.2+git20080214.600fc29+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/b1/amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/b2/amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_29-21277.service Warning: program compiled against libxml 212 using older 209 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/amap-align_2.2+git20080214.600fc29+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/amap-align_2.2+git20080214.600fc29+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/amap-align_2.2+git20080214.600fc29+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/b1/amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.sR4KIppD/b2/amap-align_2.2+git20080214.600fc29+dfsg-2_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: 0.466s) 0.466s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.033s) 0.033s 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: 862ms CPU time consumed: 860ms _ _ __ _ _ __ ___ __ _ _ __ __ _| (_) __ _ _ __ / _` | '_ ` _ \ / _` | '_ \ _____ / _` | | |/ _` | '_ \ | (_| | | | | | | (_| | |_) |_____| (_| | | | (_| | | | | \__,_|_| |_| |_|\__,_| .__/ \__,_|_|_|\__, |_| |_| |_| |___/ Sat Sep 28 10:41:39 UTC 2024 I: diffoscope 278 found no differences in the changes files, and a .buildinfo file also exists. Sat Sep 28 10:41:39 UTC 2024 I: amap-align from unstable built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-09-28 10:41:40] INFO: Starting at 2024-09-28 10:41:40.185620 [2024-09-28 10:41:40] INFO: Generating the pages of 1 package(s) [2024-09-28 10:41:40] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/amap-align didn't produce a buildlog, even though it has been built. [2024-09-28 10:41:40] INFO: Finished at 2024-09-28 10:41:40.857961, took: 0:00:00.672355 Sat Sep 28 10:41:40 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/amap-align.html Sat Sep 28 10:41:40 UTC 2024 I: Submitting .buildinfo files to external archives: Sat Sep 28 10:41:40 UTC 2024 I: Submitting 8.0K b1/amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo.asc https://buildinfo.debian.net/a8c0ae5d91799a0aa35f7d8de11a85262f567a6a/amap-align_2.2+git20080214.600fc29+dfsg-2_amd64 Sat Sep 28 10:41:41 UTC 2024 I: Submitting 8.0K b2/amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo.asc https://buildinfo.debian.net/e96bbdca97eb67497e1b491e76289f06e43aae5f/amap-align_2.2+git20080214.600fc29+dfsg-2_amd64 Sat Sep 28 10:41:42 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Sep 28 10:41:42 UTC 2024 I: Done submitting .buildinfo files. Sat Sep 28 10:41:42 UTC 2024 I: Removing signed amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo.asc files: removed './b1/amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo.asc' removed './b2/amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.buildinfo.asc' 1727520102 amd64 unstable amap-align Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/amap-align_2.2+git20080214.600fc29+dfsg-2.rbuild.log: 73.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/amap-align_2.2+git20080214.600fc29+dfsg-2.rbuild.log.gz [2024-09-28 10:41:43] INFO: Starting at 2024-09-28 10:41:43.187218 [2024-09-28 10:41:43] INFO: Generating the pages of 1 package(s) [2024-09-28 10:41:43] INFO: Finished at 2024-09-28 10:41:43.702177, took: 0:00:00.514969 All cleanup done. Sat Sep 28 10:41:43 UTC 2024 - total duration: 0h 4m 12s. Sat Sep 28 10:41:43 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-8j03ZDpH, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 4min 15.946s CPU time consumed: 8.540s