Fri Aug 20 09:07:15 UTC 2021 I: starting to build amap-align/bullseye/armhf on jenkins on '2021-08-20 09:07' Fri Aug 20 09:07:15 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_31/3824/console.log Fri Aug 20 09:07:15 UTC 2021 I: Downloading source for bullseye/amap-align=2.2+git20080214.600fc29+dfsg-2 --2021-08-20 09:07:15-- http://cdn-fastly.deb.debian.org/debian/pool/main/a/amap-align/amap-align_2.2%2bgit20080214.600fc29%2bdfsg-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2176 (2.1K) Saving to: ‘amap-align_2.2+git20080214.600fc29+dfsg-2.dsc’ 0K .. 100% 186M=0s 2021-08-20 09:07:15 (186 MB/s) - ‘amap-align_2.2+git20080214.600fc29+dfsg-2.dsc’ saved [2176/2176] Fri Aug 20 09:07:15 UTC 2021 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----- Fri Aug 20 09:07:15 UTC 2021 I: Checking whether the package is not for us Fri Aug 20 09:07:15 UTC 2021 I: Starting 1st build on remote node virt64c-armhf-rb.debian.net. Fri Aug 20 09:07:15 UTC 2021 I: Preparing to do remote build '1' on virt64c-armhf-rb.debian.net. Fri Aug 20 09:09:17 UTC 2021 I: Deleting $TMPDIR on virt64c-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Aug 19 21:07:21 -12 2021 I: pbuilder-time-stamp: 1629450441 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.f_6amQ4O/trustedkeys.kbx': General error gpgv: Signature made Sun Nov 15 21:15:40 2020 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./amap-align_2.2+git20080214.600fc29+dfsg-2.dsc 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/4248/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='0be60bd15dc7476cb30bd88c377ea042' 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='4248' 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/tmp.7M6BwjuQDw/pbuilderrc_34pU --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.7M6BwjuQDw/b1 --logfile b1/build.log amap-align_2.2+git20080214.600fc29+dfsg-2.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux virt64c 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 26668 Sep 22 2020 cat -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash -rwxr-xr-x 1 root root 75880 Sep 22 2020 date -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd -rwxr-xr-x 1 root root 59912 Sep 22 2020 df -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir -rwxr-xr-x 1 root root 55012 Jul 28 07:09 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 22496 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln -rwxr-xr-x 1 root root 35068 Feb 7 2020 login -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls -rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 34408 Jul 28 07:09 more -rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount -rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 13 21:24 sh -> dash -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty -rwsr-xr-x 1 root root 46704 Jul 28 07:09 su -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync -rwxr-xr-x 1 root root 340872 Feb 16 2021 tar -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch -rwxr-xr-x 1 root root 22496 Sep 22 2020 true -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir -rwxr-xr-x 1 root root 38512 Jul 28 07:09 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/4248/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: armhf 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 ... 19398 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} libelf1{a} libfile-stripnondeterminism-perl{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 17.7 MB of archives. After unpacking 62.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-8 [138 kB] Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB] Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB] Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB] Get: 6 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB] Get: 9 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB] Get: 11 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB] Get: 12 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB] Get: 13 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB] Get: 25 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB] Get: 26 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB] Get: 27 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB] Get: 28 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB] Get: 29 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Fetched 17.7 MB in 9s (1947 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19398 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_armhf.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_armhf.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../03-libpipeline1_1.5.3-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_armhf.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_armhf.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../07-libmagic1_1%3a5.39-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_armhf.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_armhf.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../10-libsigsegv2_2.13-1_armhf.deb ... Unpacking libsigsegv2:armhf (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_armhf.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../23-libelf1_0.183-1_armhf.deb ... Unpacking libelf1:armhf (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.13+20210201-1_armhf.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:armhf. Preparing to unpack .../25-libicu67_67.1-7_armhf.deb ... Unpacking libicu67:armhf (67.1-7) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../26-libxml2_2.9.10+dfsg-6.7_armhf.deb ... Unpacking libxml2:armhf (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-4_armhf.deb ... Unpacking gettext (0.21-4) ... 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Setting up libsigsegv2:armhf (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libelf1:armhf (0.183-1) ... Setting up libxml2:armhf (2.9.10+dfsg-6.7) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-13) ... 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/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 armhf debian/rules clean dh clean --sourcedirectory=align dh_auto_clean -O--sourcedirectory=align cd align && make -j3 clean make[1]: Entering directory '/build/amap-align-2.2+git20080214.600fc29+dfsg/align' rm -f amap make[1]: Leaving directory '/build/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/amap-align-2.2+git20080214.600fc29+dfsg' dh_auto_build cd align && make -j3 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/amap-align-2.2+git20080214.600fc29+dfsg/align' g++ -g -O2 -fdebug-prefix-map=/build/amap-align-2.2+git20080214.600fc29+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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: In member function 'std::string MultiSequenceDag::GetSequences()': MultiSequenceDag.h:749:92: 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:849:67: warning: operation on 'guiFrame' may be undefined [-Wsequence-point] 849 | if (outputForGUI && guiStartWeight >= edge->weight && !(guiFrame = ++guiFrame % guiStepSize)) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MultiSequenceDag.h:849:67: 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:504:31: 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; | ^~~~~~~~~~~~~~~~~~~~~~ In file included from Amap.cc:7: 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)); | ^ In file included from Amap.cc:7: 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); | ^ In file included from Amap.cc:7: 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/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/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 -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/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/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 dpkg-shlibdeps: warning: debian/amap-align/usr/bin/amap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin 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_armhf.deb'. dpkg-deb: building package 'amap-align' in '../amap-align_2.2+git20080214.600fc29+dfsg-2_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../amap-align_2.2+git20080214.600fc29+dfsg-2_armhf.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/4248 and its subdirectories I: Current time: Thu Aug 19 21:09:12 -12 2021 I: pbuilder-time-stamp: 1629450552 Fri Aug 20 09:09:20 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ff4a-armhf-rb.debian.net. Fri Aug 20 09:09:20 UTC 2021 I: Preparing to do remote build '2' on ff4a-armhf-rb.debian.net. Fri Aug 20 09:16:28 UTC 2021 I: Deleting $TMPDIR on ff4a-armhf-rb.debian.net. Fri Aug 20 09:16:30 UTC 2021 I: amap-align_2.2+git20080214.600fc29+dfsg-2_armhf.changes: Format: 1.8 Date: Mon, 16 Nov 2020 09:45:41 +0100 Source: amap-align Binary: amap-align amap-align-dbgsym Architecture: armhf 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: cefc38554637ecab069d328beb7b6840526c368d 833164 amap-align-dbgsym_2.2+git20080214.600fc29+dfsg-2_armhf.deb 3eb8f8d2400e5bd79dc77db1fd484ad7c8528b32 4957 amap-align_2.2+git20080214.600fc29+dfsg-2_armhf.buildinfo 36f194fbba66f40b9841e33568915a7d02d1d29a 109736 amap-align_2.2+git20080214.600fc29+dfsg-2_armhf.deb Checksums-Sha256: d7258ceef9e04dc3f6c900c185770011e65c99617cf6a032901dbbf55169a339 833164 amap-align-dbgsym_2.2+git20080214.600fc29+dfsg-2_armhf.deb 500ae6fee18f73466c9ed83daa5879539726899bbed2c0b4aaf2e65a0c3e6f22 4957 amap-align_2.2+git20080214.600fc29+dfsg-2_armhf.buildinfo c2d5ef33ed4e29a18c76a275ace9e26b4ac629a57b7027b3a894e81414cb79ca 109736 amap-align_2.2+git20080214.600fc29+dfsg-2_armhf.deb Files: 555c950b2f7373fe8332f5a8348d1768 833164 debug optional amap-align-dbgsym_2.2+git20080214.600fc29+dfsg-2_armhf.deb 9b11810596e3a0b1193495296c86f3fd 4957 science optional amap-align_2.2+git20080214.600fc29+dfsg-2_armhf.buildinfo f586db389e857f69fb948a82447a8c8c 109736 science optional amap-align_2.2+git20080214.600fc29+dfsg-2_armhf.deb Fri Aug 20 09:16:32 UTC 2021 I: diffoscope 177 will be used to compare the two builds: W: /var/lib/schroot/session/jenkins-reproducible-bookworm-diffoscope-8718fa6c-d2e6-4a59-9bf9-8ce9643e314f: Failed to stat file: No such file or directory # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.7M6BwjuQDw/amap-align_2.2+git20080214.600fc29+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.7M6BwjuQDw/amap-align_2.2+git20080214.600fc29+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.7M6BwjuQDw/amap-align_2.2+git20080214.600fc29+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.7M6BwjuQDw/b1/amap-align_2.2+git20080214.600fc29+dfsg-2_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.7M6BwjuQDw/b2/amap-align_2.2+git20080214.600fc29+dfsg-2_armhf.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: 1.530s) 1.530s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.130s) 0.130s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Fri Aug 20 09:16:34 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Fri Aug 20 09:16:34 UTC 2021 I: amap-align from bullseye built successfully and reproducibly on armhf. Fri Aug 20 09:16:36 UTC 2021 I: Submitting .buildinfo files to external archives: Fri Aug 20 09:16:36 UTC 2021 I: Submitting 8.0K b1/amap-align_2.2+git20080214.600fc29+dfsg-2_armhf.buildinfo.asc Fri Aug 20 09:16:36 UTC 2021 I: Submitting 8.0K b2/amap-align_2.2+git20080214.600fc29+dfsg-2_armhf.buildinfo.asc Fri Aug 20 09:16:38 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Aug 20 09:16:38 UTC 2021 I: Done submitting .buildinfo files. Fri Aug 20 09:16:38 UTC 2021 I: Removing signed amap-align_2.2+git20080214.600fc29+dfsg-2_armhf.buildinfo.asc files: removed './b1/amap-align_2.2+git20080214.600fc29+dfsg-2_armhf.buildinfo.asc' removed './b2/amap-align_2.2+git20080214.600fc29+dfsg-2_armhf.buildinfo.asc'