Fri Jul 24 01:00:21 UTC 2020 I: starting to build gff2aplot/buster/arm64 on jenkins on '2020-07-24 01:00' Fri Jul 24 01:00:21 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_4/1796/console.log Fri Jul 24 01:00:21 UTC 2020 I: Downloading source for buster/gff2aplot=2.0-11 --2020-07-24 01:00:21-- http://deb.debian.org/debian/pool/main/g/gff2aplot/gff2aplot_2.0-11.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2082 (2.0K) Saving to: ‘gff2aplot_2.0-11.dsc’ 0K .. 100% 13.3M=0s 2020-07-24 01:00:21 (13.3 MB/s) - ‘gff2aplot_2.0-11.dsc’ saved [2082/2082] Fri Jul 24 01:00:21 UTC 2020 I: gff2aplot_2.0-11.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: gff2aplot Binary: gff2aplot Architecture: any Version: 2.0-11 Maintainer: Debian Med Packaging Team Uploaders: Nelson A. de Oliveira , Andreas Tille Homepage: http://genome.imim.es/software/gfftools/GFF2APLOT.html Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/gff2aplot Vcs-Git: https://salsa.debian.org/med-team/gff2aplot.git Testsuite: autopkgtest Testsuite-Triggers: ghostscript, graphicsmagick, imagemagick Build-Depends: debhelper (>= 11~) Package-List: gff2aplot deb science optional arch=any Checksums-Sha1: 469f99901a437f8b539b8b29be9cb0f392d6633b 328439 gff2aplot_2.0.orig.tar.gz bfc6d2fd17774fd1d323cf4b23e7d1f70ddfa873 19852 gff2aplot_2.0-11.debian.tar.xz Checksums-Sha256: 33798a1f2877fc9d64aaf143c2e5bb909021b1f147c6718e61fbcc96cc65ccc3 328439 gff2aplot_2.0.orig.tar.gz a3ed0beb0134981b88997d7f4bafc09f25b7b1075260bb24c8331b1d77edaa84 19852 gff2aplot_2.0-11.debian.tar.xz Files: 8b269e236bcbacb1c70e4a3424940dc6 328439 gff2aplot_2.0.orig.tar.gz a86186908f5484b79c37945c64e86db2 19852 gff2aplot_2.0-11.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlxRo3QRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHTGQ//cLV/iDxHPqeDmsjCioOLLOOQtKTHDGuE IdyDiHhdd5ZBdRh6/9gvFACVLAgP9F3vSaXtFJ4eB+IdAOmweHoKStMxXiOOU7J0 wSzYznYV2LHTYOvJEU6wVsmONUXClUyUjvk1QBdy5eXdmHyz3XWiPWy5g/9/ziDd h3Kp67EfNkcft6hAxxcyRNE1ae3YDF3bUSn1aH2IsItnplSuLPJHVir7Gq1ifS/k LzAQsAnIPRSCgZee+UUlGSy6Dtjy6GPvW3XvKytSndPMN2h7JeAPzandBFiNlm/k WsikvUEhzE1VzaK1jZPPnl8gtMVf+Lna6pcGds1hrOnSNArla8kgNGnlc6Akt0do rv4HMrGbJ3Dw8t8rX19IX2Oj++BuaeARweOx1AWv62m1eoaJ69wW3XOHjAqU1NAj ZH6uDmbwRKnUTPQl+1IeSqttN7W6IT6f3BZ6yb3p02c6W6r4pLexbg4V5Byze0aR h0FG01t3I3WCQNRLn3hdR1LZ5GeS04FPbkL47FX2y0Y4jofcSpurZnmldqAkvIyW E07iMqfVtygfOmsxaGUV9Qpluho5J6iXGdot34RXpd/DAVG1AfWUi+EkSe2OxGle ylbwUfxfdG7jw+lthZIvhkTsYYskFerjeAv3l19eMC8v34HagVzOucEAD071CbRU w/XGucEGpd0= =iwLa -----END PGP SIGNATURE----- Fri Jul 24 01:00:21 UTC 2020 I: Checking whether the package is not for us Fri Jul 24 01:00:21 UTC 2020 I: Starting 1st build on remote node codethink-sled9-arm64.debian.net. Fri Jul 24 01:00:21 UTC 2020 I: Preparing to do remote build '1' on codethink-sled9-arm64.debian.net. Fri Jul 24 01:01:29 UTC 2020 I: Deleting $TMPDIR on codethink-sled9-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Aug 25 19:23:32 -12 2021 I: pbuilder-time-stamp: 1629962612 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-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 [gff2aplot_2.0-11.dsc] I: copying [./gff2aplot_2.0.orig.tar.gz] I: copying [./gff2aplot_2.0-11.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Jan 30 01:15:32 2019 -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 ./gff2aplot_2.0-11.dsc dpkg-source: info: extracting gff2aplot in gff2aplot-2.0 dpkg-source: info: unpacking gff2aplot_2.0.orig.tar.gz dpkg-source: info: unpacking gff2aplot_2.0-11.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying non_lexical_loop_iterator.patch dpkg-source: info: applying 02-blat2gff.diff dpkg-source: info: applying 03-parseblast.diff dpkg-source: info: applying use-dpkg-buildflags.patch dpkg-source: info: applying mayhem.patch dpkg-source: info: applying fis-privacy-breach.patch dpkg-source: info: applying perl_5.28.patch dpkg-source: info: applying fix_install_ali2gff.patch dpkg-source: info: applying enhance_sprintf_buffer.patch dpkg-source: info: applying fix_README_used_for_test.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4301/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='4301' 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.X36LghkSxJ/pbuilderrc_6wBj --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.X36LghkSxJ/b1 --logfile b1/build.log gff2aplot_2.0-11.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink-sled9-arm64 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 24 02:48 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/4301/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: arm64 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 (>= 11~) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19168 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 (>= 11~); however: Package debhelper 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} bsdmainutils{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} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{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 libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 18.6 MB of archives. After unpacking 69.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Fetched 18.6 MB in 1s (21.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_arm64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_arm64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../11-libsigsegv2_2.12-2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_arm64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. 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Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/gff2aplot-2.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package gff2aplot dpkg-buildpackage: info: source version 2.0-11 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/gff2aplot-2.0' rm -f src/ali2gff/ali2gff bin/ali2gff make[1]: Leaving directory '/build/gff2aplot-2.0' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j8 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/gff2aplot-2.0' ### ### RUNNING MAKEFILE ### ### Wed Aug 25 19:24:11 -12 2021 -- pbuilder1 ### ### Finishing PERL script from "src/gff2aplot.pl" -> "bin/gff2aplot.pl" ### Finishing PERL script from "src/parseblast.pl" -> "bin/parseblast.pl" ### Finishing PERL script from "src/blat2gff.pl" -> "bin/blat2gff.pl" ### Finishing PERL script from "src/sim2gff.pl" -> "bin/sim2gff.pl" ### Making ALI2GFF... ### make[2]: Entering directory '/build/gff2aplot-2.0/src/ali2gff' ### MAKEFILE DONE... ### ali2gff.c: In function 'main': ali2gff.c:88:8: warning: variable 'ptr' set but not used [-Wunused-but-set-variable] char *ptr; ^~~ ali2gff.c: In function 'processMumfile': ali2gff.c:527:51: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] if (DEBUG) fprintf(stderr,"gap data: length %d-20=%d\n%s\n%s\n%s\n",strlen(seq1),strlen(seq1)-20,seq1,seq2,err); ~^ ~~~~~~~~~~~~ %ld ali2gff.c:527:57: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] if (DEBUG) fprintf(stderr,"gap data: length %d-20=%d\n%s\n%s\n%s\n",strlen(seq1),strlen(seq1)-20,seq1,seq2,err); ~^ ~~~~~~~~~~~~~~~ %ld ali2gff.c:768:51: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] if (DEBUG) fprintf(stderr,"gap data: length %d-20=%d\n%s\n%s\n%s\n",strlen(seq1),strlen(seq1)-20,seq1,seq2,err); ~^ ~~~~~~~~~~~~ %ld ali2gff.c:768:57: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] if (DEBUG) fprintf(stderr,"gap data: length %d-20=%d\n%s\n%s\n%s\n",strlen(seq1),strlen(seq1)-20,seq1,seq2,err); ~^ ~~~~~~~~~~~~~~~ %ld ali2gff.c: In function 'processGFFfile': ali2gff.c:355:71: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] else sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%s\t%s\t%s\n", xName,yName,source,xb,yb,xe,ye,scores,strands,frames); ^~ ~~~~~ In file included from /usr/include/stdio.h:873, from ali2gff.h:20, from ali2gff.c:64: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 25 and 5103 bytes into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:354:71: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] if (sscanf(scores,"%f",&score) == 1) sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%s\t%s\n",xName,yName,source,xb,yb,xe,ye,score ,strands,frames); ^~ ~~~~~ In file included from /usr/include/stdio.h:873, from ali2gff.h:20, from ali2gff.c:64: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 30 and 3418 bytes into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:351:71: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] else sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%s\t%s\t%s\t%s", xName,yName,source,xb,yb,xe,ye,scores,strands,frames,cptr); ^~ ~~~~~ In file included from /usr/include/stdio.h:873, from ali2gff.h:20, from ali2gff.c:64: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 25 or more bytes (assuming 5027) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:350:71: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] if (sscanf(scores,"%f",&score) == 1) sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%s\t%s\t%s",xName,yName,source,xb,yb,xe,ye,score ,strands,frames,cptr); ^~ ~~~~~ In file included from /usr/include/stdio.h:873, from ali2gff.h:20, from ali2gff.c:64: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 30 or more bytes (assuming 3033) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:300:71: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] else sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%s\t%s\t%s\n", yName,xName,source,yb,xb,ye,xe,scores,strands,frames); ^~ ~~~~~ In file included from /usr/include/stdio.h:873, from ali2gff.h:20, from ali2gff.c:64: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 25 and 5103 bytes into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:299:71: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] if (sscanf(scores,"%f",&score) == 1) sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%s\t%s\n",yName,xName,source,yb,xb,ye,xe,score,strands,frames); ^~ ~~~~~ In file included from /usr/include/stdio.h:873, from ali2gff.h:20, from ali2gff.c:64: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 30 and 3418 bytes into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:296:71: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] else sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%s\t%s\t%s\t%s", yName,xName,source,yb,xb,ye,xe,scores,strands,frames,cptr); ^~ ~~~~~ In file included from /usr/include/stdio.h:873, from ali2gff.h:20, from ali2gff.c:64: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 25 or more bytes (assuming 5027) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:295:71: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] if (sscanf(scores,"%f",&score) == 1) sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%s\t%s\t%s",yName,xName,source,yb,xb,ye,xe,score,strands,frames,cptr); ^~ ~~~~~ In file included from /usr/include/stdio.h:873, from ali2gff.h:20, from ali2gff.c:64: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 30 or more bytes (assuming 3033) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c: In function 'processMumfile': ali2gff.c:421:30: warning: 'fyb' may be used uninitialized in this function [-Wmaybe-uninitialized] unsigned long int fxb, fxe, fyb, fye; // start and end positions of gaps resp. fragments of gaps ^~~ ali2gff.c:732:12: warning: 'score' may be used uninitialized in this function [-Wmaybe-uninitialized] score = (score - errCount)/score; // match percentage ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:421:20: warning: 'fxb' may be used uninitialized in this function [-Wmaybe-uninitialized] unsigned long int fxb, fxe, fyb, fye; // start and end positions of gaps resp. fragments of gaps ^~~ ali2gff.c: In function 'processSimfile': ali2gff.c:1073:15: warning: 'yrev' may be used uninitialized in this function [-Wmaybe-uninitialized] ye = yrev-ye; ~~~~^~~ ali2gff.c:1064:41: warning: 'yseqLen_4' may be used uninitialized in this function [-Wmaybe-uninitialized] if (!opt_i || ((xe - xb < xseqLen_4) && (ye - yb < yseqLen_4))) { ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:1064:15: warning: 'xseqLen_4' may be used uninitialized in this function [-Wmaybe-uninitialized] if (!opt_i || ((xe - xb < xseqLen_4) && (ye - yb < yseqLen_4))) { ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/build/gff2aplot-2.0/src/ali2gff' mkdir -p ./bin cp ./src/ali2gff/ali2gff \ ./bin/ali2gff mode of 'bin/gff2aplot.pl' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x) mode of 'bin/parseblast.pl' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x) mode of 'bin/blat2gff.pl' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x) mode of 'bin/sim2gff.pl' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x) make[1]: Leaving directory '/build/gff2aplot-2.0' dh_auto_test make -j8 test make[1]: Entering directory '/build/gff2aplot-2.0' ### SORRY !!! Tests were not implemented yet... make[1]: Leaving directory '/build/gff2aplot-2.0' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/build/gff2aplot-2.0' for script in `find bin -name "*.pl"` ; do mv $script bin/`basename $script .pl` ; done make[1]: Leaving directory '/build/gff2aplot-2.0' dh_install dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/gff2aplot-2.0' dh_installexamples # Fix path names, silence GS find debian/*/usr/share/doc/*/examples -name README -exec sed -i \ -e 's?^$BIN/\([0-9a-z]\+\)\.pl?\1?' \ -e 's?^$BIN/\([0-9a-z]\+\) ?\1 ?' \ -e 's?^GS=.*;?GS="gs -q" ;?' \{\} \; make[1]: Leaving directory '/build/gff2aplot-2.0' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'gff2aplot' in '../gff2aplot_2.0-11_arm64.deb'. dpkg-deb: building package 'gff2aplot-dbgsym' in '../gff2aplot-dbgsym_2.0-11_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../gff2aplot_2.0-11_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/4301 and its subdirectories I: Current time: Wed Aug 25 19:24:26 -12 2021 I: pbuilder-time-stamp: 1629962666 Fri Jul 24 01:01:30 UTC 2020 I: 1st build successful. Starting 2nd build on remote node codethink-sled16-arm64.debian.net. Fri Jul 24 01:01:30 UTC 2020 I: Preparing to do remote build '2' on codethink-sled16-arm64.debian.net. Fri Jul 24 01:02:09 UTC 2020 I: Deleting $TMPDIR on codethink-sled16-arm64.debian.net. Fri Jul 24 01:02:10 UTC 2020 I: gff2aplot_2.0-11_arm64.changes: Format: 1.8 Date: Wed, 30 Jan 2019 14:12:34 +0100 Source: gff2aplot Binary: gff2aplot gff2aplot-dbgsym Architecture: arm64 Version: 2.0-11 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: gff2aplot - pair-wise alignment-plots for genomic sequences in PostScript Closes: 890789 909714 Changes: gff2aplot (2.0-11) unstable; urgency=medium . * README files in examples are actually scripts - fix PATH to gff2aplot * Add autopkgtest Closes: #890789, #909714 * Fix issue with Perl 5.28 * Fix definition of CP in upstream makefile * Try hard to make sprint buffers have proper size * Recommends: graphicsmagick | imagemagick, ghostscript (+ Test-Depends) * Fix README used as shell script for testing * hardening=+all Checksums-Sha1: 516b2ecab58a3f339f2a0564dce67a6e1e18e10c 25640 gff2aplot-dbgsym_2.0-11_arm64.deb 93223c78e628746e9b626609d393590f174009e2 4550 gff2aplot_2.0-11_arm64.buildinfo d85f89749cdb42da2ad4ac06ee5eb364453ee287 313624 gff2aplot_2.0-11_arm64.deb Checksums-Sha256: b17b45cfb68dede7760f78d0f690157848b4d94b9448692713a52118b90fa2ef 25640 gff2aplot-dbgsym_2.0-11_arm64.deb b8cd992f87cd1012231facf50f28207344363460e9e6511836455fa4e4755192 4550 gff2aplot_2.0-11_arm64.buildinfo ae334911a4c6fa5a639e58298cda066fa0c1067a22269707f794c9d7a354f22a 313624 gff2aplot_2.0-11_arm64.deb Files: 00cdf3cbcda980e8879559dacf26572e 25640 debug optional gff2aplot-dbgsym_2.0-11_arm64.deb 94d62322c602eacb75bd5f6bd9faca84 4550 science optional gff2aplot_2.0-11_arm64.buildinfo e52a5cff29b6a9ab3e21b3c5103daeb8 313624 science optional gff2aplot_2.0-11_arm64.deb Fri Jul 24 01:02:11 UTC 2020 I: diffoscope 152 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.X36LghkSxJ/gff2aplot_2.0-11.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.X36LghkSxJ/gff2aplot_2.0-11.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.X36LghkSxJ/gff2aplot_2.0-11.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.X36LghkSxJ/b1/gff2aplot_2.0-11_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.X36LghkSxJ/b2/gff2aplot_2.0-11_arm64.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: 0.284s) 0.284s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.030s) 0.030s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Fri Jul 24 01:02:21 UTC 2020 I: diffoscope 152 found no differences in the changes files, and a .buildinfo file also exists. Fri Jul 24 01:02:21 UTC 2020 I: gff2aplot from buster built successfully and reproducibly on arm64. Fri Jul 24 01:02:25 UTC 2020 I: Submitting .buildinfo files to external archives: Fri Jul 24 01:02:25 UTC 2020 I: Submitting 8.0K b1/gff2aplot_2.0-11_arm64.buildinfo.asc Fri Jul 24 01:02:27 UTC 2020 I: Submitting 8.0K b2/gff2aplot_2.0-11_arm64.buildinfo.asc Fri Jul 24 01:02:28 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Jul 24 01:02:28 UTC 2020 I: Done submitting .buildinfo files. Fri Jul 24 01:02:28 UTC 2020 I: Removing signed gff2aplot_2.0-11_arm64.buildinfo.asc files: removed './b1/gff2aplot_2.0-11_arm64.buildinfo.asc' removed './b2/gff2aplot_2.0-11_arm64.buildinfo.asc'