Mon Jun 29 05:31:40 UTC 2020 I: starting to build genometester/buster/armhf on jenkins on '2020-06-29 05:31' Mon Jun 29 05:31:40 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_52/5148/console.log Mon Jun 29 05:31:40 UTC 2020 I: Downloading source for buster/genometester=4.0+git20180508.a9c14a6+dfsg-1 --2020-06-29 05:31:41-- http://deb.debian.org/debian/pool/main/g/genometester/genometester_4.0+git20180508.a9c14a6+dfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2215 (2.2K) Saving to: ‘genometester_4.0+git20180508.a9c14a6+dfsg-1.dsc’ 0K .. 100% 127M=0s 2020-06-29 05:31:41 (127 MB/s) - ‘genometester_4.0+git20180508.a9c14a6+dfsg-1.dsc’ saved [2215/2215] Mon Jun 29 05:31:41 UTC 2020 I: genometester_4.0+git20180508.a9c14a6+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: genometester Binary: genometester Architecture: any Version: 4.0+git20180508.a9c14a6+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Liubov Chuprikova , Andreas Tille Homepage: https://github.com/bioinfo-ut/GenomeTester4 Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/genometester Vcs-Git: https://salsa.debian.org/med-team/genometester.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~) Package-List: genometester deb science optional arch=any Checksums-Sha1: e970ffcbcf431f5864898b39e5436c95a9abc009 87828 genometester_4.0+git20180508.a9c14a6+dfsg.orig.tar.xz 040d5dcef056d6fb37849b1ddeeadf904893614e 232440 genometester_4.0+git20180508.a9c14a6+dfsg-1.debian.tar.xz Checksums-Sha256: 4faf9b253028119c7e59745f179ea295562809124844e54ca722dc62cc283a85 87828 genometester_4.0+git20180508.a9c14a6+dfsg.orig.tar.xz e04baa915a0751bd8f2ff3a1244aaaa229b9bd3b118b3d7f58342d9b92a54122 232440 genometester_4.0+git20180508.a9c14a6+dfsg-1.debian.tar.xz Files: d2808f4ad0af8ea5adc955717939e699 87828 genometester_4.0+git20180508.a9c14a6+dfsg.orig.tar.xz 583c23164de14abfeb3a7a8283e8adea 232440 genometester_4.0+git20180508.a9c14a6+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlu4jWkRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtF13Q/+Piuw2e+5XHAloFdPqz37cKGOkMlNfDrL ua1kEvxdVjR0amkBFJIbEgGhIUG1WCxOeFAwMZVBg+aFXCdgzpX1/mLfooK8oi6i /FuyGv5893I7dzsZ9lmWOP9TGH8aLcVbdw+GdOX6KHg41TJNTM8qxVDKgQLq5duC Oj6x+nccRmg2JpEHzBUj0/L2qu22FDM2My1PdUzpLgVCkOdSlDMLjPQsKdxI+uT/ vMmH01w3ZJvvR+wQMnZT1Hke4SXnjpvBp8r4pCNNtIJ5RC4mV6LQIdVANwFTQnEw FWmJVMtqaOEgxhPlqvNbQmpNGYbP71R0qZuPZTBwM0jCcxwmqEyYmACl4/qS6pMb ENyED5oK4oE9FoaNODCGVA8ryErK3A146RttGFMUPDLvyyOgGn8B0NlcDIp/9uxP A6QHwK4aZ+BOjzN8LURo0JlT6U/UhYmCYVFJHtuG62korQdPhvhxp/dcICjq897W JkZUveqCWwPo2ugBBpSETDYjJjyzknKeBtQUJspqNW0K8qI6eZfhywpTVY6JIrzF cxJnTefUoCRH2QXT+xNX4eIUS04AAlqEo5lnSJnJ1olcaYjRS8eINZh9EBf8sNmL pYFMVD5xS6Qhc8Obz0vZnBqCXXt+D9kq9coKukb2EfRgdm5fXEMrfYT5MpMjsbew coCQm0x/dNs= =/vj9 -----END PGP SIGNATURE----- Mon Jun 29 05:31:41 UTC 2020 I: Checking whether the package is not for us Mon Jun 29 05:31:41 UTC 2020 I: Starting 1st build on remote node jtx1c-armhf-rb.debian.net. Mon Jun 29 05:31:41 UTC 2020 I: Preparing to do remote build '1' on jtx1c-armhf-rb.debian.net. Mon Jun 29 05:33:33 UTC 2020 I: Deleting $TMPDIR on jtx1c-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 28 17:31:56 -12 2020 I: pbuilder-time-stamp: 1593408716 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 [genometester_4.0+git20180508.a9c14a6+dfsg-1.dsc] I: copying [./genometester_4.0+git20180508.a9c14a6+dfsg.orig.tar.xz] I: copying [./genometester_4.0+git20180508.a9c14a6+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Oct 5 22:24:41 2018 -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 ./genometester_4.0+git20180508.a9c14a6+dfsg-1.dsc dpkg-source: info: extracting genometester in genometester-4.0+git20180508.a9c14a6+dfsg dpkg-source: info: unpacking genometester_4.0+git20180508.a9c14a6+dfsg.orig.tar.xz dpkg-source: info: unpacking genometester_4.0+git20180508.a9c14a6+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add_debug_symbols.patch dpkg-source: info: applying hardening.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/30546/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 parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='04ed6d26e7ba44c1baee1ec43f4cbb0d' 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='30546' 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.8NkTIAwd6t/pbuilderrc_1nSs --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.8NkTIAwd6t/b1 --logfile b1/build.log genometester_4.0+git20180508.a9c14a6+dfsg-1.dsc' SUDO_GID='111' 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 jtx1c 4.19.0-9-arm64 #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) aarch64 GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 26052 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 26052 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 9636 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 22432 Feb 28 2019 cat -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash -rwxr-xr-x 1 root root 71648 Feb 28 2019 date -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd -rwxr-xr-x 1 root root 55672 Feb 28 2019 df -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir -rwxr-xr-x 1 root root 54872 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 22364 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 18260 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 124508 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 64232 Jan 5 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln -rwxr-xr-x 1 root root 34932 Jul 26 2018 login -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 9 2019 more -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 84284 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 22416 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jun 26 20:25 sh -> dash -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty -rwsr-xr-x 1 root root 42472 Jan 9 2019 su -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch -rwxr-xr-x 1 root root 18260 Feb 28 2019 true -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir -rwxr-xr-x 1 root root 21980 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/30546/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 (>= 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 ... 18932 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 18.2 MB of archives. After unpacking 63.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 10 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 11 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 12 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 13 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 14 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 24 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 25 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 30 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 31 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Fetched 18.2 MB in 4s (4164 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (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 ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_armhf.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_armhf.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic1:armhf (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_armhf.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_armhf.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../11-libsigsegv2_2.12-2_armhf.deb ... Unpacking libsigsegv2:armhf (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_armhf.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. Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. 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Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:armhf (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libmagic1:armhf (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:armhf (63.1-6+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up libbsd0:armhf (0.9.1-2) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+b3) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up m4 (1.4.18-2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:armhf (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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 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/genometester-4.0+git20180508.a9c14a6+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package genometester dpkg-buildpackage: info: source version 4.0+git20180508.a9c14a6+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j3 clean make[1]: Entering directory '/build/genometester-4.0+git20180508.a9c14a6+dfsg/src' rm -f *.o glistmaker glistquery glistcompare make[1]: Leaving directory '/build/genometester-4.0+git20180508.a9c14a6+dfsg/src' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules build dh build --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src debian/rules override_dh_auto_build make[1]: Entering directory '/build/genometester-4.0+git20180508.a9c14a6+dfsg' dh_auto_build cd src && make -j3 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/genometester-4.0+git20180508.a9c14a6+dfsg/src' gcc glistmaker.c common.c common.h fasta.c fasta.h wordtable.c wordtable.h wordmap.c wordmap.h buffer.c buffer.h sequence.c sequence.h sequence-file.c sequence-file.h queue.c queue.h utils.c utils.h -o glistmaker -lm -lpthread -lrt -g -O2 -ffile-prefix-map=/build/genometester-4.0+git20180508.a9c14a6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -O3 -g -Wall -Wl,-z,relro -Wl,-z,now gcc glistquery.c wordtable.c wordtable.h wordmap.c wordmap.h fasta.c fasta.h buffer.c buffer.h sequence.c sequence.h sequence-file.c sequence-file.h common.c common.h queue.c queue.h utils.c utils.h -o glistquery -lm -lpthread -lrt -g -O2 -ffile-prefix-map=/build/genometester-4.0+git20180508.a9c14a6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -O3 -g -Wall -Wl,-z,relro -Wl,-z,now gcc glistcompare.c wordtable.c wordmap.c fasta.c buffer.c sequence.c sequence-file.c sequence-file.h common.c queue.c queue.h utils.c -o glistcompare -lm -lpthread -lrt -g -O2 -ffile-prefix-map=/build/genometester-4.0+git20180508.a9c14a6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -O3 -g -Wall -Wl,-z,relro -Wl,-z,now glistquery.c: In function ‘main’: glistquery.c:277:95: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] fprintf (stderr, "Error: Incompatible wordlengths! Wordlength in list: %u, query length: %lu\n", p.wordlength, strlen (querystring)); ~~^ ~~~~~~~~~~~~~~~~~~~~ %u glistquery.c: In function ‘search_n_query_strings’: glistquery.c:339:96: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] fprintf (stderr, "Error: Incompatible wordlengths! Wordlength in list: %u, query length: %lu\n", p->wordlength, strlen (querystring)); ~~^ ~~~~~~~~~~~~~~~~~~~~ %u glistmaker.c: In function ‘process’: glistmaker.c:380:5: warning: ‘t[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] wordtable_build_filename (t[0], c, 1024, outputname); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ queue.c: In function ‘scout_map’: queue.c:251:10: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] return (void *) val; ^ queue.c: In function ‘scout_map’: queue.c:251:10: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] return (void *) val; ^ queue.c: In function ‘scout_map’: queue.c:251:10: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] return (void *) val; ^ make[2]: Leaving directory '/build/genometester-4.0+git20180508.a9c14a6+dfsg/src' dh_auto_build -- gmer_counter cd src && make -j3 "INSTALL=install --strip-program=true" gmer_counter make[2]: Entering directory '/build/genometester-4.0+git20180508.a9c14a6+dfsg/src' gcc gmer_counter.c index.c index.h trie.c trie.h wordmap.c wordmap.h sequence.c sequence.h sequence-file.c sequence-file.h wordtable.c wordtable.h fasta.c fasta.h thread-pool.c thread-pool.h queue.c queue.h utils.c utils.h database.c database.h -o gmer_counter -lm -lpthread -lrt -g -O2 -ffile-prefix-map=/build/genometester-4.0+git20180508.a9c14a6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -O3 -g -Wall -Wl,-z,relro -Wl,-z,now -Wall thread-pool.c: In function ‘aosora_thread_pool_delete’: thread-pool.c:88:90: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] fprintf (stderr, "aosora_thread_pool_delete: Thread %d exited with result %llu\n", i, (unsigned long long) res); ^ queue.c: In function ‘scout_map’: queue.c:251:10: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] return (void *) val; ^ make[2]: Leaving directory '/build/genometester-4.0+git20180508.a9c14a6+dfsg/src' dh_auto_build -- gmer_caller cd src && make -j3 "INSTALL=install --strip-program=true" gmer_caller make[2]: Entering directory '/build/genometester-4.0+git20180508.a9c14a6+dfsg/src' gcc binomial.c binomial.h genotypes.c genotypes.h simplex.c simplex.h thread-pool.c thread-pool.h utils.c utils.h gmer_caller.c -o gmer_caller -lm -lpthread -lrt -g -O2 -ffile-prefix-map=/build/genometester-4.0+git20180508.a9c14a6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -O3 -g -Wall -Wl,-z,relro -Wl,-z,now -Wall thread-pool.c: In function ‘aosora_thread_pool_delete’: thread-pool.c:88:90: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] fprintf (stderr, "aosora_thread_pool_delete: Thread %d exited with result %llu\n", i, (unsigned long long) res); ^ gmer_caller.c: In function ‘main’: gmer_caller.c:495:16: warning: variable ‘coverage_specified’ set but not used [-Wunused-but-set-variable] unsigned int coverage_specified = 0; ^~~~~~~~~~~~~~~~~~ At top level: gmer_caller.c:903:1: warning: ‘logL2’ defined but not used [-Wunused-function] logL2 (const float arg[], unsigned int count, unsigned int tulem2[], unsigned int katvus2[]) ^~~~~ gmer_caller.c: In function ‘parse_calls’: gmer_caller.c:168:24: warning: ‘best_b’ may be used uninitialized in this function [-Wmaybe-uninitialized] calls[i].counts[1] = best_b; ~~~~~~~~~~~~~~~~~~~^~~~~~~~ gmer_caller.c:167:24: warning: ‘best_a’ may be used uninitialized in this function [-Wmaybe-uninitialized] calls[i].counts[0] = best_a; ~~~~~~~~~~~~~~~~~~~^~~~~~~~ gmer_caller.c: In function ‘main’: gmer_caller.c:785:9: warning: ‘calls_x’ may be used uninitialized in this function [-Wmaybe-uninitialized] print_genotypes (lines, calls_x, nx, params, pB, (non_canonical) ? 0 : 2, prob_cutoff, alternatives, nthreads); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/build/genometester-4.0+git20180508.a9c14a6+dfsg/src' dh_auto_build -- gdistribution cd src && make -j3 "INSTALL=install --strip-program=true" gdistribution make[2]: Entering directory '/build/genometester-4.0+git20180508.a9c14a6+dfsg/src' gcc gdistribution.c wordtable.c wordmap.c fasta.c buffer.c sequence.c sequence-file.c sequence-file.h common.c queue.c queue.h utils.c -o gdistribution -lm -lpthread -lrt -g -O2 -ffile-prefix-map=/build/genometester-4.0+git20180508.a9c14a6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -O3 -g -Wall -Wl,-z,relro -Wl,-z,now gdistribution.c: In function ‘main’: gdistribution.c:55:9: warning: unused variable ‘freqs’ [-Wunused-variable] Freq *freqs; ^~~~~ queue.c: In function ‘scout_map’: queue.c:251:10: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] return (void *) val; ^ make[2]: Leaving directory '/build/genometester-4.0+git20180508.a9c14a6+dfsg/src' make[1]: Leaving directory '/build/genometester-4.0+git20180508.a9c14a6+dfsg' dh_auto_test -O--sourcedirectory=src create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --sourcedirectory=src dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_auto_install -O--sourcedirectory=src dh_install -O--sourcedirectory=src dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src dh_installman -O--sourcedirectory=src dh_installinit -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_strip -O--sourcedirectory=src dh_makeshlibs -O--sourcedirectory=src dh_shlibdeps -O--sourcedirectory=src dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'genometester-dbgsym' in '../genometester-dbgsym_4.0+git20180508.a9c14a6+dfsg-1_armhf.deb'. dpkg-deb: building package 'genometester' in '../genometester_4.0+git20180508.a9c14a6+dfsg-1_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../genometester_4.0+git20180508.a9c14a6+dfsg-1_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) 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/30546 and its subdirectories I: Current time: Sun Jun 28 17:33:28 -12 2020 I: pbuilder-time-stamp: 1593408808 Mon Jun 29 05:33:36 UTC 2020 I: 1st build successful. Starting 2nd build on remote node odu3a-armhf-rb.debian.net. Mon Jun 29 05:33:36 UTC 2020 I: Preparing to do remote build '2' on odu3a-armhf-rb.debian.net. Mon Jun 29 05:37:07 UTC 2020 I: Deleting $TMPDIR on odu3a-armhf-rb.debian.net. Mon Jun 29 05:37:10 UTC 2020 I: genometester_4.0+git20180508.a9c14a6+dfsg-1_armhf.changes: Format: 1.8 Date: Sat, 06 Oct 2018 12:04:26 +0200 Source: genometester Binary: genometester genometester-dbgsym Architecture: armhf Version: 4.0+git20180508.a9c14a6+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: genometester - toolkit for performing set operations on k-mer lists Changes: genometester (4.0+git20180508.a9c14a6+dfsg-1) unstable; urgency=medium . * Remove binaries from upstream source * Use git mode in watch file since gdistribution is needed by some dependencies * Standards-Version: 4.2.1 * Install gdistribution Checksums-Sha1: 7a72fd58cab850df21634754b347f3a058898a56 312324 genometester-dbgsym_4.0+git20180508.a9c14a6+dfsg-1_armhf.deb f69cb4c857b24a69ca3ce6a74a2158cea7507e5d 4706 genometester_4.0+git20180508.a9c14a6+dfsg-1_armhf.buildinfo 4f87d4727211e73279cf7988f940198cc81894b2 297004 genometester_4.0+git20180508.a9c14a6+dfsg-1_armhf.deb Checksums-Sha256: 79d368de5481e2584bf4c741ea8548b7e39a98d86d44d1bd634ccfb7e03662eb 312324 genometester-dbgsym_4.0+git20180508.a9c14a6+dfsg-1_armhf.deb 9b0e4d6775a8f505f56c7992d448a9b3095ecf7f58fdbea0375704a167e94b4f 4706 genometester_4.0+git20180508.a9c14a6+dfsg-1_armhf.buildinfo 0b2fa8de6492b01eb3ee3a8b9d286883bc4c0699c586702b6dbb149539a77a2a 297004 genometester_4.0+git20180508.a9c14a6+dfsg-1_armhf.deb Files: 983530072b2318c383f120eeca839551 312324 debug optional genometester-dbgsym_4.0+git20180508.a9c14a6+dfsg-1_armhf.deb d32d6bb64b875a54d3fbc77e7bc73d56 4706 science optional genometester_4.0+git20180508.a9c14a6+dfsg-1_armhf.buildinfo 0c42651baa7499f0265f3ee5102e8b26 297004 science optional genometester_4.0+git20180508.a9c14a6+dfsg-1_armhf.deb Mon Jun 29 05:37:11 UTC 2020 I: diffoscope 149 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.8NkTIAwd6t/genometester_4.0+git20180508.a9c14a6+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.8NkTIAwd6t/genometester_4.0+git20180508.a9c14a6+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.8NkTIAwd6t/genometester_4.0+git20180508.a9c14a6+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.8NkTIAwd6t/b1/genometester_4.0+git20180508.a9c14a6+dfsg-1_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.8NkTIAwd6t/b2/genometester_4.0+git20180508.a9c14a6+dfsg-1_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: 0.264s) 0.264s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.028s) 0.028s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Mon Jun 29 05:37:13 UTC 2020 I: diffoscope 149 found no differences in the changes files, and a .buildinfo file also exists. Mon Jun 29 05:37:13 UTC 2020 I: genometester from buster built successfully and reproducibly on armhf. Mon Jun 29 05:37:14 UTC 2020 I: Submitting .buildinfo files to external archives: Mon Jun 29 05:37:14 UTC 2020 I: Submitting 8.0K b1/genometester_4.0+git20180508.a9c14a6+dfsg-1_armhf.buildinfo.asc Mon Jun 29 05:37:15 UTC 2020 I: Submitting 8.0K b2/genometester_4.0+git20180508.a9c14a6+dfsg-1_armhf.buildinfo.asc Mon Jun 29 05:37:16 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jun 29 05:37:16 UTC 2020 I: Done submitting .buildinfo files. Mon Jun 29 05:37:16 UTC 2020 I: Removing signed genometester_4.0+git20180508.a9c14a6+dfsg-1_armhf.buildinfo.asc files: removed './b1/genometester_4.0+git20180508.a9c14a6+dfsg-1_armhf.buildinfo.asc' removed './b2/genometester_4.0+git20180508.a9c14a6+dfsg-1_armhf.buildinfo.asc'