Diff of the two buildlogs: -- --- b1/build.log 2020-08-10 19:03:32.244645296 +0000 +++ b2/build.log 2020-08-10 19:15:27.878497742 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Aug 10 07:00:49 -12 2020 -I: pbuilder-time-stamp: 1597086049 +I: Current time: Mon Sep 13 15:26:46 +14 2021 +I: pbuilder-time-stamp: 1631496406 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ 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 Dec 12 19:20:19 2018 -12 +gpgv: Signature made Thu Dec 13 21:20:19 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -34,136 +34,170 @@ dpkg-source: info: applying use_debian_packaged_smithwaterman.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/20585/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/18645/tmp/hooks/D01_modify_environment starting +debug: Running on codethink-sled13-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/18645/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/18645/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' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + 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='20585' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=18645 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.wwpfBf2moF/pbuilderrc_P6la --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.wwpfBf2moF/b1 --logfile b1/build.log tvc_5.0.3+git20151221.80e144e+dfsg-2.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' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.wwpfBf2moF/pbuilderrc_s8Eo --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.wwpfBf2moF/b2 --logfile b2/build.log tvc_5.0.3+git20151221.80e144e+dfsg-2.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink-sled14-arm64 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux + Linux i-capture-the-hostname 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 07:38 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 8 20:27 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 07:38 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/20585/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1216928 Apr 18 2019 bash + -rwxr-xr-x 3 root root 34808 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 34808 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 34808 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14264 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 35576 Mar 1 2019 cat + -rwxr-xr-x 1 root root 60256 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 56096 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 64368 Mar 1 2019 chown + -rwxr-xr-x 1 root root 134632 Mar 1 2019 cp + -rwxr-xr-x 1 root root 129536 Jan 18 2019 dash + -rwxr-xr-x 1 root root 97136 Mar 1 2019 date + -rwxr-xr-x 1 root root 76736 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93752 Mar 1 2019 df + -rwxr-xr-x 1 root root 138848 Mar 1 2019 dir + -rwxr-xr-x 1 root root 75984 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 31368 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 27256 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68792 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34824 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 174304 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 89656 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 18440 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 64472 Mar 1 2019 ln + -rwxr-xr-x 1 root root 52544 Jul 27 2018 login + -rwxr-xr-x 1 root root 138848 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108552 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 76840 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 64480 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 39736 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 38840 Jan 10 2019 more + -rwsr-xr-x 1 root root 47112 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14344 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138736 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 35560 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 43712 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68440 Mar 1 2019 rm + -rwxr-xr-x 1 root root 39624 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 19144 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Sep 13 15:27 sh -> bash + lrwxrwxrwx 1 root root 4 Sep 12 04:48 sh.distrib -> dash + -rwxr-xr-x 1 root root 31384 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 72480 Mar 1 2019 stty + -rwsr-xr-x 1 root root 59424 Jan 10 2019 su + -rwxr-xr-x 1 root root 31416 Mar 1 2019 sync + -rwxr-xr-x 1 root root 449416 Apr 24 2019 tar + -rwxr-xr-x 1 root root 10560 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 88968 Mar 1 2019 touch + -rwxr-xr-x 1 root root 27256 Mar 1 2019 true + -rwxr-xr-x 1 root root 14264 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 30728 Jan 10 2019 umount + -rwxr-xr-x 1 root root 31384 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138848 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34824 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/18645/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -302,7 +336,7 @@ Get: 89 http://deb.debian.org/debian buster/main arm64 libjsoncpp-dev arm64 1.7.4-3 [85.5 kB] Get: 90 http://deb.debian.org/debian buster/main arm64 libsmithwaterman0 arm64 0.0+git20160702.2610e25-7 [32.9 kB] Get: 91 http://deb.debian.org/debian buster/main arm64 libsmithwaterman-dev arm64 0.0+git20160702.2610e25-7 [37.4 kB] -Fetched 46.1 MB in 3s (15.0 MB/s) +Fetched 46.1 MB in 2s (18.9 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.) @@ -695,7 +729,7 @@ 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/tvc-5.0.3+git20151221.80e144e+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package tvc dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -748,14 +782,14 @@ make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend -make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend -make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' -cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake --color= +make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake --color= +make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend +make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' +cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake --color= Scanning dependencies of target tvcassembly make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build @@ -763,17 +797,17 @@ Scanning dependencies of target tvcutils make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build -[ 3%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o -[ 3%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o -[ 4%] Building CXX object 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TheSilenceOfTheArmadillos(std::ofstream&)': /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:9: warning: 'void arma::set_stream_err1(std::ostream&)' is deprecated [-Wdeprecated-declarations] arma::set_stream_err1(null_ostream); @@ -849,45 +885,43 @@ /usr/include/armadillo_bits/debug.hpp:101:1: note: declared here set_stream_err2(std::ostream& user_stream) ^~~~~~~~~~~~~~~ -[ 26%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o -/usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src/AlleleParser.cpp /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function '_bgzf_check_EOF': /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c:678:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(buf, 1, 28, fp->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 84%] Building CXX object CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o -/usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src/AlleleParser.cpp [ 85%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller/PIDloop.cpp [ 87%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o @@ -979,18 +1013,18 @@ Start 6: tvcutils_validate_bed_call Start 7: tvcutils_unify_vcf_call Start 8: tvcassembly_call -1/8 Test #1: tvc_call ......................................... Passed 0.02 sec -2/8 Test #4: tvcutils_call .................................... Passed 0.01 sec -3/8 Test #5: tvcutils_prepare_hotspots_call ................... Passed 0.01 sec -4/8 Test #6: tvcutils_validate_bed_call ....................... Passed 0.01 sec -5/8 Test #7: tvcutils_unify_vcf_call .......................... Passed 0.01 sec -6/8 Test #8: tvcassembly_call ................................. Passed 0.01 sec -7/8 Test #2: tvc_test_1_thread_sse_off ........................ Passed 1.75 sec -8/8 Test #3: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 1.77 sec +1/8 Test #1: tvc_call ......................................... Passed 0.11 sec +2/8 Test #4: tvcutils_call .................................... Passed 0.08 sec +3/8 Test #5: tvcutils_prepare_hotspots_call ................... Passed 0.07 sec +4/8 Test #6: tvcutils_validate_bed_call ....................... Passed 0.07 sec +5/8 Test #7: tvcutils_unify_vcf_call .......................... Passed 0.05 sec +6/8 Test #8: tvcassembly_call ................................. Passed 0.04 sec +7/8 Test #2: tvc_test_1_thread_sse_off ........................ Passed 2.64 sec +8/8 Test #3: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 2.77 sec 100% tests passed, 0 tests failed out of 8 -Total Test time (real) = 1.77 sec +Total Test time (real) = 2.80 sec make[1]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary @@ -1006,26 +1040,26 @@ make[2]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend -make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color= +make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build -make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvcassembly.dir/build'. make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' +make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build +[ 10%] Built target tvcassembly make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvcutils.dir/build'. make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build -[ 21%] Built target tvcassembly [ 31%] Built target tvcutils make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvc.dir/build'. @@ -1084,8 +1118,8 @@ dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvc was not linked against libblas.so.3 (it uses none of the library's symbols) -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvc was not linked against liblapack.so.3 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvcutils debian/tvc/usr/bin/tvc were not linked against libdisorder.so.0 (they use none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvc was not linked against liblapack.so.3 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums @@ -1098,12 +1132,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/18645/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/18645/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/20585 and its subdirectories -I: Current time: Mon Aug 10 07:03:30 -12 2020 -I: pbuilder-time-stamp: 1597086210 +I: removing directory /srv/workspace/pbuilder/18645 and its subdirectories +I: Current time: Mon Sep 13 15:38:25 +14 2021 +I: pbuilder-time-stamp: 1631497105