Diff of the two buildlogs: -- --- b1/build.log 2021-08-06 05:32:31.206620866 +0000 +++ b2/build.log 2021-08-06 05:40:01.817628080 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Aug 5 17:24:40 -12 2021 -I: pbuilder-time-stamp: 1628227480 +I: Current time: Fri Sep 9 01:55:34 +14 2022 +I: pbuilder-time-stamp: 1662638134 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./beast2-mcmc_2.6.3+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.vGsFVMog/trustedkeys.kbx': General error -gpgv: Signature made Sat Oct 3 06:52:00 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.5zTjZTyo/trustedkeys.kbx': General error +gpgv: Signature made Sun Oct 4 08:52:00 2020 +14 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./beast2-mcmc_2.6.3+dfsg-2.dsc @@ -36,135 +36,169 @@ dpkg-source: info: applying handling_minor_issues_in_tests.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/13987/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/5447/tmp/hooks/D01_modify_environment starting +debug: Running on codethink13-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/5447/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/5447/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]="1" [2]="4" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.1.4(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,-fixfilepath 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='13987' - 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=5447 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.bcxP4TiKmj/pbuilderrc_Ntbj --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.bcxP4TiKmj/b1 --logfile b1/build.log beast2-mcmc_2.6.3+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.bcxP4TiKmj/pbuilderrc_skp6 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.bcxP4TiKmj/b2 --logfile b2/build.log --extrapackages usrmerge beast2-mcmc_2.6.3+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 codethink14-arm64 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 - -rwxr-xr-x 1 root root 1282512 Aug 4 08:25 bash - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat - -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown - -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp - -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash - -rwxr-xr-x 1 root root 101384 Sep 22 2020 date - -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd - -rwxr-xr-x 1 root root 89824 Sep 22 2020 df - -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir - -rwxr-xr-x 1 root root 76152 Jul 28 07:09 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 31512 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 64856 Jul 28 07:09 findmnt - -rwsr-xr-x 1 root root 34824 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 93744 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln - -rwxr-xr-x 1 root root 52720 Feb 7 2020 login - -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls - -rwxr-xr-x 1 root root 161960 Jul 28 07:09 lsblk - -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 51368 Jul 28 07:09 more - -rwsr-xr-x 1 root root 51360 Jul 28 07:09 mount - -rwxr-xr-x 1 root root 14496 Jul 28 07:09 mountpoint - -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash - -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm - -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 3 21:25 sh -> dash - -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty - -rwsr-xr-x 1 root root 67776 Jul 28 07:09 su - -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync - -rwxr-xr-x 1 root root 535768 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch - -rwxr-xr-x 1 root root 31512 Sep 22 2020 true - -rwxr-xr-x 1 root root 14264 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 30880 Jul 28 07:09 umount - -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 59584 Jul 28 07:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/13987/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1282512 Aug 5 2021 bash + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 14264 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 39832 Sep 23 2020 cat + -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown + -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp + -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash + -rwxr-xr-x 1 root root 101384 Sep 23 2020 date + -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd + -rwxr-xr-x 1 root root 89824 Sep 23 2020 df + -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir + -rwxr-xr-x 1 root root 76152 Jul 29 2021 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 35632 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 31512 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 64856 Jul 29 2021 findmnt + -rwsr-xr-x 1 root root 34824 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 93744 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln + -rwxr-xr-x 1 root root 52720 Feb 8 2020 login + -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls + -rwxr-xr-x 1 root root 161960 Jul 29 2021 lsblk + -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 51368 Jul 29 2021 more + -rwsr-xr-x 1 root root 51360 Jul 29 2021 mount + -rwxr-xr-x 1 root root 14496 Jul 29 2021 mountpoint + -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 2021 rbash -> bash + -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm + -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Sep 9 01:55 sh -> bash + lrwxrwxrwx 1 root root 4 Sep 8 05:47 sh.distrib -> dash + -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty + -rwsr-xr-x 1 root root 67776 Jul 29 2021 su + -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync + -rwxr-xr-x 1 root root 535768 Feb 17 2021 tar + -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch + -rwxr-xr-x 1 root root 31512 Sep 23 2020 true + -rwxr-xr-x 1 root root 14264 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 30880 Jul 29 2021 umount + -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 59584 Jul 29 2021 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/5447/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -455,7 +489,7 @@ Get: 229 http://deb.debian.org/debian bullseye/main arm64 texlive-latex-recommended all 2020.20210202-3 [14.5 MB] Get: 230 http://deb.debian.org/debian bullseye/main arm64 texlive-pictures all 2020.20210202-3 [6743 kB] Get: 231 http://deb.debian.org/debian bullseye/main arm64 texlive-latex-extra all 2020.20210202-3 [13.7 MB] -Fetched 426 MB in 35s (12.0 MB/s) +Fetched 426 MB in 33s (13.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19646 files and directories currently installed.) @@ -1589,8 +1623,45 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (3030 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 44350 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/beast2-mcmc-2.6.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../beast2-mcmc_2.6.3+dfsg-2_source.changes +hostname: Temporary failure in name resolution +I: Running cd /build/beast2-mcmc-2.6.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../beast2-mcmc_2.6.3+dfsg-2_source.changes dpkg-buildpackage: info: source package beast2-mcmc dpkg-buildpackage: info: source version 2.6.3+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -1654,37 +1725,37 @@ junit: [mkdir] Created dir: /build/beast2-mcmc-2.6.3+dfsg/build/junitreport [junit] Running test.beast.app.BeautiSubTemplateTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.298 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.695 sec [junit] Running test.beast.app.BeautiTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.766 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.191 sec [junit] Running test.beast.app.tools.LogCombinerTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.253 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.085 sec [junit] Running test.beast.core.BEASTInterfaceTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.703 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.363 sec [junit] Running test.beast.core.InputForAnnotatedConstructorTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.988 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.243 sec [junit] Running test.beast.core.InputTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.52 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.356 sec [junit] Running test.beast.core.LoggerTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.512 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.363 sec [junit] Running test.beast.core.OperatorScheduleTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.502 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.428 sec [junit] Running test.beast.core.StateNodeInitialiserTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.032 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.939 sec [junit] Running test.beast.core.parameter.BooleanParameterListTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.404 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.373 sec [junit] Running test.beast.core.parameter.IntegerParameterListTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.401 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.343 sec [junit] Running test.beast.core.parameter.ParameterTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.377 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.328 sec [junit] Running test.beast.core.parameter.RealParameterListTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.402 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.38 sec [junit] Running test.beast.core.util.SumTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.407 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.336 sec [junit] Running test.beast.evolution.alignment.FilteredAlignmentTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.991 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.845 sec [junit] Running test.beast.evolution.alignment.UncertainAlignmentTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.739 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.666 sec [junit] Running test.beast.evolution.alignment.UnorderedAlignmentsTest [junit] [junit] OpenCL error: CL_DEVICE_NOT_FOUND from file , line 122. @@ -1692,9 +1763,9 @@ [junit] Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0 sec [junit] Test test.beast.evolution.alignment.UnorderedAlignmentsTest FAILED (crashed) [junit] Running test.beast.evolution.datatype.DataTypeDeEncodeTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.361 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.337 sec [junit] Running test.beast.evolution.datatype.IntegerDataTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.353 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.311 sec [junit] Running test.beast.evolution.likelihood.TreeLikelihoodTest [junit] [junit] OpenCL error: CL_DEVICE_NOT_FOUND from file , line 122. @@ -1702,49 +1773,49 @@ [junit] Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0 sec [junit] Test test.beast.evolution.likelihood.TreeLikelihoodTest FAILED (crashed) [junit] Running test.beast.evolution.operator.CompoundParameterHelperTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.349 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.34 sec [junit] Running test.beast.evolution.operator.DeltaExchangeOperatorTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.374 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.351 sec [junit] Running test.beast.evolution.operator.ExchangeOperatorTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 45.304 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 38.85 sec [junit] Running test.beast.evolution.operator.IntRandomWalkOperatorTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 27.032 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 41.088 sec [junit] Running test.beast.evolution.operator.ScaleOperatorTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.517 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.531 sec [junit] Running test.beast.evolution.operator.UniformIntegerOperatorTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.359 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.356 sec [junit] Running test.beast.evolution.operator.WilsonBaldingTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.303 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.232 sec [junit] Running test.beast.evolution.speciation.BirthDeathGernhard08ModelTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.857 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.889 sec [junit] Running test.beast.evolution.speciation.YuleModelTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.538 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.54 sec [junit] Running test.beast.evolution.substmodel.BinaryCovarionModelTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.467 sec [junit] Running test.beast.evolution.substmodel.GTRTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.436 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.389 sec [junit] Running test.beast.evolution.substmodel.GeneralSubstitutionModelTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.34 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.373 sec [junit] Running test.beast.evolution.substmodel.HKYTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.348 sec [junit] Running test.beast.evolution.tree.NodeTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.544 sec [junit] Running test.beast.evolution.tree.RandomTreeTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 27.263 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 27.775 sec [junit] Running test.beast.evolution.tree.TraitSetTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.659 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.674 sec [junit] Running test.beast.evolution.tree.TreeAnnotatorTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.626 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.682 sec [junit] Running test.beast.evolution.tree.TreeTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.487 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.516 sec [junit] Running test.beast.evolution.tree.TreeUtilsTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.481 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.525 sec [junit] Running test.beast.evolution.tree.coalescent.BayesianSkylineTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.492 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.537 sec [junit] Running test.beast.evolution.tree.coalescent.CoalescentTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.895 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.881 sec [junit] Running test.beast.integration.DocumentationTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.642 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.768 sec [junit] Running test.beast.integration.ExampleJSONParsingTest [junit] [junit] OpenCL error: CL_DEVICE_NOT_FOUND from file , line 122. @@ -1758,7 +1829,7 @@ [junit] Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0 sec [junit] Test test.beast.integration.ExampleXmlParsingTest FAILED (crashed) [junit] Running test.beast.integration.InputTypeTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.806 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.809 sec [junit] Running test.beast.integration.ResumeTest [junit] [junit] OpenCL error: CL_DEVICE_NOT_FOUND from file , line 122. @@ -1766,27 +1837,27 @@ [junit] Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0 sec [junit] Test test.beast.integration.ResumeTest FAILED (crashed) [junit] Running test.beast.integration.XMLElementNameTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.626 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.71 sec [junit] Running test.beast.integration.XMLProducerTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.315 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.069 sec [junit] Running test.beast.math.distributions.GammaTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.274 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.138 sec [junit] Running test.beast.math.distributions.InvGammaTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.338 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.35 sec [junit] Running test.beast.math.distributions.LaplaceDistributionTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.242 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.052 sec [junit] Running test.beast.math.distributions.LogNormalDistributionModelTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.382 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.899 sec [junit] Running test.beast.math.distributions.MRCAPriorTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.891 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.95 sec [junit] Running test.beast.math.distributions.MeanOfParametricDistributionTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.115 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.132 sec [junit] Running test.beast.math.distributions.NormalDistributionTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.489 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.567 sec [junit] Running test.beast.statistic.RPNCalculatorTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.365 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.407 sec [junit] Running test.beast.util.ClusterTreeTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.757 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.801 sec [junit] Running test.beast.util.JSONTest [junit] [junit] OpenCL error: CL_DEVICE_NOT_FOUND from file , line 122. @@ -1794,15 +1865,15 @@ [junit] Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0 sec [junit] Test test.beast.util.JSONTest FAILED (crashed) [junit] Running test.beast.util.NexusParserTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.213 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.36 sec [junit] Running test.beast.util.RandomizerTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.808 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.8 sec [junit] Running test.beast.util.TreeParserTest - [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.534 sec + [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.533 sec [junit] Running test.beast.util.XMLParserTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.025 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.031 sec [junit] Running test.beast.util.XMLTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.953 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.876 sec [echo] JUnit test finished. dist_all_BEAST: @@ -1820,7 +1891,7 @@ build_jar_all_BEAST: BUILD SUCCESSFUL -Total time: 4 minutes 44 seconds +Total time: 4 minutes 24 seconds mv debian/fest_swing_tests src/test/beast/app/beauti make[1]: Leaving directory '/build/beast2-mcmc-2.6.3+dfsg' dh_auto_test @@ -1848,13 +1919,13 @@ dh_missing dh_installdeb dh_gencontrol -dpkg-gencontrol: warning: Depends field of package beast2-mcmc-doc: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package beast2-mcmc: substitution variable ${shlibs:Depends} used, but is not defined +dpkg-gencontrol: warning: Depends field of package beast2-mcmc-doc: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package beast2-mcmc-examples: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb -dpkg-deb: building package 'beast2-mcmc-examples' in '../beast2-mcmc-examples_2.6.3+dfsg-2_all.deb'. dpkg-deb: building package 'beast2-mcmc' in '../beast2-mcmc_2.6.3+dfsg-2_all.deb'. +dpkg-deb: building package 'beast2-mcmc-examples' in '../beast2-mcmc-examples_2.6.3+dfsg-2_all.deb'. dpkg-deb: building package 'beast2-mcmc-doc' in '../beast2-mcmc-doc_2.6.3+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../beast2-mcmc_2.6.3+dfsg-2_arm64.changes @@ -1863,12 +1934,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/5447/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/5447/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/13987 and its subdirectories -I: Current time: Thu Aug 5 17:32:29 -12 2021 -I: pbuilder-time-stamp: 1628227949 +I: removing directory /srv/workspace/pbuilder/5447 and its subdirectories +I: Current time: Fri Sep 9 02:02:59 +14 2022 +I: pbuilder-time-stamp: 1662638579