Diff of the two buildlogs: -- --- b1/build.log 2021-07-06 20:05:18.303680082 +0000 +++ b2/build.log 2021-07-06 20:10:24.704168031 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jul 6 07:57:16 -12 2021 -I: pbuilder-time-stamp: 1625601436 +I: Current time: Tue Aug 9 16:28:21 +14 2022 +I: pbuilder-time-stamp: 1660012101 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 [./jalview_2.11.1.3+dfsg2-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.tiR5XcsR/trustedkeys.kbx': General error -gpgv: Signature made Thu Mar 18 09:12:22 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.T6NLgUtM/trustedkeys.kbx': General error +gpgv: Signature made Fri Mar 19 11:12:22 2021 +14 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./jalview_2.11.1.3+dfsg2-5.dsc @@ -36,135 +36,169 @@ dpkg-source: info: applying controlling_web_services.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/10957/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4845/tmp/hooks/D01_modify_environment starting +debug: Running on codethink11-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/4845/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4845/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='10957' - 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=4845 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.D0vwubzQgw/pbuilderrc_F4x2 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.D0vwubzQgw/b1 --logfile b1/build.log jalview_2.11.1.3+dfsg2-5.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.D0vwubzQgw/pbuilderrc_06j5 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.D0vwubzQgw/b2 --logfile b2/build.log --extrapackages usrmerge jalview_2.11.1.3+dfsg2-5.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 codethink16-arm64 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 - -rwxr-xr-x 1 root root 1282512 Jun 21 14:26 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 Feb 7 02:38 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 Feb 7 02:38 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 Feb 7 02:38 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 Feb 7 02:38 more - -rwsr-xr-x 1 root root 51360 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 14496 Feb 7 02:38 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 Jun 21 14:26 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 Jul 5 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 Feb 7 02:38 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 Feb 7 02:38 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 Feb 7 02:38 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/10957/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1282512 Jun 22 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 Feb 8 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 Feb 8 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 Feb 8 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 Feb 8 2021 more + -rwsr-xr-x 1 root root 51360 Feb 8 2021 mount + -rwxr-xr-x 1 root root 14496 Feb 8 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 Jun 22 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 Aug 9 16:28 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 9 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 Feb 8 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 Feb 8 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 Feb 8 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/4845/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -668,7 +702,7 @@ Get: 402 http://deb.debian.org/debian bullseye/main arm64 maven-debian-helper all 2.6 [117 kB] Get: 403 http://deb.debian.org/debian bullseye/main arm64 testng all 6.9.12-4 [795 kB] Get: 404 http://deb.debian.org/debian bullseye/main arm64 varna all 3-93+ds-3 [787 kB] -Fetched 437 MB in 33s (13.4 MB/s) +Fetched 437 MB in 35s (12.5 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.) @@ -2511,8 +2545,45 @@ 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 (2666 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 ... 32715 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/jalview-2.11.1.3+dfsg2/ && 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 > ../jalview_2.11.1.3+dfsg2-5_source.changes +hostname: Temporary failure in name resolution +I: Running cd /build/jalview-2.11.1.3+dfsg2/ && 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 > ../jalview_2.11.1.3+dfsg2-5_source.changes dpkg-buildpackage: info: source package jalview dpkg-buildpackage: info: source version 2.11.1.3+dfsg2-5 dpkg-buildpackage: info: source distribution unstable @@ -2522,7 +2593,7 @@ debian/rules clean dh clean debian/rules override_dh_clean -make[1]: Entering directory '/build/jalview-2.11.1.3+dfsg2' +make[1]: Map '/build/jalview-2.11.1.3+dfsg2' wordt binnengegaan dh_clean # Removing the help/ folder that was put into resources/ rm -f -rf resources/help/ @@ -2532,13 +2603,13 @@ # Putting gradle file back in place, removing Maven's pom. if [ -e buildUpstream.gradle ] ; then mv buildUpstream.gradle build.gradle ; fi rm -f pom.xml -make[1]: Leaving directory '/build/jalview-2.11.1.3+dfsg2' +make[1]: Map '/build/jalview-2.11.1.3+dfsg2' wordt verlaten debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure -make[1]: Entering directory '/build/jalview-2.11.1.3+dfsg2' +make[1]: Map '/build/jalview-2.11.1.3+dfsg2' wordt binnengegaan # Putting help folder inside resources so that it enters the jar. cp -a help/help/ resources/ # Putting the .build_properties file needed by upstream in the resources. @@ -2551,7 +2622,7 @@ sed 's/\(VERSION_PACKAGE\)/\12.11.1.3+dfsg2/; s/VERSION_PACKAGE\(.*\)+dfsg[0-9]*/\1/' debian/pom.xml > pom.xml dh_auto_configure mh_patchpoms -pjalview --debian-build --keep-pom-version --maven-repo=/build/jalview-2.11.1.3\+dfsg2/debian/maven-repo -make[1]: Leaving directory '/build/jalview-2.11.1.3+dfsg2' +make[1]: Map '/build/jalview-2.11.1.3+dfsg2' wordt verlaten dh_auto_build /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/jalview-2.11.1.3\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/jalview-2.11.1.3\+dfsg2/debian -Dmaven.repo.local=/build/jalview-2.11.1.3\+dfsg2/debian/maven-repo --batch-mode package -DskipTests -Dnotimestamp=true -Dlocale=en_US [INFO] Scanning for projects... @@ -2607,8 +2678,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 02:35 min -[INFO] Finished at: 2021-07-06T08:03:15-12:00 +[INFO] Total time: 57.013 s +[INFO] Finished at: 2022-08-09T16:31:59+14:00 [INFO] ------------------------------------------------------------------------ dh_auto_test /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/jalview-2.11.1.3\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/jalview-2.11.1.3\+dfsg2/debian -Dmaven.repo.local=/build/jalview-2.11.1.3\+dfsg2/debian/maven-repo --batch-mode test @@ -2717,21 +2788,21 @@ >SEQ2/1-7 CFCVVEV -Jul 06, 2021 8:03:32 AM jalview.util.MessageManager +Aug 09, 2022 4:32:07 PM jalview.util.MessageManager INFO: Getting messages for lang: en -Error reading author details: java.io.FileNotFoundException: /build/jalview-2.11.1.3+dfsg2/target/classes (Is a directory) -Error reading build details: java.io.FileNotFoundException: /build/jalview-2.11.1.3+dfsg2/target/classes (Is a directory) -Error reading author details: java.io.FileNotFoundException: /build/jalview-2.11.1.3+dfsg2/target/classes (Is a directory) -Error reading build details: java.io.FileNotFoundException: /build/jalview-2.11.1.3+dfsg2/target/classes (Is a directory) +Error reading author details: java.io.FileNotFoundException: /build/jalview-2.11.1.3+dfsg2/target/classes (Is een map) +Error reading build details: java.io.FileNotFoundException: /build/jalview-2.11.1.3+dfsg2/target/classes (Is een map) +Error reading author details: java.io.FileNotFoundException: /build/jalview-2.11.1.3+dfsg2/target/classes (Is een map) +Error reading build details: java.io.FileNotFoundException: /build/jalview-2.11.1.3+dfsg2/target/classes (Is een map) Overwriting file format: mmCIF -findMinMax for 1000 x 1000 took 35ms -Error reading author details: java.io.FileNotFoundException: /build/jalview-2.11.1.3+dfsg2/target/classes (Is a directory) -Error reading build details: java.io.FileNotFoundException: /build/jalview-2.11.1.3+dfsg2/target/classes (Is a directory) -Error reading author details: java.io.FileNotFoundException: /build/jalview-2.11.1.3+dfsg2/target/classes (Is a directory) -Error reading build details: java.io.FileNotFoundException: /build/jalview-2.11.1.3+dfsg2/target/classes (Is a directory) +findMinMax for 1000 x 1000 took 22ms +Error reading author details: java.io.FileNotFoundException: /build/jalview-2.11.1.3+dfsg2/target/classes (Is een map) +Error reading build details: java.io.FileNotFoundException: /build/jalview-2.11.1.3+dfsg2/target/classes (Is een map) +Error reading author details: java.io.FileNotFoundException: /build/jalview-2.11.1.3+dfsg2/target/classes (Is een map) +Error reading build details: java.io.FileNotFoundException: /build/jalview-2.11.1.3+dfsg2/target/classes (Is een map) DEBUG - Jalview Debugging Output Follows. -Error reading author details: java.io.FileNotFoundException: /build/jalview-2.11.1.3+dfsg2/target/classes (Is a directory) -Error reading build details: java.io.FileNotFoundException: /build/jalview-2.11.1.3+dfsg2/target/classes (Is a directory) +Error reading author details: java.io.FileNotFoundException: /build/jalview-2.11.1.3+dfsg2/target/classes (Is een map) +Error reading build details: java.io.FileNotFoundException: /build/jalview-2.11.1.3+dfsg2/target/classes (Is een map) >SEQ1/1-20 PTEIICYRTWRAPNNPMRWN >SEQ2/1-20 @@ -2874,9 +2945,9 @@ >SEQ20/1-50 TTEIICYRTWRAPNNPMRWNLIDVIILWTGQNPNKGNMIPESDFHI-WLWT -Jul 06, 2021 8:03:38 AM jalview.util.MessageManager formatMessage +Aug 09, 2022 4:32:10 PM jalview.util.MessageManager formatMessage WARNING: I18N missing: en label.rubbish -Jul 06, 2021 8:03:38 AM jalview.util.MessageManager getString +Aug 09, 2022 4:32:10 PM jalview.util.MessageManager getString WARNING: I18N missing: en label.rubbish Invalid matcher format: 'Score ge 12.2 Invalid matcher format: 'Score' ge '12.2 @@ -7613,7 +7684,7 @@ MemorySetting Property 'jvmmemmax' (1B) too small, using minimum (536870912). MemorySetting Property 'jvmmempc' (0.000000001) too small. Using minimum (536870912). MemorySetting Property 'jvmmempc' (100) too large. Leaving free space for OS and reducing to (67021094912). -[INFO] Tests run: 344, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.632 s - in TestSuite +[INFO] Tests run: 344, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.374 s - in TestSuite [INFO] [INFO] Results: [INFO] @@ -7622,13 +7693,13 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 25.483 s -[INFO] Finished at: 2021-07-06T08:03:47-12:00 +[INFO] Total time: 12.746 s +[INFO] Finished at: 2022-08-09T16:32:15+14:00 [INFO] ------------------------------------------------------------------------ create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install -make[1]: Entering directory '/build/jalview-2.11.1.3+dfsg2' +make[1]: Map '/build/jalview-2.11.1.3+dfsg2' wordt binnengegaan dh_auto_install /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/jalview-2.11.1.3\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/jalview-2.11.1.3\+dfsg2/debian -Dmaven.repo.local=/build/jalview-2.11.1.3\+dfsg2/debian/maven-repo --batch-mode -Ddebian.dir=/build/jalview-2.11.1.3\+dfsg2/debian -Ddebian.package=jalview -Dmaven.repo.local=/build/jalview-2.11.1.3\+dfsg2/debian/maven-repo -Dinstall.to.usj=true org.debian.maven:debian-maven-plugin:2.6:install [INFO] Scanning for projects... @@ -7660,15 +7731,15 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 2.650 s -[INFO] Finished at: 2021-07-06T08:03:58-12:00 +[INFO] Total time: 1.529 s +[INFO] Finished at: 2022-08-09T16:32:21+14:00 [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -pjalview --base-directory=/build/jalview-2.11.1.3\+dfsg2 --non-explore Analysing pom.xml... > dpkg --search /usr/share/maven-repo/compbio/min-jaba-client/*/* dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/maven-repo/compbio/min-jaba-client -Jul 06, 2021 8:04:14 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +Aug 09, 2022 4:32:31 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/jalview-2.11.1.3+dfsg2/pom.xml: Dependency not found compbio:min-jaba-client:jar:debian ERROR: pom.xml: dependency is not packaged in the Maven repository for Debian: compbio:min-jaba-client:debian @@ -7682,16 +7753,16 @@ jh_installlibs jh_manifest jh_depends -make[1]: Leaving directory '/build/jalview-2.11.1.3+dfsg2' +make[1]: Map '/build/jalview-2.11.1.3+dfsg2' wordt verlaten dh_install dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples -make[1]: Entering directory '/build/jalview-2.11.1.3+dfsg2' +make[1]: Map '/build/jalview-2.11.1.3+dfsg2' wordt binnengegaan dh_installexamples # Providing an example at startup instead of having to load it from the Internet. cp examples/exampleFile_2_7.jar debian/jalview/usr/share/doc/jalview/examples/exampleFile_2_7.jvp -make[1]: Leaving directory '/build/jalview-2.11.1.3+dfsg2' +make[1]: Map '/build/jalview-2.11.1.3+dfsg2' wordt verlaten dh_installman dh_installdebconf dh_icons @@ -7700,18 +7771,18 @@ dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms -make[1]: Entering directory '/build/jalview-2.11.1.3+dfsg2' +make[1]: Map '/build/jalview-2.11.1.3+dfsg2' wordt binnengegaan # Setting the packaged example file as not executable. chmod a-x debian/jalview/usr/share/doc/jalview/examples/uniref50.fa dh_fixperms -make[1]: Leaving directory '/build/jalview-2.11.1.3+dfsg2' +make[1]: Map '/build/jalview-2.11.1.3+dfsg2' wordt verlaten dh_missing dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package jalview: substitution variable ${maven:CompileDepends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'jalview' in '../jalview_2.11.1.3+dfsg2-5_all.deb'. +dpkg-deb: pakket 'jalview' wordt gebouwd in '../jalview_2.11.1.3+dfsg2-5_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../jalview_2.11.1.3+dfsg2-5_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -7719,12 +7790,14 @@ 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/4845/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4845/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/10957 and its subdirectories -I: Current time: Tue Jul 6 08:05:17 -12 2021 -I: pbuilder-time-stamp: 1625601917 +I: removing directory /srv/workspace/pbuilder/4845 and its subdirectories +I: Current time: Tue Aug 9 16:33:23 +14 2022 +I: pbuilder-time-stamp: 1660012403