Diff of the two buildlogs: -- --- b1/build.log 2021-07-23 06:01:41.790669326 +0000 +++ b2/build.log 2021-07-23 07:19:07.096338645 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jul 22 16:34:05 -12 2021 -I: pbuilder-time-stamp: 1627014845 +I: Current time: Fri Jul 23 20:04:33 +14 2021 +I: pbuilder-time-stamp: 1627020273 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 [./primer3_2.4.0-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.GdFAG6D7/trustedkeys.kbx': General error -gpgv: Signature made Thu Jul 2 17:56:39 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.XX55likf/trustedkeys.kbx': General error +gpgv: Signature made Fri Jul 3 19:56:39 2020 +14 gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./primer3_2.4.0-4.dsc @@ -31,135 +31,169 @@ dpkg-source: info: applying p3test_fix_exit_status.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/28716/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/29933/tmp/hooks/D01_modify_environment starting +debug: Running on virt64a. +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/29933/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/29933/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='44f5bbdef5eb4abea6367e9ac5d86486' - 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='28716' - PS1='# ' - PS2='> ' + INVOCATION_ID=5ba7181db392400585334a20b8d10fe8 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=29933 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.B4gjsE9CVv/pbuilderrc_6VOi --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.B4gjsE9CVv/b1 --logfile b1/build.log primer3_2.4.0-4.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + 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.B4gjsE9CVv/pbuilderrc_neQ1 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.B4gjsE9CVv/b2 --logfile b2/build.log --extrapackages usrmerge primer3_2.4.0-4.dsc' + SUDO_GID=114 + SUDO_UID=108 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux virt32a 5.10.0-7-armmp-lpae #1 SMP Debian 5.10.40-1 (2021-05-28) armv7l GNU/Linux + Linux i-capture-the-hostname 5.10.0-7-arm64 #1 SMP Debian 5.10.40-1 (2021-05-28) aarch64 GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Jun 21 14:26 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 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 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 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 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 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 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Feb 7 02:38 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 124508 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 64212 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Feb 7 02:38 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Feb 7 02:38 more - -rwsr-xr-x 1 root root 34400 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 9824 Feb 7 02:38 mountpoint - -rwxr-xr-x 1 root root 88524 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 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Jun 21 14:26 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 21 21:26 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Feb 7 02:38 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 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/28716/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Jun 22 16:26 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 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 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 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 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 Feb 8 04:38 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 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Feb 8 04:38 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Feb 8 04:38 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Feb 8 04:38 more + -rwsr-xr-x 1 root root 34400 Feb 8 04:38 mount + -rwxr-xr-x 1 root root 9824 Feb 8 04:38 mountpoint + -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 23 20:05 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 21 23:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Feb 8 04:38 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Feb 8 04:38 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 Feb 8 04:38 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/29933/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -226,7 +260,7 @@ Get: 29 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] -Fetched 17.7 MB in 4s (4376 kB/s) +Fetched 17.7 MB in 5s (3386 kB/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 ... 19398 files and directories currently installed.) @@ -365,8 +399,45 @@ 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 armhf libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (132 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 ... 21274 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/primer3-2.4.0/ && 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 > ../primer3_2.4.0-4_source.changes +hostname: Name or service not known +I: Running cd /build/primer3-2.4.0/ && 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 > ../primer3_2.4.0-4_source.changes dpkg-buildpackage: info: source package primer3 dpkg-buildpackage: info: source version 2.4.0-4 dpkg-buildpackage: info: source distribution unstable @@ -376,7 +447,7 @@ debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src - cd src && make -j3 clean + cd src && make -j4 clean make[1]: Entering directory '/build/primer3-2.4.0/src' rm -f *.o primer3_core ntdpal ntthal oligotm long_seq_tm_test primer3_masker *~ libprimer3.a libdpal.a libthal.a liboligotm.a libmasker.a libprimer3.so.1.0.0 libdpal.a.so.1.0.0 libthal.a.so.1.0.0 liboligotm.so.1.2.0 libmasker.a.so.1.0.0 example.for example.rev example.int core ../*~ cd ../test/; make clean @@ -424,7 +495,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/primer3-2.4.0' dh_auto_build -- 'CPP=$(CXX)' - cd src && make -j3 "INSTALL=install --strip-program=true" CPP=\$\(CXX\) + cd src && make -j4 "INSTALL=install --strip-program=true" CPP=\$\(CXX\) make[2]: Entering directory '/build/primer3-2.4.0/src' g++ -c -g -O2 -fdebug-prefix-map=/build/primer3-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 primer3_boulder_main.c g++ -c -g -O2 -fdebug-prefix-map=/build/primer3-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -o format_output.o format_output.c @@ -494,34 +565,34 @@ 1216 | atpH[0][3] = atpH[3][0] = atp_value; | ^~~~ g++ -g -O2 -fdebug-prefix-map=/build/primer3-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm -ar rv libprimer3.a libprimer3.o p3_seq_lib.o -ar: creating libprimer3.a -a - libprimer3.o -a - p3_seq_lib.o -ranlib libprimer3.a ar rv libdpal.a dpal_primer.o ar: creating libdpal.a a - dpal_primer.o ranlib libdpal.a -ar rv libthal.a thal_primer.o -ar: creating libthal.a -a - thal_primer.o -ranlib libthal.a ar rv liboligotm.a oligotm.o ar: creating liboligotm.a a - oligotm.o ranlib liboligotm.a g++ -Wl,-z,relro -Wl,-z,now -g -o ntdpal ntdpal_main.o dpal.o g++ -g -O2 -fdebug-prefix-map=/build/primer3-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -Wl,-z,relro -Wl,-z,now -g -o oligotm oligotm_main.c liboligotm.a -lm -g++ -g -O2 -fdebug-prefix-map=/build/primer3-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -o primer3_masker masker_main.c libprimer3.a libdpal.a libthal.a liboligotm.a libmasker.a -lm +ar rv libthal.a thal_primer.o +ar: creating libthal.a +a - thal_primer.o +ranlib libthal.a +ar rv libprimer3.a libprimer3.o p3_seq_lib.o +ar: creating libprimer3.a +a - libprimer3.o +a - p3_seq_lib.o +ranlib libprimer3.a g++ -Wl,-z,relro -Wl,-z,now -g -o primer3_core primer3_boulder_main.o format_output.o read_boulder.o print_boulder.o masker.o libprimer3.a libdpal.a libthal.a liboligotm.a libmasker.a -lm +g++ -g -O2 -fdebug-prefix-map=/build/primer3-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -o primer3_masker masker_main.c libprimer3.a libdpal.a libthal.a liboligotm.a libmasker.a -lm g++ -Wl,-z,relro -Wl,-z,now -g -o ntthal thal_main.o thal.o -lm make[2]: Leaving directory '/build/primer3-2.4.0/src' make[1]: Leaving directory '/build/primer3-2.4.0' debian/rules override_dh_auto_test make[1]: Entering directory '/build/primer3-2.4.0' dh_auto_test --sourcedirectory=test - cd test && make -j3 test + cd test && make -j4 test make[2]: Entering directory '/build/primer3-2.4.0/test' cd ../src; make perl cmdline_test.pl @@ -531,19 +602,24 @@ make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/primer3-2.4.0/src' echo; echo; echo 'TESTING ALIGNMENT CALCS'; echo; perl dpal_test.pl ; +echo; echo; echo 'TESTING THERMODYNAMIC ALIGNMENT CALCS'; echo; perl thal_test.pl ; TESTING ALIGNMENT CALCS + +TESTING THERMODYNAMIC ALIGNMENT CALCS + + TESTING Tm CALCULATIONS -Tm tests nr 1-Error handling of too-long sequence...[OK] -Default implementations + alignment... +Tm tests nr 1- TESTING command line arguments -Test 1... [OK] +Test 1... Error handling of too-long sequence...[OK] +Default implementations + alignment...[OK] Test 2... [OK] Test 3... [OK] Test 4... [OK] @@ -551,22 +627,16 @@ Passed all tests - [OK] -echo; echo; echo 'TESTING THERMODYNAMIC ALIGNMENT CALCS'; echo; perl thal_test.pl ; +echo; echo; echo 'TESTING MASKER'; echo; perl masker_test.pl ; -TESTING THERMODYNAMIC ALIGNMENT CALCS +TESTING MASKER Error handling of too-long sequence... 1................................... [OK] -Default implementations + alignment...50: [OK] - - -echo; echo; echo 'TESTING MASKER'; echo; perl masker_test.pl ; +Default implementations + alignment...Default implementations...50: [OK] -TESTING MASKER - -Default implementations...[OK] echo; echo; echo 'TESTING primer3_core'; echo; perl p3test.pl @@ -581,7 +651,7 @@ p3test.pl: testing ../src/primer3_core -START, Thu Jul 22 16:35:39 2021 +START, Fri Jul 23 20:06:59 2021 testing fatal errors... ./primer_global_err/bad_divalent_dntp_conc_1 @@ -615,6 +685,7 @@ ./primer_global_err/bad_self_end ./primer_global_err/bad_self_end_int ./primer_global_err/bad_settings0 +[OK] ./primer_global_err/bad_settings1 ./primer_global_err/bad_settings2 ./primer_global_err/bad_settings3 @@ -670,8 +741,7 @@ ./primer_global_err/repeat_lib_err5 ./primer_global_err/repeat_lib_err6 ./primer_global_err/repeat_lib_int_err -[OK] -Default implementations + NO alignment 1... ./primer_global_err/repeat_lib_int_err1 + ./primer_global_err/repeat_lib_int_err1 ./primer_global_err/repeat_lib_int_err2 ./primer_global_err/repeat_lib_int_err3 ./primer_global_err/repeat_lib_int_err4 @@ -685,26 +755,27 @@ ./primer_global_err/zero_min_size ./primer_global_err/zero_num_return [OK] -primer_must_use_th...0s [OK] +primer_must_use_th...1s [OK] primer_task_th...[OK] Default implementations + NO alignment 1...[OK] +Default implementations + NO alignment 1...[OK] Default implementations + NO alignment 2...[OK] Force _dpal_generic...8s [OK] primer_thal_args...2s [OK] primer_thal_max_seq_error...[OK] Force _dpal_long_nopath_generic 1...[OK] -Default implementations + NO alignment 2...2s [OK] -primer_first_base_index...1s [OK] -primer_must_match...0s [OK] +Default implementations + NO alignment 2...3s [OK] +primer_first_base_index...0s [OK] +primer_must_match...1s [OK] primer_masker...[OK] Force _dpal_long_nopath_generic 2...[OK] Force long maxgap1 functions 1...[OK] [OK] Force long maxgap1 functions 2...[OK] -9s [OK] -primer_masker_formatted...6s [OK] +11s [OK] +primer_masker_formatted...38s [OK] test_compl_error...0s [OK] -test_left_to_right_of_right...0s [OK] +test_left_to_right_of_right...1s [OK] dv_conc_vs_dntp_conc...0s [OK] primer_boundary...0s [OK] primer_boundary1...0s [OK] @@ -712,23 +783,23 @@ primer_boundary1_formatted...0s [OK] primer3_v1_1_4_default_settings...1s [OK] primer3web_v0_4_0_default_settings...0s [OK] -primer3web_v3_0_0_default_settings...7s [OK] -primer3web_v4_0_0_default_settings...1s [OK] +primer3web_v3_0_0_default_settings...11s [OK] +primer3web_v4_0_0_default_settings...0s [OK] primer_internal...0s [OK] primer_internal1...0s [OK] primer_internal_formatted...0s [OK] primer_internal1_formatted...0s [OK] primer_ok_regions...0s [OK] -primer_ok_regions_formatted...0s [OK] -primer_ok_regions2...33s [OK] +primer_ok_regions_formatted...1s [OK] +primer_ok_regions2...68s [OK] primer_tm_lc_masking...0s [OK] primer_tm_lc_masking_formatted...0s [OK] primer_start_codon...1s [OK] -primer_task...1s [OK] +primer_task...0s [OK] primer_task_formatted...0s [OK] primer_renewed_tasks...0s [OK] primer_new_tasks...1s [OK] -primer_new_tasks_formatted...0s [OK] +primer_new_tasks_formatted...2s [OK] primer_must_overlap_point...3s [OK] primer_overlap_junction...0s [OK] primer_all_settingsfiles...0s [OK] @@ -739,46 +810,46 @@ primer_must_use...0s [OK] primer_must_use_formatted...0s [OK] primer_syntax...0s [OK] -primer_end_pathology...0s [OK] -primer_num_best...1s [OK] +primer_end_pathology...1s [OK] +primer_num_best...0s [OK] primer_quality_boundary...0s [OK] primer...3s [OK] primer_list_files...[OK] primer1...0s [OK] primer1_list_files...[OK] primer_mispriming...2s [OK] -primer_mispriming_formatted...1s [OK] +primer_mispriming_formatted...2s [OK] primer_mispriming_boundary1...0s [OK] primer_mispriming_boundary1_formatted...0s [OK] primer_mispriming_boundary2...0s [OK] primer_mispriming_boundary2_formatted...0s [OK] primer_mispriming_long_lib...0s [OK] -primer_rat...2s [OK] -primer_human...2s [OK] +primer_rat...1s [OK] +primer_human...4s [OK] long_seq...1s [OK] -primer_position_penalty...2s [OK] -primer_position_penalty_formatted...2s [OK] -p3-tmpl-mispriming...0s [OK] +primer_position_penalty...3s [OK] +primer_position_penalty_formatted...3s [OK] +p3-tmpl-mispriming...1s [OK] primer_three_prime_distance...0s [OK] -primer_obj_fn...7s [OK] +primer_obj_fn...9s [OK] p3_3_prime_n...0s [OK] -primer_masker...6s [OK] -primer_masker_formatted...8s [OK] -primer_mispriming_th...60s [OK] -th-w-other-tasks...67s [OK] +primer_masker...18s [OK] +primer_masker_formatted...31s [OK] +primer_mispriming_th...168s [OK] +th-w-other-tasks...109s [OK] th-w-other-tasks_list_files...[OK] -primer_new_tasks_th...242s [OK] -primer_thermod_align...560s [OK] -primer_thermod_align_formatted...456s [OK] -primer1_th...1827s [OK] +primer_new_tasks_th...154s [OK] +primer_thermod_align...305s [OK] +primer_thermod_align_formatted...267s [OK] +primer1_th...1123s [OK] primer1_th_list_files...[OK] primer_lib_amb_codes... NOTE: this test takes _much_ longer than the others (5 to 20 minutes or more). -starting primer_lib_amb_codes at Thu Jul 22 17:31:07 2021...1091s [OK] +starting primer_lib_amb_codes at Fri Jul 23 20:46:22 2021...1218s [OK] -Tests in p3test.pl ran for 4419 s (73.65 min) +Tests in p3test.pl ran for 3581 s (59.6833333333333 min) -DONE Thu Jul 22 17:49:18 2021 Passed all tests - [OK] +DONE Fri Jul 23 21:06:40 2021 Passed all tests - [OK] echo; echo; echo "Testing completed. You must check the test output for the string FAILED"; echo; echo; @@ -790,7 +861,7 @@ make[2]: Leaving directory '/build/primer3-2.4.0/test' dh clean --sourcedirectory=test dh_auto_clean -O--sourcedirectory=test - cd test && make -j3 clean + cd test && make -j4 clean make[2]: Entering directory '/build/primer3-2.4.0/test' echo; echo; echo 'CLEAN UP TEST DIRECTORIES'; echo; echo; @@ -876,12 +947,14 @@ 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/29933/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/29933/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/28716 and its subdirectories -I: Current time: Thu Jul 22 18:01:37 -12 2021 -I: pbuilder-time-stamp: 1627020097 +I: removing directory /srv/workspace/pbuilder/29933 and its subdirectories +I: Current time: Fri Jul 23 21:18:59 +14 2021 +I: pbuilder-time-stamp: 1627024739