Diff of the two buildlogs: -- --- b1/build.log 2024-06-29 15:10:10.942554254 +0000 +++ b2/build.log 2024-06-29 15:16:09.167326104 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jun 29 02:59:50 -12 2024 -I: pbuilder-time-stamp: 1719673190 +I: Current time: Sat Aug 2 11:33:13 +14 2025 +I: pbuilder-time-stamp: 1754083993 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./bioperl-run_1.7.3-6.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.cvrlR3dC/trustedkeys.kbx': General error -gpgv: Signature made Wed Jan 6 09:46:40 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.xMKqMR7M/trustedkeys.kbx': General error +gpgv: Signature made Thu Jan 7 11:46:40 2021 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bioperl-run_1.7.3-6.dsc @@ -45,134 +45,165 @@ dpkg-source: info: applying skip-test-for-kalign.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/788413/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2298863/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-amd64. +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 +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Aug 2 11:33 /bin/sh -> /bin/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/2298863/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2298863/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - 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]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=12 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='2a8f63980fda4202bb6d9b927404eebb' - 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='788413' - PS1='# ' - PS2='> ' + INVOCATION_ID=5a75c308753249a883ce133afbd9597a + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-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=2298863 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/r-b-build.M49NWtj8/pbuilderrc_WySA --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.M49NWtj8/b1 --logfile b1/build.log bioperl-run_1.7.3-6.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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/r-b-build.M49NWtj8/pbuilderrc_7PLy --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.M49NWtj8/b2 --logfile b2/build.log bioperl-run_1.7.3-6.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 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 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 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 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Jan 20 2022 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 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jan 20 2022 more - -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount - -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jun 6 21:24 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jan 20 2022 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Jan 19 21:59 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/788413/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 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 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 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 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jan 21 2022 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 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 69032 Jan 21 2022 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jan 21 2022 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jan 21 2022 more + -rwsr-xr-x 1 root root 55528 Jan 21 2022 mount + -rwxr-xr-x 1 root root 18664 Jan 21 2022 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 9 Aug 2 11:33 sh -> /bin/bash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jan 21 2022 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Jan 20 2024 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jan 21 2022 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jan 21 2022 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/2298863/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -534,7 +565,7 @@ Get: 235 http://deb.debian.org/debian bullseye/main amd64 tigr-glimmer amd64 3.02b-5 [286 kB] Get: 236 http://deb.debian.org/debian bullseye/main amd64 wise-data all 2.4.1-23 [78.2 kB] Get: 237 http://deb.debian.org/debian bullseye/main amd64 wise amd64 2.4.1-23 [994 kB] -Fetched 221 MB in 4s (58.3 MB/s) +Fetched 221 MB in 3s (65.5 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 ... 19711 files and directories currently installed.) @@ -1524,7 +1555,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/bioperl-run-1.7.3/ && 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 > ../bioperl-run_1.7.3-6_source.changes +I: user script /srv/workspace/pbuilder/2298863/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/2298863/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/bioperl-run-1.7.3/ && 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 > ../bioperl-run_1.7.3-6_source.changes dpkg-buildpackage: info: source package bioperl-run dpkg-buildpackage: info: source version 1.7.3-6 dpkg-buildpackage: info: source distribution unstable @@ -1590,7 +1625,7 @@ gapOpen[] = { 0.01993141696 0.01993141696 } gapExtend[] = { 0.7943345308 0.7943345308 } -Loading sequence file: /tmp/ENmH5vxc7c +Loading sequence file: /tmp/zQyw12F3bF Computing posterior matrices Building DAG Starting the sequence annealing process @@ -1632,7 +1667,7 @@ ok 11 - can return output format for command 'annotate' ok 12 - result claims to be in correct format for command 'annotate' ok 13 - can return output file for command 'annotate' -ok 14 - file format of '/tmp/_JkObEW2gC/XJKQaGYPbE.bed' consistent with claim for 'annotate' +ok 14 - file format of '/tmp/j_x_ZGHn79/AvHJvrv1J6.bed' consistent with claim for 'annotate' ok 15 - can set want to IO object for command 'annotate' ok 16 - can get the basic object result for command 'annotate' ok 17 - 'returned object is correct for command 'annotate'' isa 'Bio::Root::IO' @@ -1669,7 +1704,7 @@ ok 48 - can return output format for command 'overlap' ok 49 - result claims to be in correct format for command 'overlap' ok 50 - can return output file for command 'overlap' -ok 51 - file format of '/tmp/Fd6o7x1KN4/oCFx3pwMGS.bed' consistent with claim for 'overlap' +ok 51 - file format of '/tmp/pQXDrOSDZJ/aq_ftkceKf.bed' consistent with claim for 'overlap' ok 52 - can set want to IO object for command 'overlap' ok 53 - can get the basic object result for command 'overlap' ok 54 - 'returned object is correct for command 'overlap'' isa 'Bio::Root::IO' @@ -1687,7 +1722,7 @@ ok 66 - can return output format for command 'bam_to_bed' ok 67 - result claims to be in correct format for command 'bam_to_bed' ok 68 - can return output file for command 'bam_to_bed' -ok 69 - file format of '/tmp/JkcSebj5hm/Hy3llyFm9u.bed' consistent with claim for 'bam_to_bed' +ok 69 - file format of '/tmp/XzJrxemQmd/Lsb0pPCoFm.bed' consistent with claim for 'bam_to_bed' ok 70 - can set want to IO object for command 'bam_to_bed' ok 71 - can get the basic object result for command 'bam_to_bed' ok 72 - 'returned object is correct for command 'bam_to_bed'' isa 'Bio::Root::IO' @@ -1726,7 +1761,7 @@ ok 101 - can return output format for command 'pair_to_pair' ok 102 - result claims to be in correct format for command 'pair_to_pair' ok 103 - can return output file for command 'pair_to_pair' -ok 104 - file format of '/tmp/fcGU8NS9kp/wrLfRbUiXC.bedpe' consistent with claim for 'pair_to_pair' +ok 104 - file format of '/tmp/fl5MPo2q39/tZAlOuIgLT.bedpe' consistent with claim for 'pair_to_pair' ok 105 - can set want to IO object for command 'pair_to_pair' ok 106 - can get the basic object result for command 'pair_to_pair' ok 107 - 'returned object is correct for command 'pair_to_pair'' isa 'Bio::Root::IO' @@ -1806,7 +1841,7 @@ ok 181 - can return output format for command 'group_by' ok 182 - result claims to be in correct format for command 'group_by' ok 183 - can return output file for command 'group_by' -ok 184 - file format of '/tmp/okh37XEzRv/sEzydxWHpA.bed' consistent with claim for 'group_by' +ok 184 - file format of '/tmp/dHESjDmiSJ/j9OLNlIuYP.bed' consistent with claim for 'group_by' ok 185 - can set want to IO object for command 'group_by' ok 186 - can get the basic object result for command 'group_by' ok 187 - 'returned object is correct for command 'group_by'' isa 'Bio::Root::IO' @@ -1824,7 +1859,7 @@ ok 199 - can return output format for command 'shuffle' ok 200 - result claims to be in correct format for command 'shuffle' ok 201 - can return output file for command 'shuffle' -ok 202 - file format of '/tmp/VJesO_G9lR/bc3zrGJ5g3.bed' consistent with claim for 'shuffle' +ok 202 - file format of '/tmp/egeLKMc33U/PZ_0lQEVrg.bed' consistent with claim for 'shuffle' ok 203 - can set want to IO object for command 'shuffle' ok 204 - can get the basic object result for command 'shuffle' ok 205 - 'returned object is correct for command 'shuffle'' isa 'Bio::Root::IO' @@ -1842,7 +1877,7 @@ ok 217 - can return output format for command 'b12_to_b6' ok 218 - result claims to be in correct format for command 'b12_to_b6' ok 219 - can return output file for command 'b12_to_b6' -ok 220 - file format of '/tmp/_5hMZ_hYyr/NbuJaaiSsA.bed' consistent with claim for 'b12_to_b6' +ok 220 - file format of '/tmp/qkYov9H_IJ/UQewwaNp3b.bed' consistent with claim for 'b12_to_b6' ok 221 - can set want to IO object for command 'b12_to_b6' ok 222 - can get the basic object result for command 'b12_to_b6' ok 223 - 'returned object is correct for command 'b12_to_b6'' isa 'Bio::Root::IO' @@ -1882,7 +1917,7 @@ ok 253 - can return output format for command 'slop' ok 254 - result claims to be in correct format for command 'slop' ok 255 - can return output file for command 'slop' -ok 256 - file format of '/tmp/vC8bAuzThQ/iDU3lS7WVI.bed' consistent with claim for 'slop' +ok 256 - file format of '/tmp/ylSKboIShR/C7BfAJDHEN.bed' consistent with claim for 'slop' ok 257 - can set want to IO object for command 'slop' ok 258 - can get the basic object result for command 'slop' ok 259 - 'returned object is correct for command 'slop'' isa 'Bio::Root::IO' @@ -1900,7 +1935,7 @@ ok 271 - can return output format for command 'closest' ok 272 - result claims to be in correct format for command 'closest' ok 273 - can return output file for command 'closest' -ok 274 - file format of '/tmp/EK3JyArqDz/eLAAFI_RVj.bedpe' consistent with claim for 'closest' +ok 274 - file format of '/tmp/0PNsTR6ogL/gUILGfCwEz.bedpe' consistent with claim for 'closest' ok 275 - can set want to IO object for command 'closest' ok 276 - can get the basic object result for command 'closest' ok 277 - 'returned object is correct for command 'closest'' isa 'Bio::Root::IO' @@ -1939,7 +1974,7 @@ ok 306 - can return output format for command 'sort' ok 307 - result claims to be in correct format for command 'sort' ok 308 - can return output file for command 'sort' -ok 309 - file format of '/tmp/ndo7c7DJ1p/anXQMI2aYF.bed' consistent with claim for 'sort' +ok 309 - file format of '/tmp/t1pQrIXvxv/VyfTSd7q4D.bed' consistent with claim for 'sort' ok 310 - can set want to IO object for command 'sort' ok 311 - can get the basic object result for command 'sort' ok 312 - 'returned object is correct for command 'sort'' isa 'Bio::Root::IO' @@ -1957,7 +1992,7 @@ ok 324 - can return output format for command 'complement' ok 325 - result claims to be in correct format for command 'complement' ok 326 - can return output file for command 'complement' -ok 327 - file format of '/tmp/c8VeeUtMUO/n8HLKuuUv9.bed' consistent with claim for 'complement' +ok 327 - file format of '/tmp/EE04OZWR_6/9sXdySSMm1.bed' consistent with claim for 'complement' ok 328 - can set want to IO object for command 'complement' ok 329 - can get the basic object result for command 'complement' ok 330 - 'returned object is correct for command 'complement'' isa 'Bio::Root::IO' @@ -1997,7 +2032,7 @@ ok 360 - can return output format for command 'subtract' ok 361 - result claims to be in correct format for command 'subtract' ok 362 - can return output file for command 'subtract' -ok 363 - file format of '/tmp/8y3hpJzfP9/R5E3xPBpBH.bed' consistent with claim for 'subtract' +ok 363 - file format of '/tmp/pMBRlFoz8A/D8ftH_nbRj.bed' consistent with claim for 'subtract' ok 364 - can set want to IO object for command 'subtract' ok 365 - can get the basic object result for command 'subtract' ok 366 - 'returned object is correct for command 'subtract'' isa 'Bio::Root::IO' @@ -2019,7 +2054,7 @@ ok 378 - can return output format for command 'coverage' ok 379 - result claims to be in correct format for command 'coverage' ok 380 - can return output file for command 'coverage' -ok 381 - file format of '/tmp/bZilbv1I9W/nLP5896Hqw.bed' consistent with claim for 'coverage' +ok 381 - file format of '/tmp/uTRkaQGgrw/TGyXO9h0qW.bed' consistent with claim for 'coverage' ok 382 - can set want to IO object for command 'coverage' ok 383 - can get the basic object result for command 'coverage' ok 384 - 'returned object is correct for command 'coverage'' isa 'Bio::Root::IO' @@ -2041,7 +2076,7 @@ ok 396 - can return output format for command 'merge' ok 397 - result claims to be in correct format for command 'merge' ok 398 - can return output file for command 'merge' -ok 399 - file format of '/tmp/3owwDV8mif/G0bD1F3TdM.bed' consistent with claim for 'merge' +ok 399 - file format of '/tmp/xofUVUsMlJ/OtqYRoGXv_.bed' consistent with claim for 'merge' ok 400 - can set want to IO object for command 'merge' ok 401 - can get the basic object result for command 'merge' ok 402 - 'returned object is correct for command 'merge'' isa 'Bio::Root::IO' @@ -2059,7 +2094,7 @@ ok 414 - can return output format for command 'window' ok 415 - result claims to be in correct format for command 'window' ok 416 - can return output file for command 'window' -ok 417 - file format of '/tmp/YOxZMqpZNT/NHJb3JZDlX.bedpe' consistent with claim for 'window' +ok 417 - file format of '/tmp/C2BCwgM8bx/X579scPMzy.bedpe' consistent with claim for 'window' ok 418 - can set want to IO object for command 'window' ok 419 - can get the basic object result for command 'window' ok 420 - 'returned object is correct for command 'window'' isa 'Bio::Root::IO' @@ -2687,16 +2722,16 @@ WARNING: AVX2 instruction set not found! Kalign will not run optimally. -[2024-06-29 03:08:51] : LOG : Detected protein sequences. -[2024-06-29 03:08:51] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -[2024-06-29 03:08:51] : LOG : Detected: 7 sequences. -[2024-06-29 03:08:51] : LOG : Calculating pairwise distances -[2024-06-29 03:08:51] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 -[2024-06-29 03:08:51] : LOG : 7 anchors -[2024-06-29 03:08:51] : LOG : Building guide tree. -[2024-06-29 03:08:51] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -[2024-06-29 03:08:51] : LOG : Aligning -[2024-06-29 03:08:51] : LOG : CPU Time: 0.22u 00:00:00.21 Elapsed: 00:00:00.00 +[2025-08-02 11:38:10] : LOG : Detected protein sequences. +[2025-08-02 11:38:10] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2025-08-02 11:38:10] : LOG : Detected: 7 sequences. +[2025-08-02 11:38:10] : LOG : Calculating pairwise distances +[2025-08-02 11:38:10] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2025-08-02 11:38:10] : LOG : 7 anchors +[2025-08-02 11:38:10] : LOG : Building guide tree. +[2025-08-02 11:38:10] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2025-08-02 11:38:10] : LOG : Aligning +[2025-08-02 11:38:10] : LOG : CPU Time: 0.19u 00:00:00.18 Elapsed: 00:00:00.00 ok 5 ok 6 @@ -2719,16 +2754,16 @@ WARNING: AVX2 instruction set not found! Kalign will not run optimally. -[2024-06-29 03:08:51] : LOG : Detected protein sequences. -[2024-06-29 03:08:51] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -[2024-06-29 03:08:51] : LOG : Detected: 7 sequences. -[2024-06-29 03:08:51] : LOG : Calculating pairwise distances -[2024-06-29 03:08:51] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -[2024-06-29 03:08:51] : LOG : 7 anchors -[2024-06-29 03:08:51] : LOG : Building guide tree. -[2024-06-29 03:08:51] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -[2024-06-29 03:08:51] : LOG : Aligning -[2024-06-29 03:08:51] : LOG : CPU Time: 0.22u 00:00:00.22 Elapsed: 00:00:00.00 +[2025-08-02 11:38:10] : LOG : Detected protein sequences. +[2025-08-02 11:38:11] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:01.00 +[2025-08-02 11:38:11] : LOG : Detected: 7 sequences. +[2025-08-02 11:38:11] : LOG : Calculating pairwise distances +[2025-08-02 11:38:11] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 +[2025-08-02 11:38:11] : LOG : 7 anchors +[2025-08-02 11:38:11] : LOG : Building guide tree. +[2025-08-02 11:38:11] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2025-08-02 11:38:11] : LOG : Aligning +[2025-08-02 11:38:11] : LOG : CPU Time: 0.16u 00:00:00.15 Elapsed: 00:00:00.00 ok 7 ok # Required executable for Bio::Tools::Run::Phylo::LVB is not present @@ -2985,7 +3020,7 @@ gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } -Loading sequence file: /tmp/gd8LMVkFUo +Loading sequence file: /tmp/j12gc5H6Oq Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) @@ -2998,7 +3033,7 @@ gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } -Loading sequence file: /tmp/eWgCjzSEwz +Loading sequence file: /tmp/VCtetMsZ0Q Computing posterior matrix: (1) CYS1_DICDI vs. (2) ALEU_HORVU -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (3) CATH_HUMAN -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (4) CATH_RAT -- done. @@ -3034,7 +3069,7 @@ gapOpen[] = { 0.01386300847 0.01386300847 0.006556313485 0.006556313485 } gapExtend[] = { 0.360332042 0.360332042 0.7831901312 0.7831901312 } -Loading sequence file: /tmp/kYdh9u92js +Loading sequence file: /tmp/4cXJPHV_VW Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) @@ -3497,7 +3532,7 @@ t/BEDTools.t (Wstat: 0 Tests: 423 Failed: 0) TODO passed: 20, 57, 75, 110, 155, 190, 208, 226, 262 315, 405 -Files=60, Tests=1454, 241 wallclock secs ( 0.33 usr 0.11 sys + 191.85 cusr 14.31 csys = 206.60 CPU) +Files=60, Tests=1454, 199 wallclock secs ( 0.33 usr 0.10 sys + 196.71 cusr 8.65 csys = 205.79 CPU) Result: PASS mv t.skip/* t rm -rf t.skip @@ -3509,208 +3544,208 @@ Building BioPerl-Run Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_papplmaker.pl.1p Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_neighbor.pl.1p -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_protdist.pl.1p -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_multi_hmmsearch.pl.1p Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_panalysis.pl.1p -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primer3.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSacd.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Ensembl.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/tRNAscanSE.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_multi_hmmsearch.pl.1p +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_protdist.pl.1p Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneNCBIBlast.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genemark.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSApplication.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSacd.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/FootPrinter.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneWUBlast.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Hmmer.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/TribeMCL.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genscan.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Infernal.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Seg.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RepeatMasker.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/ERPIN.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneWUBlast.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Simprot.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Signalp.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Prints.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Eponine.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genewise.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Coil.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Glimmer.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/MCS.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Vista.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Mdust.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Match.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/FootPrinter.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Tmhmm.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Eponine.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RNAMotif.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Glimmer.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genscan.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Coil.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Pseudowise.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Profile.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Vista.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Seg.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Prints.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Promoterwise.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/ERPIN.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/TribeMCL.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genemark.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSApplication.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Simprot.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Signalp.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/tRNAscanSE.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Ensembl.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RepeatMasker.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primate.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Mdust.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Profile.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primer3.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Tmhmm.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus/Config.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools/Config.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools/Config.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/AnalysisFactory/soap.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Analysis/soap.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probcons.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Pal2Nal.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/DBA.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Kalign.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MAFFT.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Amap.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Proda.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Sim4.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Exonerate.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/StandAloneFasta.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MAFFT.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Blat.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probalign.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MSAProbs.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Muscle.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Exonerate.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Gmap.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Blat.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Proda.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Sim4.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Amap.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Lagan.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/SLR.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Raxml.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probcons.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Pal2Nal.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Kalign.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Gmap.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/DBA.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MSAProbs.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/AnalysisFactory/soap.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools/Config.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/LVB.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/FastTree.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phyml.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Gerp.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/SLR.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Semphy.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phyml.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/QuickTree.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/LVB.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/FastTree.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Njtree/Best.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Raxml.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Base.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/FEL.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/REL.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Base.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Consense.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Base.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Molphy/ProtML.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Base.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/REL.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/FEL.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhastCons.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Factory/EMBOSS.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Molphy/ProtML.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Njtree/Best.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools/Config.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/ESoap.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/Result.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/LinkAdaptor.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/ESoap/WSDL.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/DocSumAdaptor.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/Result.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/GQueryAdaptor.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/LinkAdaptor.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/ESoap/WSDL.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::LVB.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Muscle.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::PhylipConf.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Simprot.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Seg.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genemark.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Consense.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::GQueryAdaptor.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Profile.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Amap.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneNCBIBlast.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Eponine.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BlastPlus.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::ERPIN.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Factory/EMBOSS.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Njtree::Best.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Samtools::Config.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Gerp.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::SLR.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::SLAC.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Ensembl.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phyml.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Blat.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genscan.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::tRNAscanSE.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::RNAMotif.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Coil.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::DocSumAdaptor.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Infernal.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genewise.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlast.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Analysis::soap.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Kalign.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Neighbor.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Mdust.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Samtools.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Vista.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::FastTree.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Molphy::ProtML.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Semphy.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor::species.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Samtools::Config.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Raxml.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Probalign.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Sim4.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Signalp.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneWUBlast.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::Modeltest.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::EMBOSSacd.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::StandAloneFasta.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phast::PhyloFit.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::REL.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Tmhmm.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Primate.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor::species.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlast.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Semphy.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::TribeMCL.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::LinkAdaptor.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Mdust.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::BatchFile.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::MSAProbs.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::RepeatMasker.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Njtree::Best.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::EMBOSSApplication.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Proda.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Prints.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::FEL.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawGram.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Lagan.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Glimmer.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Probcons.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneNCBIBlast.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Promoterwise.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Hmmer.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Match.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::ESoap::WSDL.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::LinkAdaptor.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::MCS.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::Base.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::AnalysisFactory::soap.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::Result.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::ESoap.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Kalign.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Raxml.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Amap.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BEDTools::Config.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::Modeltest.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Simprot.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::EMBOSSApplication.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::MSAProbs.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Gmap.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Exonerate.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Glimmer.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus::BlastMethods.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genewise.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor::seq.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BEDTools::Config.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Probalign.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phast::PhastCons.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Base.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Primate.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Tmhmm.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawTree.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus::BlastMethods.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::StandAloneFasta.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Blat.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Infernal.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::QuickTree.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::RNAMotif.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Lagan.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::SeqBoot.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BEDTools.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::ERPIN.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Eponine.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::DocSumAdaptor.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BlastPlus.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::Result.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genemark.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::FootPrinter.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Primer3.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Gerp.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::ESoap.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::REL.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Match.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::EMBOSSacd.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::DBA.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Probcons.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::MAFFT.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::SeqBoot.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::QuickTree.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Proda.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawGram.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genscan.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Seg.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phast::PhyloFit.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::ESoap::WSDL.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Pseudowise.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::TribeMCL.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtPars.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BEDTools.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Sim4.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Base.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Primer3.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::RepeatMasker.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Factory::EMBOSS.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Molphy::ProtML.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::AnalysisFactory::soap.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Exonerate.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Coil.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::LVB.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawTree.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Profile.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Neighbor.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::PhylipConf.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Muscle.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::FastTree.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtDist.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::SLR.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Pal2Nal.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::SLAC.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Vista.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtPars.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::MCS.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::tRNAscanSE.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Prints.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::MAFFT.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Ensembl.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Samtools.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phyml.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Consense.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::FEL.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::GQueryAdaptor.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Hmmer.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_multi_hmmsearch.pl +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_neighbor.pl Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_papplmaker.pl Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_protdist.pl -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_neighbor.pl Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_panalysis.pl dh_install dh_installdocs @@ -3736,12 +3771,14 @@ 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/2298863/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2298863/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/788413 and its subdirectories -I: Current time: Sat Jun 29 03:10:10 -12 2024 -I: pbuilder-time-stamp: 1719673810 +I: removing directory /srv/workspace/pbuilder/2298863 and its subdirectories +I: Current time: Sat Aug 2 11:39:08 +14 2025 +I: pbuilder-time-stamp: 1754084348