Diff of the two buildlogs: -- --- b1/build.log 2023-05-26 16:32:15.405083755 +0000 +++ b2/build.log 2023-05-26 17:03:42.870208867 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 26 04:12:31 -12 2023 -I: pbuilder-time-stamp: 1685117551 +I: Current time: Sat May 27 06:32:34 +14 2023 +I: pbuilder-time-stamp: 1685118754 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./bioperl-run_1.7.3.orig.tar.gz] I: copying [./bioperl-run_1.7.3-9.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Jan 22 01:58:02 2023 -12 +gpgv: Signature made Mon Jan 23 03:58:02 2023 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key @@ -47,135 +47,167 @@ dpkg-source: info: applying adjust-muscle-test.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/9782/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/25633/tmp/hooks/D01_modify_environment starting +debug: Running on virt32c. +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 May 27 06:33 /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/25633/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/25633/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 parallel=3 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.15(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 parallel=4 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='014dad1f9ca346c59737d97c9cbdcc6a' - 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='9782' - PS1='# ' - PS2='> ' + INVOCATION_ID=7088fed9764e4da784e2a9f22f3a9c30 + 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=25633 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.LYwycDbZ/pbuilderrc_YEcm --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.LYwycDbZ/b1 --logfile b1/build.log bioperl-run_1.7.3-9.dsc' - SUDO_GID='114' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.LYwycDbZ/pbuilderrc_EBNv --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.LYwycDbZ/b2 --logfile b2/build.log --extrapackages usrmerge bioperl-run_1.7.3-9.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux jtx1b 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-23-armmp-lpae #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux I: ls -l /bin total 5072 - -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 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 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 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 6460 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 8103 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/9782/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 67632 Sep 21 2022 cat + -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown + -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp + -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 133220 Sep 21 2022 date + -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd + -rwxr-xr-x 1 root root 68104 Sep 21 2022 df + -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir + -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 67548 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount + -rwxr-xr-x 1 root root 128608 Jan 25 04:43 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 64220 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln + -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login + -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls + -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk + -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more + -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount + -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint + -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm + -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 May 27 06:33 sh -> /bin/bash + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty + -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync + -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch + -rwxr-xr-x 1 root root 67548 Sep 21 2022 true + -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount + -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 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 6460 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 8103 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/25633/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -529,7 +561,7 @@ Get: 233 http://deb.debian.org/debian bookworm/main armhf tigr-glimmer armhf 3.02b-6+b1 [261 kB] Get: 234 http://deb.debian.org/debian bookworm/main armhf wise-data all 2.4.1-23 [78.2 kB] Get: 235 http://deb.debian.org/debian bookworm/main armhf wise armhf 2.4.1-23 [792 kB] -Fetched 165 MB in 15s (11.3 MB/s) +Fetched 165 MB in 5s (33.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (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 ... 19326 files and directories currently installed.) @@ -1508,8 +1540,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/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_1.7.3-9_source.changes +I: user script /srv/workspace/pbuilder/25633/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/25633/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/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_1.7.3-9_source.changes dpkg-buildpackage: info: source package bioperl-run dpkg-buildpackage: info: source version 1.7.3-9 dpkg-buildpackage: info: source distribution unstable @@ -1575,7 +1618,7 @@ gapOpen[] = { 0.01993141696 0.01993141696 } gapExtend[] = { 0.7943345308 0.7943345308 } -Loading sequence file: /tmp/G_rJ0qQE8A +Loading sequence file: /tmp/evig9lRh_4 Computing posterior matrices Building DAG Starting the sequence annealing process @@ -1617,7 +1660,7 @@ 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/yHviatKER_/XOzqGMea5x.bed' consistent with claim for 'annotate' +ok 14 - file format of '/tmp/dvVb_hmyQc/RxHHHMPxPg.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' @@ -1654,7 +1697,7 @@ 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/XJqQMpxVmq/YqL11MR91M.bed' consistent with claim for 'overlap' +ok 51 - file format of '/tmp/tnMp24q5TQ/903agslVgk.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' @@ -1672,7 +1715,7 @@ 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/E_975RvYtr/X32rXPCXZj.bed' consistent with claim for 'bam_to_bed' +ok 69 - file format of '/tmp/iHT1jbQ52G/Gic2EaPXno.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' @@ -1707,7 +1750,7 @@ 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/E5EC6sMM9d/ElGIy_qPEk.bedpe' consistent with claim for 'pair_to_pair' +ok 104 - file format of '/tmp/FiOigjW2N6/mLcwksB3bx.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' @@ -1787,7 +1830,7 @@ 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/h3gkj10_9L/PI5xLn5VWE.bed' consistent with claim for 'group_by' +ok 184 - file format of '/tmp/kb6DXccoMF/D40JmAEkLL.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' @@ -1805,7 +1848,7 @@ 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/yoXUB0QnZD/1DnjIPHNLY.bed' consistent with claim for 'shuffle' +ok 202 - file format of '/tmp/P09bV5wqxU/Jn1_fSYjzG.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' @@ -1823,7 +1866,7 @@ 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/NZoZVQtDhE/ush32a0ANz.bed' consistent with claim for 'b12_to_b6' +ok 220 - file format of '/tmp/br8EzKO_Bj/BJpmp9eMSB.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' @@ -1863,7 +1906,7 @@ 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/8OJxWlrbTS/QGB53AZFXk.bed' consistent with claim for 'slop' +ok 256 - file format of '/tmp/uA7QP27z7o/6yA6muYT7q.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' @@ -1881,7 +1924,7 @@ 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/Pn4DH7askU/X6hoPd8U6r.bedpe' consistent with claim for 'closest' +ok 274 - file format of '/tmp/0moMIE7Af5/CmRrhp0SoW.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' @@ -1916,7 +1959,7 @@ 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/_Z0Kj1VGOU/4h_ihfzj7y.bed' consistent with claim for 'sort' +ok 309 - file format of '/tmp/9pZwoi6BRs/mUVD8u6uJe.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' @@ -1934,7 +1977,7 @@ 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/TqEGhirJ9h/RnnDZqGnnk.bed' consistent with claim for 'complement' +ok 327 - file format of '/tmp/Dn9YMDEAaH/ROfzcsVGFC.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' @@ -1970,7 +2013,7 @@ 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/9Q2PiJdt1X/8RVgE3htlj.bed' consistent with claim for 'subtract' +ok 363 - file format of '/tmp/g5Ac29Jed1/aJt0LAQdWb.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' @@ -1992,7 +2035,7 @@ 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/toTPdM1HDY/fScpHwOUI1.bed' consistent with claim for 'coverage' +ok 381 - file format of '/tmp/o86MDz3lgq/pZvBY8N0I1.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' @@ -2014,7 +2057,7 @@ 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/8inyBAGYIc/SV3CiRGeWz.bed' consistent with claim for 'merge' +ok 399 - file format of '/tmp/dxtd40HZ_X/4LDvB9W4Xv.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' @@ -2032,7 +2075,7 @@ 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/Q6Q5pdIou2/bUKJ6PPjia.bedpe' consistent with claim for 'window' +ok 417 - file format of '/tmp/v_cGF8mNJI/vnJvk6ifFk.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' @@ -2668,15 +2711,15 @@ Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795 -[2023-05-26 04:30:22] : LOG : Detected protein sequences. -[2023-05-26 04:30:22] : LOG : Read 7 sequences from standard input. -[2023-05-26 04:30:22] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -[2023-05-26 04:30:22] : LOG : Calculating pairwise distances -[2023-05-26 04:30:22] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -[2023-05-26 04:30:22] : LOG : Building guide tree. -[2023-05-26 04:30:22] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -[2023-05-26 04:30:22] : LOG : Aligning -[2023-05-26 04:30:22] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 +[2023-05-27 06:57:42] : LOG : Detected protein sequences. +[2023-05-27 06:57:42] : LOG : Read 7 sequences from standard input. +[2023-05-27 06:57:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2023-05-27 06:57:42] : LOG : Calculating pairwise distances +[2023-05-27 06:57:42] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +[2023-05-27 06:57:42] : LOG : Building guide tree. +[2023-05-27 06:57:42] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +[2023-05-27 06:57:42] : LOG : Aligning +[2023-05-27 06:57:42] : LOG : CPU Time: 0.07u 00:00:00.06 Elapsed: 00:00:00.00 ok 5 ok 6 @@ -2695,15 +2738,15 @@ Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795 -[2023-05-26 04:30:23] : LOG : Detected protein sequences. -[2023-05-26 04:30:23] : LOG : Read 7 sequences from standard input. -[2023-05-26 04:30:23] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -[2023-05-26 04:30:23] : LOG : Calculating pairwise distances -[2023-05-26 04:30:23] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -[2023-05-26 04:30:23] : LOG : Building guide tree. -[2023-05-26 04:30:23] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -[2023-05-26 04:30:23] : LOG : Aligning -[2023-05-26 04:30:23] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 +[2023-05-27 06:57:42] : LOG : Detected protein sequences. +[2023-05-27 06:57:42] : LOG : Read 7 sequences from standard input. +[2023-05-27 06:57:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2023-05-27 06:57:42] : LOG : Calculating pairwise distances +[2023-05-27 06:57:42] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +[2023-05-27 06:57:42] : LOG : Building guide tree. +[2023-05-27 06:57:42] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +[2023-05-27 06:57:42] : LOG : Aligning +[2023-05-27 06:57:42] : LOG : CPU Time: 0.07u 00:00:00.06 Elapsed: 00:00:00.00 ok 7 ok # Required executable for Bio::Tools::Run::Phylo::LVB is not present @@ -3163,7 +3206,7 @@ gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } -Loading sequence file: /tmp/RLCQmcPV0G +Loading sequence file: /tmp/5Dxt9qyglh Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) @@ -3176,7 +3219,7 @@ gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } -Loading sequence file: /tmp/qSggP8YMDx +Loading sequence file: /tmp/ReRQUUSWi_ 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. @@ -3212,7 +3255,7 @@ gapOpen[] = { 0.01386300847 0.01386300847 0.006556313485 0.006556313485 } gapExtend[] = { 0.360332042 0.360332042 0.7831901312 0.7831901312 } -Loading sequence file: /tmp/L4b02zlFyY +Loading sequence file: /tmp/hxwKl6tQXI Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) @@ -3672,7 +3715,7 @@ t/BEDTools.t (Wstat: 0 Tests: 423 Failed: 0) TODO passed: 20, 57, 75, 88, 110, 155, 190, 208, 226 262, 280, 315, 333, 405 -Files=60, Tests=1652, 928 wallclock secs ( 0.70 usr 0.24 sys + 831.46 cusr 29.54 csys = 861.94 CPU) +Files=60, Tests=1652, 1579 wallclock secs ( 0.92 usr 0.42 sys + 841.91 cusr 27.23 csys = 870.48 CPU) Result: PASS mv t.skip/* t rm -rf t.skip @@ -3682,210 +3725,210 @@ dh_auto_install /usr/bin/perl Build install --destdir /build/bioperl-run-1.7.3/debian/tmp --create_packlist 0 Building BioPerl-Run +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_multi_hmmsearch.pl.1p +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_neighbor.pl.1p Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_papplmaker.pl.1p Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_protdist.pl.1p -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_neighbor.pl.1p Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_panalysis.pl.1p -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_multi_hmmsearch.pl.1p -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Profile.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primer3.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/FootPrinter.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Pseudowise.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genemark.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Glimmer.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Match.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneWUBlast.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Infernal.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Eponine.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Signalp.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RNAMotif.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSApplication.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Tmhmm.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RepeatMasker.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Infernal.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genewise.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Coil.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Simprot.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Vista.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Hmmer.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Ensembl.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/TribeMCL.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/tRNAscanSE.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Seg.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Signalp.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneNCBIBlast.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Profile.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Eponine.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genemark.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Prints.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Coil.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/ERPIN.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Pseudowise.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primate.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSacd.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Promoterwise.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/MCS.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/ERPIN.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSApplication.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Simprot.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Mdust.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Tmhmm.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genewise.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Ensembl.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genscan.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Hmmer.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Glimmer.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/FootPrinter.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RepeatMasker.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RNAMotif.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneNCBIBlast.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/AnalysisFactory/soap.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Muscle.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/StandAloneFasta.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probalign.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genscan.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneWUBlast.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Promoterwise.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Mdust.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/MCS.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Seg.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Sim4.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MSAProbs.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Amap.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Exonerate.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MAFFT.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Kalign.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Gmap.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Pal2Nal.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Blat.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probalign.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Lagan.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Pal2Nal.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/StandAloneFasta.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Muscle.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Kalign.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Proda.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Exonerate.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MSAProbs.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MAFFT.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/DBA.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Blat.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probcons.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools/Config.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus/Config.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Analysis/soap.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Raxml.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Semphy.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Amap.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Gmap.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/QuickTree.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phyml.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/FastTree.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Gerp.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/LVB.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phyml.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/SLR.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Molphy/ProtML.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhastCons.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/LVB.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Semphy.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/FastTree.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Raxml.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Base.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/FEL.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/REL.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Consense.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Base.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Consense.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Base.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/REL.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/FEL.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Base.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhastCons.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Molphy/ProtML.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Njtree/Best.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools/Config.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/AnalysisFactory/soap.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools/Config.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus/Config.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Analysis/soap.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Factory/EMBOSS.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/ESoap.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/LinkAdaptor.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/GQueryAdaptor.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/Result.pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/DocSumAdaptor.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/GQueryAdaptor.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/ESoap/WSDL.pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Factory/EMBOSS.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Pal2Nal.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genscan.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtPars.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Simprot.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::FEL.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtDist.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Primer3.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::EMBOSSacd.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Vista.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::EMBOSSApplication.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::QuickTree.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Raxml.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlast.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::EMBOSSApplication.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BEDTools::Config.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Signalp.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::MSAProbs.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BlastPlus.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor::species.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::MCS.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phast::PhyloFit.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Probalign.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::PhylipConf.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Samtools::Config.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Glimmer.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Amap.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Match.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Blat.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawGram.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Proda.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::TribeMCL.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::ESoap.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::RNAMotif.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus::BlastMethods.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Profile.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Prints.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::DBA.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::FastTree.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Analysis::soap.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Seg.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::ESoap::WSDL.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::Modeltest.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BEDTools.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Muscle.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Sim4.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Tmhmm.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::SLR.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawTree.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Neighbor.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::SeqBoot.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::MCS.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::tRNAscanSE.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phyml.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::ESoap::WSDL.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Sim4.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Kalign.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Primate.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::StandAloneFasta.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Proda.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor::species.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Neighbor.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genemark.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Probcons.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::REL.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Analysis::soap.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Samtools.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phast::PhyloFit.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phast::PhastCons.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Vista.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BEDTools::Config.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Gmap.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::DocSumAdaptor.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::BatchFile.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Profile.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Factory::EMBOSS.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities.3pm -Installing 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+Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawTree.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Consense.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::PhylipConf.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Gerp.3pm +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_panalysis.pl Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_protdist.pl -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_papplmaker.pl Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_multi_hmmsearch.pl -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_panalysis.pl +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_papplmaker.pl Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_neighbor.pl dh_install dh_installdocs @@ -3902,8 +3945,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libbio-perl-run-perl' in '../libbio-perl-run-perl_1.7.3-9_all.deb'. dpkg-deb: building package 'bioperl-run' in '../bioperl-run_1.7.3-9_all.deb'. +dpkg-deb: building package 'libbio-perl-run-perl' in '../libbio-perl-run-perl_1.7.3-9_all.deb'. dpkg-genbuildinfo --build=binary -O../bioperl-run_1.7.3-9_armhf.buildinfo dpkg-genchanges --build=binary -O../bioperl-run_1.7.3-9_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3911,12 +3954,14 @@ 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/25633/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/25633/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/9782 and its subdirectories -I: Current time: Fri May 26 04:32:08 -12 2023 -I: pbuilder-time-stamp: 1685118728 +I: removing directory /srv/workspace/pbuilder/25633 and its subdirectories +I: Current time: Sat May 27 07:03:38 +14 2023 +I: pbuilder-time-stamp: 1685120618