Diff of the two buildlogs: -- --- b1/build.log 2023-05-28 16:03:33.810070240 +0000 +++ b2/build.log 2023-05-28 16:13:01.517199904 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun May 28 03:56:51 -12 2023 -I: pbuilder-time-stamp: 1685289411 +I: Current time: Mon May 29 06:03:53 +14 2023 +I: pbuilder-time-stamp: 1685289833 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 [./roary_3.13.0+dfsg.orig.tar.xz] I: copying [./roary_3.13.0+dfsg-1.debian.tar.xz] I: Extracting source -gpgv: Signature made Fri Nov 8 01:51:49 2019 -12 +gpgv: Signature made Sat Nov 9 03:51:49 2019 +14 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./roary_3.13.0+dfsg-1.dsc: no acceptable signature found @@ -30,135 +30,167 @@ dpkg-source: info: applying new-bioperl-require.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/20863/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/726/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 29 06:04 /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/726/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/726/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='8f40b41abc2343328df451ca3b913e36' - 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='20863' - PS1='# ' - PS2='> ' + INVOCATION_ID=4df523b89837431dacd874833753dca1 + 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=726 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.hjOENBnI/pbuilderrc_yMub --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.hjOENBnI/b1 --logfile b1/build.log roary_3.13.0+dfsg-1.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.hjOENBnI/pbuilderrc_jhNe --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.hjOENBnI/b2 --logfile b2/build.log --extrapackages usrmerge roary_3.13.0+dfsg-1.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/20863/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 29 06:04 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/726/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -551,7 +583,7 @@ Get: 297 http://deb.debian.org/debian bookworm/main armhf unzip armhf 6.0-28 [152 kB] Get: 298 http://deb.debian.org/debian bookworm/main armhf xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 299 http://deb.debian.org/debian bookworm/main armhf r-base-core armhf 4.2.2.20221110-2 [25.6 MB] -Fetched 101 MB in 12s (8756 kB/s) +Fetched 101 MB in 4s (24.4 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 ... 19324 files and directories currently installed.) @@ -1790,10 +1822,17 @@ Reading package lists... Building dependency tree... Reading state information... +usrmerge is already the newest version (35). fakeroot is already the newest version (1.31-1.2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/roary-3.13.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../roary_3.13.0+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/726/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/726/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/roary-3.13.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../roary_3.13.0+dfsg-1_source.changes dpkg-buildpackage: info: source package roary dpkg-buildpackage: info: source version 3.13.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -1825,87 +1864,87 @@ Writing Makefile for Bio::Roary Writing MYMETA.yml and MYMETA.json dh_auto_build -D .build/debian-build - cd .build/debian-build && make -j3 + cd .build/debian-build && make -j4 make[1]: Entering directory '/build/roary-3.13.0+dfsg/.build/debian-build' -cp lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm -cp lib/Bio/Roary/AnnotateGroups.pm blib/lib/Bio/Roary/AnnotateGroups.pm -cp lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm -cp lib/Bio/Roary/CommandLine/AssemblyStatistics.pm blib/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm +cp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.pm -cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm -cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm -cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm -cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.pm -cp lib/Bio/Roary/AccessoryClustering.pm blib/lib/Bio/Roary/AccessoryClustering.pm -cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm -cp lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm blib/lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm -cp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm -cp lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm cp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm +cp lib/Bio/Roary/AccessoryClustering.pm blib/lib/Bio/Roary/AccessoryClustering.pm +cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm +cp lib/Bio/Roary/AccessoryBinaryFasta.pm blib/lib/Bio/Roary/AccessoryBinaryFasta.pm cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm -cp lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm blib/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm -cp lib/Bio/Roary/AssemblyStatistics.pm blib/lib/Bio/Roary/AssemblyStatistics.pm -cp lib/Bio/Roary/CommandLine/IterativeCdhit.pm blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pm +cp lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm +cp lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm -cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm -cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.pm +cp lib/Bio/Roary/CommandLine/AssemblyStatistics.pm blib/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm +cp lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm -cp lib/Bio/Roary/AccessoryBinaryFasta.pm blib/lib/Bio/Roary/AccessoryBinaryFasta.pm +cp lib/Bio/Roary/AssemblyStatistics.pm blib/lib/Bio/Roary/AssemblyStatistics.pm cp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm -cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.pm +cp lib/Bio/Roary/AnnotateGroups.pm blib/lib/Bio/Roary/AnnotateGroups.pm +cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm +cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm +cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm +cp lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm blib/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm +cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm +cp lib/Bio/Roary/CommandLine/IterativeCdhit.pm blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pm +cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.pm +cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.pm +cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.pm +cp lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm blib/lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm +cp lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm +cp lib/Bio/Roary/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm +cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.pm +cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm +cp lib/Bio/Roary/External/Mcl.pm blib/lib/Bio/Roary/External/Mcl.pm +cp lib/Bio/Roary/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pm +cp lib/Bio/Roary/External/Mafft.pm blib/lib/Bio/Roary/External/Mafft.pm +cp lib/Bio/Roary/GeneNamesFromGFF.pm blib/lib/Bio/Roary/GeneNamesFromGFF.pm +cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm +cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm +cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm +cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pm cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm -cp lib/Bio/Roary/Output/GroupMultifasta.pm blib/lib/Bio/Roary/Output/GroupMultifasta.pm -cp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm -cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.pm -cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm -cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm -cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm -cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm -cp lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm -cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.pm cp lib/Bio/Roary/MergeMultifastaAlignments.pm blib/lib/Bio/Roary/MergeMultifastaAlignments.pm -cp lib/Bio/Roary/External/IterativeCdhit.pm blib/lib/Bio/Roary/External/IterativeCdhit.pm cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm -cp lib/Bio/Roary/GeneNamesFromGFF.pm blib/lib/Bio/Roary/GeneNamesFromGFF.pm -cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm cp lib/Bio/Roary/Output/EMBLHeaderCommon.pm blib/lib/Bio/Roary/Output/EMBLHeaderCommon.pm -cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm -cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm -cp lib/Bio/Roary/External/Mafft.pm blib/lib/Bio/Roary/External/Mafft.pm -cp lib/Bio/Roary/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pm -cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm cp lib/Bio/Roary/JobRunner/Parallel.pm blib/lib/Bio/Roary/JobRunner/Parallel.pm -cp lib/Bio/Roary/External/Mcl.pm blib/lib/Bio/Roary/External/Mcl.pm -cp lib/Bio/Roary/External/Fasttree.pm blib/lib/Bio/Roary/External/Fasttree.pm -cp lib/Bio/Roary/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm +cp lib/Bio/Roary/External/IterativeCdhit.pm blib/lib/Bio/Roary/External/IterativeCdhit.pm +cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm -cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm -cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm -cp lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm -cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm -cp lib/Bio/Roary/Output/QueryGroups.pm blib/lib/Bio/Roary/Output/QueryGroups.pm -cp lib/Bio/Roary/ReorderSpreadsheet.pm blib/lib/Bio/Roary/ReorderSpreadsheet.pm -cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm -cp lib/Bio/Roary/PresenceAbsenceMatrix.pm blib/lib/Bio/Roary/PresenceAbsenceMatrix.pm +cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm +cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm +cp lib/Bio/Roary/Output/GroupMultifasta.pm blib/lib/Bio/Roary/Output/GroupMultifasta.pm +cp lib/Bio/Roary/External/Fasttree.pm blib/lib/Bio/Roary/External/Fasttree.pm +cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm +cp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm +cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm +cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm -cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm -cp lib/Bio/Roary/SpreadsheetRole.pm blib/lib/Bio/Roary/SpreadsheetRole.pm cp lib/Bio/Roary/UniqueGenesPerSample.pm blib/lib/Bio/Roary/UniqueGenesPerSample.pm -cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm +cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm +cp lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm +cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm +cp lib/Bio/Roary/SampleOrder.pm blib/lib/Bio/Roary/SampleOrder.pm +cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm -cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm -cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm +cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm +cp lib/Bio/Roary/SpreadsheetRole.pm blib/lib/Bio/Roary/SpreadsheetRole.pm +cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm +cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm +cp lib/Bio/Roary/ReorderSpreadsheet.pm blib/lib/Bio/Roary/ReorderSpreadsheet.pm cp lib/Bio/Roary/SequenceLengths.pm blib/lib/Bio/Roary/SequenceLengths.pm -cp lib/Bio/Roary/SampleOrder.pm blib/lib/Bio/Roary/SampleOrder.pm -cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm cp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm +cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm +cp lib/Bio/Roary/PresenceAbsenceMatrix.pm blib/lib/Bio/Roary/PresenceAbsenceMatrix.pm +cp lib/Bio/Roary/Output/QueryGroups.pm blib/lib/Bio/Roary/Output/QueryGroups.pm cp bin/create_pan_genome blib/script/create_pan_genome cp bin/create_pan_genome_plots blib/script/create_pan_genome_plots cp bin/extract_proteome_from_gff blib/script/extract_proteome_from_gff @@ -1913,32 +1952,32 @@ "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome_plots "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/extract_proteome_from_gff cp bin/iterative_cdhit blib/script/iterative_cdhit -cp bin/pan_genome_assembly_statistics blib/script/pan_genome_assembly_statistics -cp bin/pan_genome_core_alignment blib/script/pan_genome_core_alignment "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/iterative_cdhit +cp bin/pan_genome_assembly_statistics blib/script/pan_genome_assembly_statistics "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_assembly_statistics +cp bin/pan_genome_core_alignment blib/script/pan_genome_core_alignment "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_core_alignment cp bin/pan_genome_post_analysis blib/script/pan_genome_post_analysis -cp bin/pan_genome_reorder_spreadsheet blib/script/pan_genome_reorder_spreadsheet -cp bin/parallel_all_against_all_blastp blib/script/parallel_all_against_all_blastp "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_post_analysis +cp bin/pan_genome_reorder_spreadsheet blib/script/pan_genome_reorder_spreadsheet "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_reorder_spreadsheet +cp bin/parallel_all_against_all_blastp blib/script/parallel_all_against_all_blastp "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/parallel_all_against_all_blastp cp bin/protein_alignment_from_nucleotides blib/script/protein_alignment_from_nucleotides -cp bin/query_pan_genome blib/script/query_pan_genome -cp bin/roary blib/script/roary "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/protein_alignment_from_nucleotides +cp bin/query_pan_genome blib/script/query_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/query_pan_genome +cp bin/roary blib/script/roary "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary cp bin/roary-create_pan_genome_plots.R blib/script/roary-create_pan_genome_plots.R -cp bin/roary-pan_genome_reorder_spreadsheet blib/script/roary-pan_genome_reorder_spreadsheet -cp bin/roary-query_pan_genome blib/script/roary-query_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-create_pan_genome_plots.R +cp bin/roary-pan_genome_reorder_spreadsheet blib/script/roary-pan_genome_reorder_spreadsheet "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-pan_genome_reorder_spreadsheet +cp bin/roary-query_pan_genome blib/script/roary-query_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-query_pan_genome cp bin/roary-unique_genes_per_sample blib/script/roary-unique_genes_per_sample -cp bin/transfer_annotation_to_groups blib/script/transfer_annotation_to_groups "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-unique_genes_per_sample +cp bin/transfer_annotation_to_groups blib/script/transfer_annotation_to_groups "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/transfer_annotation_to_groups Manifying 16 pod documents Manifying 26 pod documents @@ -1956,203 +1995,203 @@ dh_testroot dh_prep dh_auto_install -D .build/debian-build --destdir=debian/roary/ - cd .build/debian-build && make -j3 install DESTDIR=/build/roary-3.13.0\+dfsg/debian/roary AM_UPDATE_INFO_DIR=no PREFIX=/usr + cd .build/debian-build && make -j4 install DESTDIR=/build/roary-3.13.0\+dfsg/debian/roary AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/roary-3.13.0+dfsg/.build/debian-build' Manifying 16 pod documents Manifying 26 pod documents Manifying 28 pod documents Manifying 25 pod documents Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PrepareInputFiles.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PostAnalysis.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AssemblyStatistics.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParseGFFAnnotationRole.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/LookupGeneFiles.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/BedFromGFFRole.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryClustering.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterFullClusters.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SpreadsheetRole.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupLabels.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ClustersRole.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterUnknownsFromFasta.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SampleOrder.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFF.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CombinedProteome.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParallelAllAgainstAllBlast.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SequenceLengths.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/UniqueGenesPerSample.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryBinaryFasta.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ContigsToGeneIDsFromGFF.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PostAnalysis.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParseGFFAnnotationRole.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/InflateClusters.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PresenceAbsenceMatrix.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReformatInputGFFs.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFFs.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SplitGroups.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/IterativeCdhit.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnnotateGroups.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryBinaryFasta.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/UniqueGenesPerSample.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReorderSpreadsheet.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ClustersRole.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterUnknownsFromFasta.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupStatistics.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnalyseGroups.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SortFasta.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Exceptions.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SampleOrder.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupLabels.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/OrderGenes.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SequenceLengths.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupStatistics.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterFullClusters.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ChunkFastaFile.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFF.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GeneNamesFromGFF.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SpreadsheetRole.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnnotateGroups.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryClustering.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/MergeMultifastaAlignments.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ContigsToGeneIDsFromGFF.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/NumberOfGroups.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnalyseGroups.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AssemblyStatistics.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/LookupGeneFiles.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/IterativeCdhit.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReformatInputGFFs.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/BedFromGFFRole.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFFs.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Exceptions.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PresenceAbsenceMatrix.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReorderSpreadsheet.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/OrderGenes.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PrepareInputFiles.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/DifferenceBetweenSets.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EMBLHeaderCommon.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaProtein.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastas.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaNucleotide.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupMultifasta.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/QueryGroups.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EmblGroups.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaNucleotide.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaProtein.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/BlastIdentityFrequency.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EMBLHeaderCommon.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastasNucleotide.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/CheckTools.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/PostAnalysis.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/GeneAlignmentFromNucleotides.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mafft.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mcl.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Cdhit.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/IterativeCdhit.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Makeblastdb.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Blastp.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Prank.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Fasttree.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/QC/Report.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Common.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryCoreAlignment.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/AssemblyStatistics.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryPostAnalysis.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/QueryGroups.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/BlastIdentityFrequency.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/NumberOfGroups.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/CreatePanGenome.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/IterativeCdhit.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryCoreAlignment.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/QueryRoary.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/UniqueGenesPerSample.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/QueryRoary.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Common.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Roary.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Local.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/AssemblyStatistics.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/IterativeCdhit.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryPostAnalysis.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/QC/Report.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/GeneAlignmentFromNucleotides.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Fasttree.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mcl.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Prank.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/PostAnalysis.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Cdhit.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/CheckTools.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Blastp.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mafft.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/IterativeCdhit.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Makeblastdb.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Role.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Parallel.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/transfer_annotation_to_groups.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/protein_alignment_from_nucleotides.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_core_alignment.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/parallel_all_against_all_blastp.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Local.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_post_analysis.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_assembly_statistics.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/query_pan_genome.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-query_pan_genome.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-unique_genes_per_sample.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-pan_genome_reorder_spreadsheet.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/iterative_cdhit.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-pan_genome_reorder_spreadsheet.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_assembly_statistics.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome_plots.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/query_pan_genome.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/extract_proteome_from_gff.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/protein_alignment_from_nucleotides.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_core_alignment.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome_plots.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/transfer_annotation_to_groups.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/parallel_all_against_all_blastp.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-unique_genes_per_sample.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_reorder_spreadsheet.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::BlastIdentityFrequency.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CombinedProteome.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnalyseGroups.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Cdhit.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::QC::Report.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReorderSpreadsheet.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PostAnalysis.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastasNucleotide.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Parallel.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::UniqueGenesPerSample.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::CheckTools.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::InflateClusters.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Blastp.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SpreadsheetRole.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::FilterFullClusters.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GroupStatistics.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReformatInputGFFs.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::BlastIdentityFrequency.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::QC::Report.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SampleOrder.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::OrderGenes.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::DifferenceBetweenSets.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::EmblGroups.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::TransferAnnotationToGroups.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::IterativeCdhit.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PresenceAbsenceMatrix.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::GeneAlignmentFromNucleotides.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::FilterUnknownsFromFasta.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ClustersRole.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnnotateGroups.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::AssemblyStatistics.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::CreatePanGenome.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryCoreAlignment.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::PostAnalysis.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GeneNamesFromGFF.3pm -Installing 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-Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ContigsToGeneIDsFromGFF.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::IterativeCdhit.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Fasttree.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Mafft.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::CreatePanGenome.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::UniqueGenesPerSample.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::NumberOfGroups.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::UniqueGenesPerSample.3pm -Installing 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/build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::PostAnalysis.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::LookupGeneFiles.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CombinedProteome.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/protein_alignment_from_nucleotides +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/parallel_all_against_all_blastp Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/create_pan_genome +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_assembly_statistics +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-pan_genome_reorder_spreadsheet Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-unique_genes_per_sample -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/query_pan_genome +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/create_pan_genome_plots Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-create_pan_genome_plots.R +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_reorder_spreadsheet +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/transfer_annotation_to_groups Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_core_alignment -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/extract_proteome_from_gff -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_assembly_statistics +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_post_analysis Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-query_pan_genome -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/transfer_annotation_to_groups -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/parallel_all_against_all_blastp -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_reorder_spreadsheet +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/extract_proteome_from_gff +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/query_pan_genome Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/iterative_cdhit -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_post_analysis -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/create_pan_genome_plots -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/protein_alignment_from_nucleotides +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary make[1]: Leaving directory '/build/roary-3.13.0+dfsg/.build/debian-build' dh_installdocs dh_installchangelogs @@ -2176,12 +2215,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/726/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/726/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/20863 and its subdirectories -I: Current time: Sun May 28 04:03:25 -12 2023 -I: pbuilder-time-stamp: 1685289805 +I: removing directory /srv/workspace/pbuilder/726 and its subdirectories +I: Current time: Mon May 29 06:12:57 +14 2023 +I: pbuilder-time-stamp: 1685290377