Running as unit: rb-build-amd64_34-36868.service ==================================================================================== Mon Nov 25 07:32:52 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_34) on jenkins, called using "infom02-amd64 infom01-amd64" as arguments. Mon Nov 25 07:32:52 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-u22m2YjF" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Nov 25 07:32:53 UTC 2024 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Mon Nov 25 07:32:53 UTC 2024 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-k76po6' Mon Nov 25 07:32:53 UTC 2024 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Mon Nov 25 07:32:53 UTC 2024 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-fOPqOj' ok, let's check if roary is building anywhere yet… ok, roary is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of roary in trixie on amd64 on jenkins now. 1st build will be done on infom02-amd64.debian.net. 2nd build will be done on infom01-amd64.debian.net. ============================================================================= Mon Nov 25 07:32:59 UTC 2024 I: starting to build roary/trixie/amd64 on jenkins on '2024-11-25 07:32' Mon Nov 25 07:32:59 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_34/36868/console.log 1732519979 amd64 trixie roary Mon Nov 25 07:32:59 UTC 2024 I: Downloading source for trixie/roary=3.13.0+dfsg-1 --2024-11-25 07:32:59-- http://deb.debian.org/debian/pool/main/r/roary/roary_3.13.0%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2501 (2.4K) [text/prs.lines.tag] Saving to: ‘roary_3.13.0+dfsg-1.dsc’ 0K .. 100% 299M=0s 2024-11-25 07:32:59 (299 MB/s) - ‘roary_3.13.0+dfsg-1.dsc’ saved [2501/2501] --2024-11-25 07:32:59-- http://deb.debian.org/debian/pool/main/r/roary/roary_3.13.0%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2501 (2.4K) [text/prs.lines.tag] Saving to: ‘roary_3.13.0+dfsg-1.dsc’ 0K .. 100% 299M=0s 2024-11-25 07:32:59 (299 MB/s) - ‘roary_3.13.0+dfsg-1.dsc’ saved [2501/2501] Mon Nov 25 07:33:00 UTC 2024 I: roary_3.13.0+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: roary Binary: roary Architecture: all Version: 3.13.0+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Sascha Steinbiss Homepage: http://sanger-pathogens.github.io/Roary/ Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/roary Vcs-Git: https://salsa.debian.org/med-team/roary.git Testsuite: autopkgtest Build-Depends: debhelper (>= 12~), dh-dist-zilla, libdist-zilla-plugin-podweaver-perl, bioperl (>= 1.7.4), libarray-utils-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, mafft, fasttree Build-Depends-Indep: perl Package-List: roary deb science optional arch=all Checksums-Sha1: ec41e9813412b1e168328131cabc91ae1ea06162 207348 roary_3.13.0+dfsg.orig.tar.xz 00f683879e2465a2f91d2214d806d3209ace2dcd 6612 roary_3.13.0+dfsg-1.debian.tar.xz Checksums-Sha256: 5450fe6f4bab8b27829d2ec6836c0a8c9a38d42b3891fab29b10a9587dee2fd1 207348 roary_3.13.0+dfsg.orig.tar.xz f316c055c6c368084b80133c39749d78c70f229ecb1e5a8134ee35c4e7d1e830 6612 roary_3.13.0+dfsg-1.debian.tar.xz Files: fe3935332843c9d4dfb4d4c5cb9080a6 207348 roary_3.13.0+dfsg.orig.tar.xz 5e189111d062819d48d66eff830c7c36 6612 roary_3.13.0+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAl3FcvUACgkQ6NN64vCf SHIkCw//bXPQle1oBgKz8vCLiooiAPBtRcz6YLBaHWO3ZdkMiGa2H/05t98nAaxE luasIS44vFXJggCWEce7DvGAhu6VPlLjhZirZfHlGl/PISyJsYvH2/chaYbaslVF Ql/KG0lx5NUDp1aaPtoRrv2KDcqeJsTNXRmyel3yuSwsHJvtPee4f1aBIV0QjVDB 3NJu5hUCTKtC9P42Qaz/YrXJKoWIEI2jl8oaj8PygRSvL+238bnowDPTJNyQmS/j FiubtiuwsDNiKglVNHO8nyLJG7+0MinpKYl5jGtT3sqrASZsLgE01YXY0kS/05el KSEGIIa7yAl0d/k/x9YPx7svWwX0UfomWlrmSI++09r8OAqFbswi0wzXS75hnO7w 7hkKL9VfddKkSDol+ILRKJM6qQuy+fTlQz8HOWNXpXYsEqnOMQ0nHNW9d7nNa38f pjkoPbbqtrMZL6YOuygb3aIuTXfGjZMa3j8pemnx7K8fm2epiefFVYFia46u+bsJ KEtx8vwfYp+voak/r6Edjob/J7EeFI46oYfy5o2u3TGnQ3XOQM00m8pv3os/+g7P dn6NprfUztjCEpzpYfQAFSxqpC/yuPfnbLpy5+y1iqqy3BGXdMBee+Ej9M0p0hRq UD+PbkpQTLTqGjHEymTL8bwTsYARC7V/LQhbyalFKCPBm6fc+Vc= =4hyZ -----END PGP SIGNATURE----- Mon Nov 25 07:33:00 UTC 2024 I: Checking whether the package is not for us Mon Nov 25 07:33:00 UTC 2024 I: Starting 1st build on remote node infom02-amd64.debian.net. Mon Nov 25 07:33:00 UTC 2024 I: Preparing to do remote build '1' on infom02-amd64.debian.net. Mon Nov 25 07:33:00 UTC 2024 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Mon Nov 25 07:33:00 UTC 2024 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-5zbHKw' ==================================================================================== Sun Dec 28 13:56:01 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom02-amd64, called using "1 roary trixie /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ 3.13.0+dfsg-1" as arguments. Sun Dec 28 13:56:01 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-cPytVOA6" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun Dec 28 13:56:01 UTC 2025 I: Downloading source for trixie/roary=3.13.0+dfsg-1 Reading package lists... NOTICE: 'roary' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/roary.git Please use: git clone https://salsa.debian.org/med-team/roary.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 216 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main roary 3.13.0+dfsg-1 (dsc) [2501 B] Get:2 http://deb.debian.org/debian trixie/main roary 3.13.0+dfsg-1 (tar) [207 kB] Get:3 http://deb.debian.org/debian trixie/main roary 3.13.0+dfsg-1 (diff) [6612 B] Fetched 216 kB in 0s (2167 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'roary' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/roary.git Please use: git clone https://salsa.debian.org/med-team/roary.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 216 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main roary 3.13.0+dfsg-1 (dsc) [2501 B] Get:2 http://deb.debian.org/debian trixie/main roary 3.13.0+dfsg-1 (tar) [207 kB] Get:3 http://deb.debian.org/debian trixie/main roary 3.13.0+dfsg-1 (diff) [6612 B] Fetched 216 kB in 0s (2167 kB/s) Download complete and in download only mode ============================================================================= Building roary in trixie on amd64 on infom02-amd64 now. Date: Sun Dec 28 13:56:01 UTC 2025 Date UTC: Sun Dec 28 13:56:01 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Sun Dec 28 01:56:01 -12 2025 I: pbuilder-time-stamp: 1766930161 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [roary_3.13.0+dfsg-1.dsc] 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 13:51:49 2019 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 dpkg-source: info: extracting roary in roary-3.13.0+dfsg dpkg-source: info: unpacking roary_3.13.0+dfsg.orig.tar.xz dpkg-source: info: unpacking roary_3.13.0+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying rename_R_script.patch dpkg-source: info: applying use-dz-starter.patch dpkg-source: info: applying use-debian-perl-path.patch dpkg-source: info: applying new-bioperl-require.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2221921/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='ada19eb8f6c441e19002ecde773b8ad5' 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='2221921' PS1='# ' PS2='> ' 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.oU2ie3pZ/pbuilderrc_IGIj --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/b1 --logfile b1/build.log roary_3.13.0+dfsg-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom02-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2221921/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 12~), dh-dist-zilla, libdist-zilla-plugin-podweaver-perl, bioperl (>= 1.7.4), libarray-utils-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, mafft, fasttree, perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19969 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 12~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-dist-zilla; however: Package dh-dist-zilla is not installed. pbuilder-satisfydepends-dummy depends on libdist-zilla-plugin-podweaver-perl; however: Package libdist-zilla-plugin-podweaver-perl is not installed. pbuilder-satisfydepends-dummy depends on bioperl (>= 1.7.4); however: Package bioperl is not installed. pbuilder-satisfydepends-dummy depends on libarray-utils-perl; however: Package libarray-utils-perl is not installed. pbuilder-satisfydepends-dummy depends on libenv-path-perl; however: Package libenv-path-perl is not installed. pbuilder-satisfydepends-dummy depends on libexception-class-perl; however: Package libexception-class-perl is not installed. pbuilder-satisfydepends-dummy depends on libfile-find-rule-perl; however: Package libfile-find-rule-perl is not installed. pbuilder-satisfydepends-dummy depends on libfile-grep-perl; however: Package libfile-grep-perl is not installed. pbuilder-satisfydepends-dummy depends on libfile-slurper-perl; however: Package libfile-slurper-perl is not installed. pbuilder-satisfydepends-dummy depends on libfile-which-perl; however: Package libfile-which-perl is not installed. pbuilder-satisfydepends-dummy depends on libfindbin-libs-perl; however: Package libfindbin-libs-perl is not installed. pbuilder-satisfydepends-dummy depends on libgraph-perl; however: Package libgraph-perl is not installed. pbuilder-satisfydepends-dummy depends on libgraph-readwrite-perl; however: Package libgraph-readwrite-perl is not installed. pbuilder-satisfydepends-dummy depends on liblog-log4perl-perl; however: Package liblog-log4perl-perl is not installed. pbuilder-satisfydepends-dummy depends on libmoose-perl; however: Package libmoose-perl is not installed. pbuilder-satisfydepends-dummy depends on libperlio-utf8-strict-perl; however: Package libperlio-utf8-strict-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-most-perl; however: Package libtest-most-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-file-perl; however: Package libtest-file-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-files-perl; however: Package libtest-files-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-output-perl; however: Package libtest-output-perl is not installed. pbuilder-satisfydepends-dummy depends on libtext-csv-perl; however: Package libtext-csv-perl is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on cd-hit; however: Package cd-hit is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on mcl; however: Package mcl is not installed. pbuilder-satisfydepends-dummy depends on parallel; however: Package parallel is not installed. pbuilder-satisfydepends-dummy depends on prank; however: Package prank is not installed. pbuilder-satisfydepends-dummy depends on r-base-core; however: Package r-base-core is not installed. pbuilder-satisfydepends-dummy depends on mafft; however: Package mafft is not installed. pbuilder-satisfydepends-dummy depends on fasttree; however: Package fasttree is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bioperl{a} bsdextrautils{a} ca-certificates{a} cd-hit{a} debhelper{a} dh-autoreconf{a} dh-dist-zilla{a} dh-strip-nondeterminism{a} dwz{a} fasttree{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libalgorithm-c3-perl{a} libalgorithm-diff-perl{a} libaliased-perl{a} libapp-cmd-perl{a} libarchive-zip-perl{a} libarray-utils-perl{a} libautobox-perl{a} libb-hooks-endofscope-perl{a} libb-hooks-op-check-perl{a} libbio-perl-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcapture-tiny-perl{a} libcarp-clan-perl{a} libclass-c3-perl{a} libclass-data-inheritable-perl{a} libclass-inspector-perl{a} libclass-load-perl{a} libclass-load-xs-perl{a} libclass-method-modifiers-perl{a} libclass-singleton-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcom-err2{a} libconfig-ini-perl{a} libconfig-mvp-perl{a} libconfig-mvp-reader-ini-perl{a} libconst-fast-perl{a} libcpan-uploader-perl{a} libcpanel-json-xs-perl{a} libcurl4t64{a} libdata-compare-perl{a} libdata-optlist-perl{a} libdata-section-perl{a} libdata-stag-perl{a} libdatetime-locale-perl{a} libdatetime-perl{a} libdatetime-timezone-perl{a} libdatrie1{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-globaldestruction-perl{a} libdevel-overloadinfo-perl{a} libdevel-stacktrace-perl{a} libdist-checkconflicts-perl{a} libdist-zilla-perl{a} libdist-zilla-plugin-podweaver-perl{a} libdynaloader-functions-perl{a} libelf1t64{a} libencode-locale-perl{a} libenv-path-perl{a} libeval-closure-perl{a} libexception-class-perl{a} libexpat1{a} libexporter-tiny-perl{a} libfile-chdir-perl{a} libfile-copy-recursive-perl{a} libfile-find-rule-perl{a} libfile-grep-perl{a} libfile-listing-perl{a} libfile-pushd-perl{a} libfile-sharedir-install-perl{a} libfile-sharedir-perl{a} libfile-slurper-perl{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libfindbin-libs-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgetopt-long-descriptive-perl{a} libgfortran5{a} libglib2.0-0t64{a} libgraph-perl{a} libgraph-readwrite-perl{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhash-merge-simple-perl{a} libheap-perl{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libice6{a} libicu72{a} libimport-into-perl{a} libio-all-perl{a} libio-html-perl{a} libio-socket-ssl-perl{a} libio-string-perl{a} libio-stringy-perl{a} libio-tiecombine-perl{a} libjbig0{a} libjpeg62-turbo{a} libjson-maybexs-perl{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap-2.5-0{a} liblerc4{a} liblist-moreutils-perl{a} liblist-moreutils-xs-perl{a} liblmdb0{a} liblog-dispatch-array-perl{a} liblog-dispatch-perl{a} liblog-dispatchouli-perl{a} liblog-log4perl-perl{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmixin-linewise-perl{a} libmodule-implementation-perl{a} libmodule-path-perl{a} libmodule-pluggable-perl{a} libmodule-runtime-conflicts-perl{a} libmodule-runtime-perl{a} libmoo-perl{a} libmoose-autobox-perl{a} libmoose-perl{a} libmoosex-lazyrequire-perl{a} libmoosex-oneargnew-perl{a} libmoosex-role-parameterized-perl{a} libmoosex-setonce-perl{a} libmoosex-types-perl{a} libmoosex-types-perl-perl{a} libmro-compat-perl{a} libnamespace-autoclean-perl{a} libnamespace-clean-perl{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libnsl2{a} libnumber-compare-perl{a} libpackage-deprecationmanager-perl{a} libpackage-stash-perl{a} libpackage-stash-xs-perl{a} libpadwalker-perl{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libparams-classify-perl{a} libparams-util-perl{a} libparams-validate-perl{a} libparams-validationcompiler-perl{a} libparse-yapp-perl{a} libpath-tiny-perl{a} libperl-prereqscanner-perl{a} libperl-version-perl{a} libperlio-utf8-strict-perl{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpod-elemental-perl{a} libpod-elemental-perlmunger-perl{a} libpod-eventual-perl{a} libpod-weaver-perl{a} libppi-perl{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librole-hasmessage-perl{a} librole-identifiable-perl{a} librole-tiny-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libscope-guard-perl{a} libsensors-config{a} libsensors5{a} libset-object-perl{a} libsharpyuv0{a} libsm6{a} libsoftware-license-perl{a} libspecio-perl{a} libspiffy-perl{a} libssh2-1t64{a} libstring-errf-perl{a} libstring-flogger-perl{a} libstring-formatter-perl{a} libstring-rewriteprefix-perl{a} libstring-truncate-perl{a} libsub-exporter-formethods-perl{a} libsub-exporter-globexporter-perl{a} libsub-exporter-perl{a} libsub-exporter-progressive-perl{a} libsub-identify-perl{a} libsub-install-perl{a} libsub-name-perl{a} libsub-quote-perl{a} libsub-uplevel-perl{a} libsyntax-keyword-junction-perl{a} libtask-weaken-perl{a} libtcl8.6{a} libterm-encoding-perl{a} libterm-readkey-perl{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-file-perl{a} libtest-files-perl{a} libtest-most-perl{a} libtest-output-perl{a} libtest-warn-perl{a} libtest2-suite-perl{a} libtext-csv-perl{a} libtext-diff-perl{a} libtext-glob-perl{a} libtext-template-perl{a} libthai-data{a} libthai0{a} libthrowable-perl{a} libtie-ixhash-perl{a} libtiff6{a} libtimedate-perl{a} libtingea0{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtry-tiny-perl{a} libtype-tiny-perl{a} libuchardet0{a} liburi-perl{a} libuv1t64{a} libvariable-magic-perl{a} libwebp7{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml-parser-perl{a} libxml-writer-perl{a} libxml2{a} libxrender1{a} libxss1{a} libxstring-perl{a} libxt6t64{a} libyaml-tiny-perl{a} m4{a} mafft{a} man-db{a} mcl{a} media-types{a} ncbi-blast+{a} ncbi-data{a} netbase{a} openssl{a} parallel{a} perl-openssl-defaults{a} po-debconf{a} prank{a} procps{a} python3{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} r-base-core{a} readline-common{a} sensible-utils{a} sysstat{a} tzdata{a} ucf{a} unzip{a} x11-common{a} xdg-utils{a} zip{a} The following packages are RECOMMENDED but will NOT be installed: bash-completion bcron bioperl-run cpanminus cron cronie curl devscripts krb5-locales libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libarchive-tar-wrapper-perl libarray-compare-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libcache-cache-perl libclass-c3-xs-perl libconvert-binary-c-perl libdata-dump-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libdevel-lexalias-perl libdevel-partialdump-perl libfile-mimeinfo-perl libgd-perl libglib2.0-data libgraphviz-perl libhtml-form-perl libhtml-format-perl libhtml-tableextract-perl libhttp-daemon-perl libio-compress-brotli-perl libipc-shareable-perl libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libmailtools-perl libmime-lite-perl libmldbm-perl libnet-dbus-perl libpod-coverage-trustpod-perl libpostscript-perl libref-util-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl libterm-readline-gnu-perl libterm-ui-perl libtest-cpan-meta-perl libtest-pod-coverage-perl libtest-pod-perl libtext-csv-xs-perl libtype-tiny-xs-perl libunicode-utf8-perl libx11-protocol-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libyaml-perl linux-sysctl-defaults lynx perl-doc perl-tk psmisc publicsuffix r-base-dev r-doc-html r-recommended ruby shared-mime-info systemd systemd-cron wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 315 newly installed, 0 to remove and 0 not upgraded. Need to get 116 MB of archives. After unpacking 392 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libclass-data-inheritable-perl all 0.10-1 [8632 B] Get: 48 http://deb.debian.org/debian trixie/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 bioperl all 1.7.8-1 [246 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 cd-hit amd64 4.8.1-4 [522 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 67 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libparams-util-perl amd64 1.102-3+b1 [24.4 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.009-1+b1 [16.2 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.5 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libclass-load-perl all 0.25-2 [15.3 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libio-stringy-perl all 2.113-2 [48.3 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libparams-validate-perl amd64 1.31-2+b3 [63.4 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libgetopt-long-descriptive-perl all 0.115-1 [27.6 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libio-tiecombine-perl all 1.005-3 [10.8 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libmodule-pluggable-perl all 5.2-5 [23.0 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libstring-rewriteprefix-perl all 0.009-1 [7140 B] Get: 94 http://deb.debian.org/debian trixie/main amd64 libapp-cmd-perl all 0.336-1 [65.8 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libscope-guard-perl all 0.21-2 [8212 B] Get: 96 http://deb.debian.org/debian trixie/main amd64 libautobox-perl amd64 3.0.2-1+b1 [33.0 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libperlio-utf8-strict-perl amd64 0.010-1+b3 [11.4 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libmixin-linewise-perl all 0.111-1 [14.4 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libconfig-ini-perl all 1:0.029-1 [23.7 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libclass-load-xs-perl amd64 0.10-2+b4 [14.2 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get: 102 http://deb.debian.org/debian trixie/main amd64 libdevel-globaldestruction-perl all 0.14-4 [7144 B] Get: 103 http://deb.debian.org/debian trixie/main amd64 libalgorithm-c3-perl all 0.11-2 [10.8 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libclass-c3-perl all 0.35-2 [21.0 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libmro-compat-perl all 0.15-2 [11.8 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libdevel-overloadinfo-perl all 0.007-1 [7896 B] Get: 107 http://deb.debian.org/debian trixie/main amd64 libeval-closure-perl all 0.14-3 [11.2 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libdist-checkconflicts-perl all 0.11-2 [10.5 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-conflicts-perl all 0.003-2 [7356 B] Get: 110 http://deb.debian.org/debian trixie/main amd64 libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libpackage-stash-xs-perl amd64 0.30-1+b4 [20.9 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libmoose-perl amd64 2.2207-1+b2 [766 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libvariable-magic-perl amd64 0.64-1+b1 [44.9 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libsub-identify-perl amd64 0.14-3+b3 [11.3 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libsub-name-perl amd64 0.27-1+b3 [12.5 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libnamespace-autoclean-perl all 0.31-1 [13.8 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libmoosex-role-parameterized-perl all 1.11-2 [41.9 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libmoosex-oneargnew-perl all 0.007-1 [8180 B] Get: 121 http://deb.debian.org/debian trixie/main amd64 libcpanel-json-xs-perl amd64 4.38-1+b1 [129 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libjson-maybexs-perl all 1.004008-1 [12.9 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libstring-formatter-perl all 1.235-1 [22.1 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libstring-errf-perl all 0.009-1 [12.9 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 librole-hasmessage-perl all 0.007-1 [9112 B] Get: 127 http://deb.debian.org/debian trixie/main amd64 librole-identifiable-perl all 0.009-1 [10.4 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b4 [36.1 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libthrowable-perl all 1.001-2 [15.7 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libtie-ixhash-perl all 1.23-4 [11.7 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libconfig-mvp-perl all 2.200013-1 [47.1 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libconfig-mvp-reader-ini-perl all 2.101465-1 [6900 B] Get: 138 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 139 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-2 [339 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.30-1 [105 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.83-1+b1 [99.7 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.47-1+b1 [13.9 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libterm-readkey-perl amd64 2.38-2+b4 [24.6 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libcpan-uploader-perl all 0.103018-1 [16.3 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libdata-section-perl all 0.200008-1 [13.1 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libclass-inspector-perl all 1.36-3 [17.5 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libfile-sharedir-perl all 1.118-3 [16.0 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libparams-validationcompiler-perl all 0.31-1 [30.9 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libxstring-perl amd64 0.005-2+b4 [8076 B] Get: 165 http://deb.debian.org/debian trixie/main amd64 libspecio-perl all 0.48-1 [142 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libdatetime-locale-perl all 1:1.41-1 [3131 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libclass-singleton-perl all 1.6-2 [12.5 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libdatetime-timezone-perl all 1:2.63-2+2024b [261 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libdatetime-perl amd64 2:1.65-1+b2 [116 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libfile-copy-recursive-perl all 0.45-4 [20.0 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libnumber-compare-perl all 0.03-3 [6332 B] Get: 172 http://deb.debian.org/debian trixie/main amd64 libtext-glob-perl all 0.11-3 [7676 B] Get: 173 http://deb.debian.org/debian trixie/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 libfile-pushd-perl all 1.016-2 [13.5 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libfile-sharedir-install-perl all 0.14-2 [11.6 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libhash-merge-simple-perl all 0.052-1 [8232 B] Get: 177 http://deb.debian.org/debian trixie/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 liblog-dispatch-perl all 2.71-1 [75.8 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 liblog-dispatch-array-perl all 1.005-1 [6700 B] Get: 180 http://deb.debian.org/debian trixie/main amd64 libstring-flogger-perl all 1.101246-1 [7380 B] Get: 181 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-globexporter-perl all 0.006-1 [8024 B] Get: 182 http://deb.debian.org/debian trixie/main amd64 liblog-dispatchouli-perl all 3.008-1 [34.4 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libexporter-tiny-perl all 1.006002-1 [38.7 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 liblist-moreutils-xs-perl amd64 0.430-4+b2 [42.1 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libsyntax-keyword-junction-perl all 0.003009-1 [12.7 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libmoose-autobox-perl all 0.16-2 [52.8 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 libaliased-perl all 0.34-3 [13.5 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libmoosex-lazyrequire-perl all 0.11-2 [9212 B] Get: 190 http://deb.debian.org/debian trixie/main amd64 libmoosex-setonce-perl all 0.200002-2 [6632 B] Get: 191 http://deb.debian.org/debian trixie/main amd64 libcarp-clan-perl all 6.08-2 [14.1 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-formethods-perl all 0.100055-1 [8024 B] Get: 193 http://deb.debian.org/debian trixie/main amd64 libmoosex-types-perl all 0.50-2 [54.6 kB] Get: 194 http://deb.debian.org/debian trixie/main amd64 libmoosex-types-perl-perl all 0.101344-1 [8160 B] Get: 195 http://deb.debian.org/debian trixie/main amd64 libpath-tiny-perl all 0.146-1 [56.2 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 libmodule-path-perl all 0.19-3 [12.3 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 libtask-weaken-perl all 1.06-2 [9364 B] Get: 198 http://deb.debian.org/debian trixie/main amd64 libppi-perl all 1.279-1 [294 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 libtype-tiny-perl all 2.004000-1 [357 kB] Get: 200 http://deb.debian.org/debian trixie/main amd64 libperl-prereqscanner-perl all 1.100-1 [31.0 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 libperl-version-perl all 1.017-1 [29.0 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 libtext-template-perl all 1.61-1 [54.4 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 libsoftware-license-perl all 0.104006-1 [116 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 libterm-encoding-perl all 0.03-2 [4980 B] Get: 205 http://deb.debian.org/debian trixie/main amd64 libyaml-tiny-perl all 1.74-1 [30.7 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 libdist-zilla-perl all 6.032-1 [343 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 dh-dist-zilla all 1.4.1 [17.9 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get: 209 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 libarray-utils-perl all 0.5-3 [6184 B] Get: 218 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3+b1 [152 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 220 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 223 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 224 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 225 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 226 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 227 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get: 229 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 230 http://deb.debian.org/debian trixie/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get: 231 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 232 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 233 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 234 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 235 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 236 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 237 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 238 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get: 239 http://deb.debian.org/debian trixie/main amd64 libdata-compare-perl all 1.29-1 [19.6 kB] Get: 240 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 241 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 242 http://deb.debian.org/debian trixie/main amd64 libpod-eventual-perl all 0.094003-1 [14.2 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 libstring-truncate-perl all 1.100603-1 [10.2 kB] Get: 244 http://deb.debian.org/debian trixie/main amd64 libpod-elemental-perl all 0.103006-1 [67.2 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 libpod-elemental-perlmunger-perl all 0.200007-1 [10.5 kB] Get: 246 http://deb.debian.org/debian trixie/main amd64 libpod-weaver-perl all 4.020-1 [70.1 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 libdist-zilla-plugin-podweaver-perl all 4.010-1 [9580 B] Get: 248 http://deb.debian.org/debian trixie/main amd64 libenv-path-perl all 0.19-4 [19.1 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 libfile-chdir-perl all 0.1008-1.2 [11.9 kB] Get: 250 http://deb.debian.org/debian trixie/main amd64 libfile-grep-perl all 0.02-3 [8352 B] Get: 251 http://deb.debian.org/debian trixie/main amd64 libfile-slurper-perl all 0.014-1 [8560 B] Get: 252 http://deb.debian.org/debian trixie/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 253 http://deb.debian.org/debian trixie/main amd64 libfindbin-libs-perl all 3.0.2-1 [29.7 kB] Get: 254 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get: 255 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 256 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get: 257 http://deb.debian.org/debian trixie/main amd64 libheap-perl all 0.80-5 [34.3 kB] Get: 258 http://deb.debian.org/debian trixie/main amd64 libset-object-perl amd64 1.42-1+b5 [37.6 kB] Get: 259 http://deb.debian.org/debian trixie/main amd64 libgraph-perl all 1:0.9729-1 [108 kB] Get: 260 http://deb.debian.org/debian trixie/main amd64 libspiffy-perl all 0.46-1 [25.7 kB] Get: 261 http://deb.debian.org/debian trixie/main amd64 libio-all-perl all 0.87-2 [67.3 kB] Get: 262 http://deb.debian.org/debian trixie/main amd64 libparse-yapp-perl all 1.21-4 [41.5 kB] Get: 263 http://deb.debian.org/debian trixie/main amd64 libxml-parser-perl amd64 2.47-1+b3 [198 kB] Get: 264 http://deb.debian.org/debian trixie/main amd64 libxml-writer-perl all 0.900-2 [26.8 kB] Get: 265 http://deb.debian.org/debian trixie/main amd64 libgraph-readwrite-perl all 2.10-1 [45.2 kB] Get: 266 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 267 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get: 268 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 269 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 270 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 271 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 272 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3+b1 [2450 kB] Get: 273 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 274 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get: 275 http://deb.debian.org/debian trixie/main amd64 liblog-log4perl-perl all 1.57-1 [367 kB] Get: 276 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB] Get: 277 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB] Get: 278 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB] Get: 279 http://deb.debian.org/debian trixie/main amd64 libpadwalker-perl amd64 2.5-1+b6 [18.6 kB] Get: 280 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 281 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 282 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [223 kB] Get: 283 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [54.2 kB] Get: 284 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [35.2 kB] Get: 285 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b2 [12.8 kB] Get: 286 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b2 [9236 B] Get: 287 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 288 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get: 289 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 290 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 291 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get: 292 http://deb.debian.org/debian trixie/main amd64 libtest-file-perl all 1.993-1 [24.5 kB] Get: 293 http://deb.debian.org/debian trixie/main amd64 libtest2-suite-perl all 0.000163-1 [383 kB] Get: 294 http://deb.debian.org/debian trixie/main amd64 libtest-files-perl all 0.26-1 [21.6 kB] Get: 295 http://deb.debian.org/debian trixie/main amd64 libtest-output-perl all 1.034-1 [16.0 kB] Get: 296 http://deb.debian.org/debian trixie/main amd64 libtext-csv-perl all 2.04-1 [112 kB] Get: 297 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 298 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 299 http://deb.debian.org/debian trixie/main amd64 libtingea0 amd64 21-361-2+b2 [52.1 kB] Get: 300 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get: 301 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get: 302 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get: 303 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 304 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get: 305 http://deb.debian.org/debian trixie/main amd64 mafft amd64 7.505-1 [1078 kB] Get: 306 http://deb.debian.org/debian trixie/main amd64 mcl amd64 1:22-282+ds-2 [474 kB] Get: 307 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get: 308 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.16.0+ds-6+b1 [15.2 MB] Get: 309 http://deb.debian.org/debian trixie/main amd64 sysstat amd64 12.7.5-2 [623 kB] Get: 310 http://deb.debian.org/debian trixie/main amd64 parallel all 20240222+ds-2 [2163 kB] Get: 311 http://deb.debian.org/debian trixie/main amd64 prank amd64 0.0.170427+dfsg-3 [395 kB] Get: 312 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-14 [233 kB] Get: 313 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 314 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 315 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Fetched 116 MB in 1s (83.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (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 ... 19969 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_amd64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:amd64 (3.12.7-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... Selecting previously unselected package python3-minimal. (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 ... 20289 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_amd64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (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 ... 21351 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package libproc2-0:amd64. 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Setting up liblog-dispatchouli-perl (3.008-1) ... Setting up libpod-weaver-perl (4.020-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libwww-perl (6.77-1) ... Setting up libcpan-uploader-perl (0.103018-1) ... Setting up libdist-zilla-perl (6.032-1) ... Setting up libdist-zilla-plugin-podweaver-perl (4.010-1) ... Setting up libxml-parser-perl (2.47-1+b3) ... Setting up dh-dist-zilla (1.4.1) ... Setting up libgraph-readwrite-perl (2.10-1) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.36-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/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 dpkg-buildpackage: info: source package roary dpkg-buildpackage: info: source version 3.13.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with dist-zilla dh_dzil_clean dh_clean debian/rules build dh build --with dist-zilla dh_update_autotools_config dh_autoreconf debian/rules override_dh_dzil_build make[1]: Entering directory '/build/reproducible-path/roary-3.13.0+dfsg' mv bin/create_pan_genome_plots.R bin/create_pan_genome_plots dh_dzil_build -- [DZ] beginning to build Bio-Roary [DZ] writing Bio-Roary in .build/debian-build [DZ] built in .build/debian-build make[1]: Leaving directory '/build/reproducible-path/roary-3.13.0+dfsg' dh_auto_configure -D .build/debian-build cd .build/debian-build && /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/roary-3.13.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/roary-3.13.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro" Warning: prerequisite Digest::MD5::File 0 not found. Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::Roary Writing MYMETA.yml and MYMETA.json dh_auto_build -D .build/debian-build cd .build/debian-build && make -j12 make[1]: Entering directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' cp lib/Bio/Roary/AccessoryClustering.pm blib/lib/Bio/Roary/AccessoryClustering.pm cp lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm cp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm cp lib/Bio/Roary/AccessoryBinaryFasta.pm blib/lib/Bio/Roary/AccessoryBinaryFasta.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/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.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/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.pm cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.pm cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.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/AssemblyStatistics.pm blib/lib/Bio/Roary/AssemblyStatistics.pm cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm cp lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm blib/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.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/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pm cp lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pm cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.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/Prank.pm blib/lib/Bio/Roary/External/Prank.pm cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm cp lib/Bio/Roary/External/Fasttree.pm blib/lib/Bio/Roary/External/Fasttree.pm cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm cp lib/Bio/Roary/Output/EMBLHeaderCommon.pm blib/lib/Bio/Roary/Output/EMBLHeaderCommon.pm cp lib/Bio/Roary/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm cp lib/Bio/Roary/JobRunner/Parallel.pm blib/lib/Bio/Roary/JobRunner/Parallel.pm cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.pm cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm cp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.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/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm cp lib/Bio/Roary/Output/GroupMultifasta.pm blib/lib/Bio/Roary/Output/GroupMultifasta.pm cp lib/Bio/Roary/External/Mcl.pm blib/lib/Bio/Roary/External/Mcl.pm cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm cp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm cp lib/Bio/Roary/Output/QueryGroups.pm blib/lib/Bio/Roary/Output/QueryGroups.pm cp lib/Bio/Roary/SampleOrder.pm blib/lib/Bio/Roary/SampleOrder.pm cp lib/Bio/Roary/ReorderSpreadsheet.pm blib/lib/Bio/Roary/ReorderSpreadsheet.pm cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm cp lib/Bio/Roary/SequenceLengths.pm blib/lib/Bio/Roary/SequenceLengths.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/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm cp lib/Bio/Roary/PresenceAbsenceMatrix.pm blib/lib/Bio/Roary/PresenceAbsenceMatrix.pm cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm cp lib/Bio/Roary/SpreadsheetRole.pm blib/lib/Bio/Roary/SpreadsheetRole.pm cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.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 cp bin/iterative_cdhit blib/script/iterative_cdhit "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome "/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 "/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 cp bin/pan_genome_core_alignment blib/script/pan_genome_core_alignment cp bin/pan_genome_post_analysis blib/script/pan_genome_post_analysis "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_assembly_statistics "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_core_alignment 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 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_reorder_spreadsheet "/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 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/protein_alignment_from_nucleotides cp bin/roary blib/script/roary "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/query_pan_genome "/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 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-create_pan_genome_plots.R "/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 "/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 Manifying 28 pod documents Manifying 25 pod documents make[1]: Leaving directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/roary-3.13.0+dfsg' # Hmmm, seems the test is not automatically run anyway by the build system dh_auto_test || true make[1]: Leaving directory '/build/reproducible-path/roary-3.13.0+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with dist-zilla dh_testroot dh_prep dh_auto_install -D .build/debian-build --destdir=debian/roary/ cd .build/debian-build && make -j12 install DESTDIR=/build/reproducible-path/roary-3.13.0\+dfsg/debian/roary AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ChunkFastaFile.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SplitGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupStatistics.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReformatInputGFFs.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Exceptions.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CombinedProteome.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SequenceLengths.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterFullClusters.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AssemblyStatistics.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFF.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/LookupGeneFiles.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParseGFFAnnotationRole.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SampleOrder.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PostAnalysis.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/BedFromGFFRole.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PresenceAbsenceMatrix.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/UniqueGenesPerSample.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ContigsToGeneIDsFromGFF.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFFs.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PrepareInputFiles.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SortFasta.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GeneNamesFromGFF.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/IterativeCdhit.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryClustering.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryBinaryFasta.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/OrderGenes.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/InflateClusters.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParallelAllAgainstAllBlast.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnnotateGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReorderSpreadsheet.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupLabels.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterUnknownsFromFasta.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/MergeMultifastaAlignments.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ClustersRole.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnalyseGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SpreadsheetRole.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupMultifasta.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/QueryGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastas.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EmblGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaNucleotide.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/BlastIdentityFrequency.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastasNucleotide.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaProtein.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/DifferenceBetweenSets.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EMBLHeaderCommon.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/NumberOfGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/AssemblyStatistics.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryPostAnalysis.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/UniqueGenesPerSample.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Roary.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/IterativeCdhit.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryCoreAlignment.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/CreatePanGenome.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Common.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/QueryRoary.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Local.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Parallel.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Role.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Cdhit.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Fasttree.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/PostAnalysis.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/CheckTools.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Makeblastdb.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Prank.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mafft.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/IterativeCdhit.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mcl.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Blastp.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/GeneAlignmentFromNucleotides.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/QC/Report.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/protein_alignment_from_nucleotides.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_core_alignment.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-query_pan_genome.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/transfer_annotation_to_groups.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_reorder_spreadsheet.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome_plots.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/query_pan_genome.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/parallel_all_against_all_blastp.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/extract_proteome_from_gff.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/iterative_cdhit.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_assembly_statistics.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_post_analysis.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-unique_genes_per_sample.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-pan_genome_reorder_spreadsheet.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ClustersRole.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnalyseGroups.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AssemblyStatistics.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Fasttree.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::NumberOfGroups.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Cdhit.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Local.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastasNucleotide.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFF.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ChunkFastaFile.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Role.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::OrderGenes.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Common.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::LookupGeneFiles.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::DifferenceBetweenSets.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Makeblastdb.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::MergeMultifastaAlignments.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::TransferAnnotationToGroups.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::AssemblyStatistics.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Prank.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SplitGroups.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SequenceLengths.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Exceptions.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::EmblGroups.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Blastp.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaNucleotide.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ParallelAllAgainstAllBlast.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PostAnalysis.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ContigsToGeneIDsFromGFF.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupMultifasta.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Roary.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReformatInputGFFs.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryReorderSpreadsheet.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::UniqueGenesPerSample.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SampleOrder.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PresenceAbsenceMatrix.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::FilterUnknownsFromFasta.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::CheckTools.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::PostAnalysis.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::BlastIdentityFrequency.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReorderSpreadsheet.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GroupLabels.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::EMBLHeaderCommon.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::UniqueGenesPerSample.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GroupStatistics.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SortFasta.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::CreatePanGenome.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::IterativeCdhit.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFFs.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Mafft.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryPostAnalysis.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::IterativeCdhit.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::IterativeCdhit.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastas.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Parallel.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GeneNamesFromGFF.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryCoreAlignment.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Mcl.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::QueryRoary.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::BedFromGFFRole.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaProtein.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::QC::Report.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ExtractProteomeFromGff.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::QueryGroups.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ParseGFFAnnotationRole.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PrepareInputFiles.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnnotateGroups.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AccessoryClustering.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SpreadsheetRole.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::FilterFullClusters.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::GeneAlignmentFromNucleotides.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractCoreGenesFromSpreadsheet.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::GeneAlignmentFromNucleotides.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CombinedProteome.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AccessoryBinaryFasta.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::InflateClusters.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_core_alignment Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/create_pan_genome Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/create_pan_genome_plots Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/extract_proteome_from_gff Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-pan_genome_reorder_spreadsheet Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/protein_alignment_from_nucleotides Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_post_analysis Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-create_pan_genome_plots.R Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/query_pan_genome Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_assembly_statistics Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-unique_genes_per_sample Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/parallel_all_against_all_blastp Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/iterative_cdhit Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_reorder_spreadsheet Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/transfer_annotation_to_groups Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-query_pan_genome make[1]: Leaving directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'roary' in '../roary_3.13.0+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../roary_3.13.0+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../roary_3.13.0+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration 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/2221921 and its subdirectories I: Current time: Sun Dec 28 01:58:26 -12 2025 I: pbuilder-time-stamp: 1766930306 Sun Dec 28 13:58:26 UTC 2025 I: Signing ./b1/roary_3.13.0+dfsg-1_amd64.buildinfo as roary_3.13.0+dfsg-1_amd64.buildinfo.asc Sun Dec 28 13:58:27 UTC 2025 I: Signed ./b1/roary_3.13.0+dfsg-1_amd64.buildinfo as ./b1/roary_3.13.0+dfsg-1_amd64.buildinfo.asc Sun Dec 28 13:58:27 UTC 2025 - build #1 for roary/trixie/amd64 on infom02-amd64 done. Starting cleanup. All cleanup done. Sun Dec 28 13:58:27 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-cPytVOA6, removing. /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 25 07:35 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 25 07:33 b2 -rw------- 1 jenkins jenkins 3617 Nov 25 07:33 rbuildlog.9YsMTsD -rw-r--r-- 1 jenkins jenkins 2501 Nov 8 2019 roary_3.13.0+dfsg-1.dsc /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/b1: total 584 -rw-r--r-- 1 jenkins jenkins 159244 Nov 25 07:35 build.log -rw-r--r-- 1 jenkins jenkins 6612 Nov 25 07:35 roary_3.13.0+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2501 Nov 25 07:35 roary_3.13.0+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 172956 Nov 25 07:35 roary_3.13.0+dfsg-1_all.deb -rw-r--r-- 1 jenkins jenkins 14497 Nov 25 07:35 roary_3.13.0+dfsg-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 15379 Nov 25 07:35 roary_3.13.0+dfsg-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1145 Nov 25 07:35 roary_3.13.0+dfsg-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 1592 Nov 25 07:35 roary_3.13.0+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 207348 Nov 25 07:35 roary_3.13.0+dfsg.orig.tar.xz /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/b2: total 0 Mon Nov 25 07:35:27 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Dec 28 01:56:01 -12 2025 I: pbuilder-time-stamp: 1766930161 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [roary_3.13.0+dfsg-1.dsc] 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 13:51:49 2019 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 dpkg-source: info: extracting roary in roary-3.13.0+dfsg dpkg-source: info: unpacking roary_3.13.0+dfsg.orig.tar.xz dpkg-source: info: unpacking roary_3.13.0+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying rename_R_script.patch dpkg-source: info: applying use-dz-starter.patch dpkg-source: info: applying use-debian-perl-path.patch dpkg-source: info: applying new-bioperl-require.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2221921/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='ada19eb8f6c441e19002ecde773b8ad5' 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='2221921' PS1='# ' PS2='> ' 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.oU2ie3pZ/pbuilderrc_IGIj --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/b1 --logfile b1/build.log roary_3.13.0+dfsg-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom02-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2221921/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 12~), dh-dist-zilla, libdist-zilla-plugin-podweaver-perl, bioperl (>= 1.7.4), libarray-utils-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, mafft, fasttree, perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19969 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 12~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-dist-zilla; however: Package dh-dist-zilla is not installed. pbuilder-satisfydepends-dummy depends on libdist-zilla-plugin-podweaver-perl; however: Package libdist-zilla-plugin-podweaver-perl is not installed. pbuilder-satisfydepends-dummy depends on bioperl (>= 1.7.4); however: Package bioperl is not installed. pbuilder-satisfydepends-dummy depends on libarray-utils-perl; however: Package libarray-utils-perl is not installed. pbuilder-satisfydepends-dummy depends on libenv-path-perl; however: Package libenv-path-perl is not installed. pbuilder-satisfydepends-dummy depends on libexception-class-perl; however: Package libexception-class-perl is not installed. pbuilder-satisfydepends-dummy depends on libfile-find-rule-perl; however: Package libfile-find-rule-perl is not installed. pbuilder-satisfydepends-dummy depends on libfile-grep-perl; however: Package libfile-grep-perl is not installed. pbuilder-satisfydepends-dummy depends on libfile-slurper-perl; however: Package libfile-slurper-perl is not installed. pbuilder-satisfydepends-dummy depends on libfile-which-perl; however: Package libfile-which-perl is not installed. pbuilder-satisfydepends-dummy depends on libfindbin-libs-perl; however: Package libfindbin-libs-perl is not installed. pbuilder-satisfydepends-dummy depends on libgraph-perl; however: Package libgraph-perl is not installed. pbuilder-satisfydepends-dummy depends on libgraph-readwrite-perl; however: Package libgraph-readwrite-perl is not installed. pbuilder-satisfydepends-dummy depends on liblog-log4perl-perl; however: Package liblog-log4perl-perl is not installed. pbuilder-satisfydepends-dummy depends on libmoose-perl; however: Package libmoose-perl is not installed. pbuilder-satisfydepends-dummy depends on libperlio-utf8-strict-perl; however: Package libperlio-utf8-strict-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-most-perl; however: Package libtest-most-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-file-perl; however: Package libtest-file-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-files-perl; however: Package libtest-files-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-output-perl; however: Package libtest-output-perl is not installed. pbuilder-satisfydepends-dummy depends on libtext-csv-perl; however: Package libtext-csv-perl is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on cd-hit; however: Package cd-hit is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on mcl; however: Package mcl is not installed. pbuilder-satisfydepends-dummy depends on parallel; however: Package parallel is not installed. pbuilder-satisfydepends-dummy depends on prank; however: Package prank is not installed. pbuilder-satisfydepends-dummy depends on r-base-core; however: Package r-base-core is not installed. pbuilder-satisfydepends-dummy depends on mafft; however: Package mafft is not installed. pbuilder-satisfydepends-dummy depends on fasttree; however: Package fasttree is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bioperl{a} bsdextrautils{a} ca-certificates{a} cd-hit{a} debhelper{a} dh-autoreconf{a} dh-dist-zilla{a} dh-strip-nondeterminism{a} dwz{a} fasttree{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libalgorithm-c3-perl{a} libalgorithm-diff-perl{a} libaliased-perl{a} libapp-cmd-perl{a} libarchive-zip-perl{a} libarray-utils-perl{a} libautobox-perl{a} libb-hooks-endofscope-perl{a} libb-hooks-op-check-perl{a} libbio-perl-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcapture-tiny-perl{a} libcarp-clan-perl{a} libclass-c3-perl{a} libclass-data-inheritable-perl{a} libclass-inspector-perl{a} libclass-load-perl{a} libclass-load-xs-perl{a} libclass-method-modifiers-perl{a} libclass-singleton-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcom-err2{a} libconfig-ini-perl{a} libconfig-mvp-perl{a} libconfig-mvp-reader-ini-perl{a} libconst-fast-perl{a} libcpan-uploader-perl{a} libcpanel-json-xs-perl{a} libcurl4t64{a} libdata-compare-perl{a} libdata-optlist-perl{a} libdata-section-perl{a} libdata-stag-perl{a} libdatetime-locale-perl{a} libdatetime-perl{a} libdatetime-timezone-perl{a} libdatrie1{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-globaldestruction-perl{a} libdevel-overloadinfo-perl{a} libdevel-stacktrace-perl{a} libdist-checkconflicts-perl{a} libdist-zilla-perl{a} libdist-zilla-plugin-podweaver-perl{a} libdynaloader-functions-perl{a} libelf1t64{a} libencode-locale-perl{a} libenv-path-perl{a} libeval-closure-perl{a} libexception-class-perl{a} libexpat1{a} libexporter-tiny-perl{a} libfile-chdir-perl{a} libfile-copy-recursive-perl{a} libfile-find-rule-perl{a} libfile-grep-perl{a} libfile-listing-perl{a} libfile-pushd-perl{a} libfile-sharedir-install-perl{a} libfile-sharedir-perl{a} libfile-slurper-perl{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libfindbin-libs-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgetopt-long-descriptive-perl{a} libgfortran5{a} libglib2.0-0t64{a} libgraph-perl{a} libgraph-readwrite-perl{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhash-merge-simple-perl{a} libheap-perl{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libice6{a} libicu72{a} libimport-into-perl{a} libio-all-perl{a} libio-html-perl{a} libio-socket-ssl-perl{a} libio-string-perl{a} libio-stringy-perl{a} libio-tiecombine-perl{a} libjbig0{a} libjpeg62-turbo{a} libjson-maybexs-perl{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap-2.5-0{a} liblerc4{a} liblist-moreutils-perl{a} liblist-moreutils-xs-perl{a} liblmdb0{a} liblog-dispatch-array-perl{a} liblog-dispatch-perl{a} liblog-dispatchouli-perl{a} liblog-log4perl-perl{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmixin-linewise-perl{a} libmodule-implementation-perl{a} libmodule-path-perl{a} libmodule-pluggable-perl{a} libmodule-runtime-conflicts-perl{a} libmodule-runtime-perl{a} libmoo-perl{a} libmoose-autobox-perl{a} libmoose-perl{a} libmoosex-lazyrequire-perl{a} libmoosex-oneargnew-perl{a} libmoosex-role-parameterized-perl{a} libmoosex-setonce-perl{a} libmoosex-types-perl{a} libmoosex-types-perl-perl{a} libmro-compat-perl{a} libnamespace-autoclean-perl{a} libnamespace-clean-perl{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libnsl2{a} libnumber-compare-perl{a} libpackage-deprecationmanager-perl{a} libpackage-stash-perl{a} libpackage-stash-xs-perl{a} libpadwalker-perl{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libparams-classify-perl{a} libparams-util-perl{a} libparams-validate-perl{a} libparams-validationcompiler-perl{a} libparse-yapp-perl{a} libpath-tiny-perl{a} libperl-prereqscanner-perl{a} libperl-version-perl{a} libperlio-utf8-strict-perl{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpod-elemental-perl{a} libpod-elemental-perlmunger-perl{a} libpod-eventual-perl{a} libpod-weaver-perl{a} libppi-perl{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librole-hasmessage-perl{a} librole-identifiable-perl{a} librole-tiny-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libscope-guard-perl{a} libsensors-config{a} libsensors5{a} libset-object-perl{a} libsharpyuv0{a} libsm6{a} libsoftware-license-perl{a} libspecio-perl{a} libspiffy-perl{a} libssh2-1t64{a} libstring-errf-perl{a} libstring-flogger-perl{a} libstring-formatter-perl{a} libstring-rewriteprefix-perl{a} libstring-truncate-perl{a} libsub-exporter-formethods-perl{a} libsub-exporter-globexporter-perl{a} libsub-exporter-perl{a} libsub-exporter-progressive-perl{a} libsub-identify-perl{a} libsub-install-perl{a} libsub-name-perl{a} libsub-quote-perl{a} libsub-uplevel-perl{a} libsyntax-keyword-junction-perl{a} libtask-weaken-perl{a} libtcl8.6{a} libterm-encoding-perl{a} libterm-readkey-perl{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-file-perl{a} libtest-files-perl{a} libtest-most-perl{a} libtest-output-perl{a} libtest-warn-perl{a} libtest2-suite-perl{a} libtext-csv-perl{a} libtext-diff-perl{a} libtext-glob-perl{a} libtext-template-perl{a} libthai-data{a} libthai0{a} libthrowable-perl{a} libtie-ixhash-perl{a} libtiff6{a} libtimedate-perl{a} libtingea0{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtry-tiny-perl{a} libtype-tiny-perl{a} libuchardet0{a} liburi-perl{a} libuv1t64{a} libvariable-magic-perl{a} libwebp7{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml-parser-perl{a} libxml-writer-perl{a} libxml2{a} libxrender1{a} libxss1{a} libxstring-perl{a} libxt6t64{a} libyaml-tiny-perl{a} m4{a} mafft{a} man-db{a} mcl{a} media-types{a} ncbi-blast+{a} ncbi-data{a} netbase{a} openssl{a} parallel{a} perl-openssl-defaults{a} po-debconf{a} prank{a} procps{a} python3{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} r-base-core{a} readline-common{a} sensible-utils{a} sysstat{a} tzdata{a} ucf{a} unzip{a} x11-common{a} xdg-utils{a} zip{a} The following packages are RECOMMENDED but will NOT be installed: bash-completion bcron bioperl-run cpanminus cron cronie curl devscripts krb5-locales libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libarchive-tar-wrapper-perl libarray-compare-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libcache-cache-perl libclass-c3-xs-perl libconvert-binary-c-perl libdata-dump-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libdevel-lexalias-perl libdevel-partialdump-perl libfile-mimeinfo-perl libgd-perl libglib2.0-data libgraphviz-perl libhtml-form-perl libhtml-format-perl libhtml-tableextract-perl libhttp-daemon-perl libio-compress-brotli-perl libipc-shareable-perl libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libmailtools-perl libmime-lite-perl libmldbm-perl libnet-dbus-perl libpod-coverage-trustpod-perl libpostscript-perl libref-util-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl libterm-readline-gnu-perl libterm-ui-perl libtest-cpan-meta-perl libtest-pod-coverage-perl libtest-pod-perl libtext-csv-xs-perl libtype-tiny-xs-perl libunicode-utf8-perl libx11-protocol-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libyaml-perl linux-sysctl-defaults lynx perl-doc perl-tk psmisc publicsuffix r-base-dev r-doc-html r-recommended ruby shared-mime-info systemd systemd-cron wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 315 newly installed, 0 to remove and 0 not upgraded. Need to get 116 MB of archives. After unpacking 392 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libclass-data-inheritable-perl all 0.10-1 [8632 B] Get: 48 http://deb.debian.org/debian trixie/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 bioperl all 1.7.8-1 [246 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 cd-hit amd64 4.8.1-4 [522 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 67 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libparams-util-perl amd64 1.102-3+b1 [24.4 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.009-1+b1 [16.2 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.5 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libclass-load-perl all 0.25-2 [15.3 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libio-stringy-perl all 2.113-2 [48.3 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libparams-validate-perl amd64 1.31-2+b3 [63.4 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libgetopt-long-descriptive-perl all 0.115-1 [27.6 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libio-tiecombine-perl all 1.005-3 [10.8 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libmodule-pluggable-perl all 5.2-5 [23.0 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libstring-rewriteprefix-perl all 0.009-1 [7140 B] Get: 94 http://deb.debian.org/debian trixie/main amd64 libapp-cmd-perl all 0.336-1 [65.8 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libscope-guard-perl all 0.21-2 [8212 B] Get: 96 http://deb.debian.org/debian trixie/main amd64 libautobox-perl amd64 3.0.2-1+b1 [33.0 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libperlio-utf8-strict-perl amd64 0.010-1+b3 [11.4 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libmixin-linewise-perl all 0.111-1 [14.4 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libconfig-ini-perl all 1:0.029-1 [23.7 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libclass-load-xs-perl amd64 0.10-2+b4 [14.2 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get: 102 http://deb.debian.org/debian trixie/main amd64 libdevel-globaldestruction-perl all 0.14-4 [7144 B] Get: 103 http://deb.debian.org/debian trixie/main amd64 libalgorithm-c3-perl all 0.11-2 [10.8 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libclass-c3-perl all 0.35-2 [21.0 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libmro-compat-perl all 0.15-2 [11.8 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libdevel-overloadinfo-perl all 0.007-1 [7896 B] Get: 107 http://deb.debian.org/debian trixie/main amd64 libeval-closure-perl all 0.14-3 [11.2 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libdist-checkconflicts-perl all 0.11-2 [10.5 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-conflicts-perl all 0.003-2 [7356 B] Get: 110 http://deb.debian.org/debian trixie/main amd64 libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libpackage-stash-xs-perl amd64 0.30-1+b4 [20.9 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libmoose-perl amd64 2.2207-1+b2 [766 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libvariable-magic-perl amd64 0.64-1+b1 [44.9 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libsub-identify-perl amd64 0.14-3+b3 [11.3 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libsub-name-perl amd64 0.27-1+b3 [12.5 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libnamespace-autoclean-perl all 0.31-1 [13.8 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libmoosex-role-parameterized-perl all 1.11-2 [41.9 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libmoosex-oneargnew-perl all 0.007-1 [8180 B] Get: 121 http://deb.debian.org/debian trixie/main amd64 libcpanel-json-xs-perl amd64 4.38-1+b1 [129 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libjson-maybexs-perl all 1.004008-1 [12.9 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libstring-formatter-perl all 1.235-1 [22.1 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libstring-errf-perl all 0.009-1 [12.9 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 librole-hasmessage-perl all 0.007-1 [9112 B] Get: 127 http://deb.debian.org/debian trixie/main amd64 librole-identifiable-perl all 0.009-1 [10.4 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b4 [36.1 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libthrowable-perl all 1.001-2 [15.7 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libtie-ixhash-perl all 1.23-4 [11.7 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libconfig-mvp-perl all 2.200013-1 [47.1 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libconfig-mvp-reader-ini-perl all 2.101465-1 [6900 B] Get: 138 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 139 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-2 [339 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.30-1 [105 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.83-1+b1 [99.7 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.47-1+b1 [13.9 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libterm-readkey-perl amd64 2.38-2+b4 [24.6 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libcpan-uploader-perl all 0.103018-1 [16.3 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libdata-section-perl all 0.200008-1 [13.1 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libclass-inspector-perl all 1.36-3 [17.5 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libfile-sharedir-perl all 1.118-3 [16.0 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libparams-validationcompiler-perl all 0.31-1 [30.9 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libxstring-perl amd64 0.005-2+b4 [8076 B] Get: 165 http://deb.debian.org/debian trixie/main amd64 libspecio-perl all 0.48-1 [142 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libdatetime-locale-perl all 1:1.41-1 [3131 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libclass-singleton-perl all 1.6-2 [12.5 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libdatetime-timezone-perl all 1:2.63-2+2024b [261 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libdatetime-perl amd64 2:1.65-1+b2 [116 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libfile-copy-recursive-perl all 0.45-4 [20.0 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libnumber-compare-perl all 0.03-3 [6332 B] Get: 172 http://deb.debian.org/debian trixie/main amd64 libtext-glob-perl all 0.11-3 [7676 B] Get: 173 http://deb.debian.org/debian trixie/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 libfile-pushd-perl all 1.016-2 [13.5 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libfile-sharedir-install-perl all 0.14-2 [11.6 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libhash-merge-simple-perl all 0.052-1 [8232 B] Get: 177 http://deb.debian.org/debian trixie/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 liblog-dispatch-perl all 2.71-1 [75.8 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 liblog-dispatch-array-perl all 1.005-1 [6700 B] Get: 180 http://deb.debian.org/debian trixie/main amd64 libstring-flogger-perl all 1.101246-1 [7380 B] Get: 181 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-globexporter-perl all 0.006-1 [8024 B] Get: 182 http://deb.debian.org/debian trixie/main amd64 liblog-dispatchouli-perl all 3.008-1 [34.4 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libexporter-tiny-perl all 1.006002-1 [38.7 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 liblist-moreutils-xs-perl amd64 0.430-4+b2 [42.1 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libsyntax-keyword-junction-perl all 0.003009-1 [12.7 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libmoose-autobox-perl all 0.16-2 [52.8 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 libaliased-perl all 0.34-3 [13.5 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libmoosex-lazyrequire-perl all 0.11-2 [9212 B] Get: 190 http://deb.debian.org/debian trixie/main amd64 libmoosex-setonce-perl all 0.200002-2 [6632 B] Get: 191 http://deb.debian.org/debian trixie/main amd64 libcarp-clan-perl all 6.08-2 [14.1 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-formethods-perl all 0.100055-1 [8024 B] Get: 193 http://deb.debian.org/debian trixie/main amd64 libmoosex-types-perl all 0.50-2 [54.6 kB] Get: 194 http://deb.debian.org/debian trixie/main amd64 libmoosex-types-perl-perl all 0.101344-1 [8160 B] Get: 195 http://deb.debian.org/debian trixie/main amd64 libpath-tiny-perl all 0.146-1 [56.2 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 libmodule-path-perl all 0.19-3 [12.3 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 libtask-weaken-perl all 1.06-2 [9364 B] Get: 198 http://deb.debian.org/debian trixie/main amd64 libppi-perl all 1.279-1 [294 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 libtype-tiny-perl all 2.004000-1 [357 kB] Get: 200 http://deb.debian.org/debian trixie/main amd64 libperl-prereqscanner-perl all 1.100-1 [31.0 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 libperl-version-perl all 1.017-1 [29.0 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 libtext-template-perl all 1.61-1 [54.4 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 libsoftware-license-perl all 0.104006-1 [116 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 libterm-encoding-perl all 0.03-2 [4980 B] Get: 205 http://deb.debian.org/debian trixie/main amd64 libyaml-tiny-perl all 1.74-1 [30.7 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 libdist-zilla-perl all 6.032-1 [343 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 dh-dist-zilla all 1.4.1 [17.9 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get: 209 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 libarray-utils-perl all 0.5-3 [6184 B] Get: 218 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3+b1 [152 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 220 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 223 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 224 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 225 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 226 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 227 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get: 229 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 230 http://deb.debian.org/debian trixie/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get: 231 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 232 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 233 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 234 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 235 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 236 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 237 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 238 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get: 239 http://deb.debian.org/debian trixie/main amd64 libdata-compare-perl all 1.29-1 [19.6 kB] Get: 240 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 241 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 242 http://deb.debian.org/debian trixie/main amd64 libpod-eventual-perl all 0.094003-1 [14.2 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 libstring-truncate-perl all 1.100603-1 [10.2 kB] Get: 244 http://deb.debian.org/debian trixie/main amd64 libpod-elemental-perl all 0.103006-1 [67.2 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 libpod-elemental-perlmunger-perl all 0.200007-1 [10.5 kB] Get: 246 http://deb.debian.org/debian trixie/main amd64 libpod-weaver-perl all 4.020-1 [70.1 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 libdist-zilla-plugin-podweaver-perl all 4.010-1 [9580 B] Get: 248 http://deb.debian.org/debian trixie/main amd64 libenv-path-perl all 0.19-4 [19.1 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 libfile-chdir-perl all 0.1008-1.2 [11.9 kB] Get: 250 http://deb.debian.org/debian trixie/main amd64 libfile-grep-perl all 0.02-3 [8352 B] Get: 251 http://deb.debian.org/debian trixie/main amd64 libfile-slurper-perl all 0.014-1 [8560 B] Get: 252 http://deb.debian.org/debian trixie/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 253 http://deb.debian.org/debian trixie/main amd64 libfindbin-libs-perl all 3.0.2-1 [29.7 kB] Get: 254 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get: 255 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 256 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get: 257 http://deb.debian.org/debian trixie/main amd64 libheap-perl all 0.80-5 [34.3 kB] Get: 258 http://deb.debian.org/debian trixie/main amd64 libset-object-perl amd64 1.42-1+b5 [37.6 kB] Get: 259 http://deb.debian.org/debian trixie/main amd64 libgraph-perl all 1:0.9729-1 [108 kB] Get: 260 http://deb.debian.org/debian trixie/main amd64 libspiffy-perl all 0.46-1 [25.7 kB] Get: 261 http://deb.debian.org/debian trixie/main amd64 libio-all-perl all 0.87-2 [67.3 kB] Get: 262 http://deb.debian.org/debian trixie/main amd64 libparse-yapp-perl all 1.21-4 [41.5 kB] Get: 263 http://deb.debian.org/debian trixie/main amd64 libxml-parser-perl amd64 2.47-1+b3 [198 kB] Get: 264 http://deb.debian.org/debian trixie/main amd64 libxml-writer-perl all 0.900-2 [26.8 kB] Get: 265 http://deb.debian.org/debian trixie/main amd64 libgraph-readwrite-perl all 2.10-1 [45.2 kB] Get: 266 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 267 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get: 268 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 269 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 270 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 271 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 272 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3+b1 [2450 kB] Get: 273 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 274 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get: 275 http://deb.debian.org/debian trixie/main amd64 liblog-log4perl-perl all 1.57-1 [367 kB] Get: 276 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB] Get: 277 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB] Get: 278 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB] Get: 279 http://deb.debian.org/debian trixie/main amd64 libpadwalker-perl amd64 2.5-1+b6 [18.6 kB] Get: 280 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 281 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 282 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [223 kB] Get: 283 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [54.2 kB] Get: 284 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [35.2 kB] Get: 285 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b2 [12.8 kB] Get: 286 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b2 [9236 B] Get: 287 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 288 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get: 289 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 290 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 291 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get: 292 http://deb.debian.org/debian trixie/main amd64 libtest-file-perl all 1.993-1 [24.5 kB] Get: 293 http://deb.debian.org/debian trixie/main amd64 libtest2-suite-perl all 0.000163-1 [383 kB] Get: 294 http://deb.debian.org/debian trixie/main amd64 libtest-files-perl all 0.26-1 [21.6 kB] Get: 295 http://deb.debian.org/debian trixie/main amd64 libtest-output-perl all 1.034-1 [16.0 kB] Get: 296 http://deb.debian.org/debian trixie/main amd64 libtext-csv-perl all 2.04-1 [112 kB] Get: 297 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 298 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 299 http://deb.debian.org/debian trixie/main amd64 libtingea0 amd64 21-361-2+b2 [52.1 kB] Get: 300 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get: 301 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get: 302 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get: 303 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 304 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get: 305 http://deb.debian.org/debian trixie/main amd64 mafft amd64 7.505-1 [1078 kB] Get: 306 http://deb.debian.org/debian trixie/main amd64 mcl amd64 1:22-282+ds-2 [474 kB] Get: 307 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get: 308 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.16.0+ds-6+b1 [15.2 MB] Get: 309 http://deb.debian.org/debian trixie/main amd64 sysstat amd64 12.7.5-2 [623 kB] Get: 310 http://deb.debian.org/debian trixie/main amd64 parallel all 20240222+ds-2 [2163 kB] Get: 311 http://deb.debian.org/debian trixie/main amd64 prank amd64 0.0.170427+dfsg-3 [395 kB] Get: 312 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-14 [233 kB] Get: 313 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 314 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 315 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Fetched 116 MB in 1s (83.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (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 ... 19969 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_amd64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:amd64 (3.12.7-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... Selecting previously unselected package python3-minimal. (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 ... 20289 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_amd64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (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 ... 21351 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package libproc2-0:amd64. 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Setting up libsharpyuv0:amd64 (1.4.0-0.1+b1) ... Setting up libfile-slurper-perl (0.014-1) ... Setting up libfile-which-perl (1.27-2) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up libtie-ixhash-perl (1.23-4) ... Setting up libtask-weaken-perl (1.06-2) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libparse-yapp-perl (1.21-4) ... Setting up libclass-inspector-perl (1.36-3) ... Setting up libdynaloader-functions-perl (0.004-1) ... Setting up libdatrie1:amd64 (0.2.13-3+b1) ... Setting up libtext-glob-perl (0.11-3) ... Setting up libtest-deep-perl (1.204-1) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up libfile-pushd-perl (1.016-2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up mafft (7.505-1) ... Setting up libclone-perl:amd64 (0.47-1+b1) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libsub-identify-perl (0.14-3+b3) ... Setting up libcpanel-json-xs-perl:amd64 (4.38-1+b1) ... Setting up libio-stringy-perl (2.113-2) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libtest-file-perl (1.993-1) ... Setting up unzip (6.0-28) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libheap-perl (0.80-5) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libuv1t64:amd64 (1.48.0-7) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libtry-tiny-perl (0.32-1) ... Setting up libsensors-config (1:3.6.0-10) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.22-1) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libclass-singleton-perl (1.6-2) ... Setting up libpadwalker-perl (2.5-1+b6) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libfindbin-libs-perl (3.0.2-1) ... Setting up libcom-err2:amd64 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libxstring-perl:amd64 (0.005-2+b4) ... Setting up libyaml-tiny-perl (1.74-1) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libsub-install-perl (0.929-1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libtest2-suite-perl (0.000163-1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libterm-encoding-perl (0.03-2) ... Setting up libnumber-compare-perl (0.03-3) ... Setting up libscope-guard-perl (0.21-2) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up libfile-copy-recursive-perl (0.45-4) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Dec 28 13:57:30 UTC 2025. Universal Time is now: Sun Dec 28 13:57:30 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libjson-maybexs-perl (1.004008-1) ... Setting up libio-string-perl (1.08-4) ... Setting up zip (3.0-14) ... Setting up libpackage-stash-xs-perl:amd64 (0.30-1+b4) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:amd64 (2.82.2-2) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libclass-data-inheritable-perl (0.10-1) ... Setting up libalgorithm-c3-perl (0.11-2) ... Setting up libset-object-perl (1.42-1+b5) ... Setting up liblog-log4perl-perl (1.57-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libtext-diff-perl (1.45-2) ... Setting up libfile-find-rule-perl (0.34-3) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libio-tiecombine-perl (1.005-3) ... Setting up libperlio-utf8-strict-perl (0.010-1+b3) ... Setting up libxml-writer-perl (0.900-2) ... Setting up libenv-path-perl (0.19-4) ... Setting up libfribidi0:amd64 (1.0.15-1) ... Setting up libproc2-0:amd64 (2:4.0.4-6) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.44-2) ... Setting up libvariable-magic-perl (0.64-1+b1) ... Setting up libio-html-perl (1.004-3) ... Setting up libtext-template-perl (1.61-1) ... Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... Setting up autopoint (0.22.5-2) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b2) ... Setting up libfile-grep-perl (0.02-3) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up liblist-moreutils-xs-perl (0.430-4+b2) ... Setting up libsensors5:amd64 (1:3.6.0-10+b1) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libparams-util-perl (1.102-3+b1) ... Setting up libspiffy-perl (0.46-1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:amd64 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libwebp7:amd64 (1.4.0-0.1+b1) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libsub-name-perl:amd64 (0.27-1+b3) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up libfile-chdir-perl (0.1008-1.2) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up libpath-tiny-perl (0.146-1) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up libjson-perl (4.10000-1) ... Setting up libtingea0:amd64 (21-361-2+b2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libfile-sharedir-perl (1.118-3) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up libaliased-perl (0.34-3) ... Setting up libthai-data (0.1.29-2) ... Setting up libcarp-clan-perl (6.08-2) ... Setting up libdevel-globaldestruction-perl (0.14-4) ... Setting up fasttree (2.1.11-2) ... Setting up netbase (6.4) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b4) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libmodule-path-perl (0.19-3) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libmbedcrypto16:amd64 (3.6.2-3) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libexporter-tiny-perl (1.006002-1) ... Setting up libterm-readkey-perl (2.38-2+b4) ... Setting up libperl-version-perl (1.017-1) ... Setting up openssl (3.3.2-2) ... Setting up libautobox-perl (3.0.2-1+b1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up bedtools (2.31.1+dfsg-2) ... Setting up liburi-perl (5.30-1) ... Setting up prank (0.0.170427+dfsg-3) ... Setting up libtext-csv-perl (2.04-1) ... Setting up libnet-ssleay-perl:amd64 (1.94-2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up liblapack3:amd64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libhash-merge-simple-perl (0.052-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b2) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up liblist-moreutils-perl (0.430-2) ... Setting up libtest-warn-perl (0.37-2) ... Setting up libtype-tiny-perl (2.004000-1) ... Setting up libtest-differences-perl (0.71-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libnet-http-perl (6.23-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libio-all-perl (0.87-2) ... Setting up libclass-c3-perl (0.35-2) ... Setting up libgraph-perl (1:0.9729-1) ... Setting up libdevel-callchecker-perl:amd64 (0.009-1+b1) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up libdata-compare-perl (1.29-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libmbedx509-7:amd64 (3.6.2-3) ... Setting up libtest-exception-perl (0.43-3) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up mcl (1:22-282+ds-2) ... Setting up libppi-perl (1.279-1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up libtest-output-perl (1.034-1) ... Setting up ucf (3.0043+nmu1) ... Setting up libsyntax-keyword-junction-perl (0.003009-1) ... Setting up libmbedtls21:amd64 (3.6.2-3) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up groff-base (1.23.0-5) ... Setting up libhtml-parser-perl:amd64 (3.83-1+b1) ... Setting up libharfbuzz0b:amd64 (10.0.1-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b2) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up libmro-compat-perl (0.15-2) ... Setting up libsm6:amd64 (2:1.2.4-1) ... Setting up sysstat (12.7.5-2) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Setting up libio-socket-ssl-perl (2.089-1) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libhttp-message-perl (7.00-2) ... Setting up libeval-closure-perl (0.14-3) ... Setting up libstring-truncate-perl (1.100603-1) ... Setting up libpaper1:amd64 (1.1.29+b2) ... Creating config file /etc/papersize with new version Setting up libstring-flogger-perl (1.101246-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up libparams-validationcompiler-perl (0.31-1) ... Setting up libxft2:amd64 (2.3.6-1+b2) ... Setting up libcurl4t64:amd64 (8.11.0-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libtest-most-perl (0.38-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libtk8.6:amd64 (8.6.15-1) ... Setting up libparams-classify-perl:amd64 (0.015-2+b4) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libsub-exporter-formethods-perl (0.100055-1) ... Setting up libpaper-utils (1.1.29+b2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libmixin-linewise-perl (0.111-1) ... Setting up libcairo2:amd64 (1.18.2-2) ... Setting up libconfig-ini-perl (1:0.029-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b1) ... 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Setting up libsoftware-license-perl (0.104006-1) ... Setting up libclass-load-perl (0.25-2) ... Setting up libstring-errf-perl (0.009-1) ... Setting up libspecio-perl (0.48-1) ... Setting up r-base-core (4.4.2-1) ... Creating config file /etc/R/Renviron with new version Setting up libpackage-deprecationmanager-perl (0.18-1) ... Setting up libdevel-overloadinfo-perl (0.007-1) ... Setting up libclass-load-xs-perl (0.10-2+b4) ... Setting up libparams-validate-perl:amd64 (1.31-2+b3) ... Setting up libb-hooks-endofscope-perl (0.28-1) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up libthrowable-perl (1.001-2) ... Setting up libmoose-perl:amd64 (2.2207-1+b2) ... Setting up python3 (3.12.6-1) ... Setting up ncbi-blast+ (2.16.0+ds-6+b1) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libmoosex-setonce-perl (0.200002-2) ... Setting up libgetopt-long-descriptive-perl (0.115-1) ... Setting up librole-identifiable-perl (0.009-1) ... Setting up libnamespace-autoclean-perl (0.31-1) ... Setting up libdatetime-locale-perl (1:1.41-1) ... Setting up libmoosex-role-parameterized-perl (1.11-2) ... Setting up libmoose-autobox-perl (0.16-2) ... Setting up libapp-cmd-perl (0.336-1) ... Setting up librole-hasmessage-perl (0.007-1) ... Setting up libperl-prereqscanner-perl (1.100-1) ... Setting up libdatetime-timezone-perl (1:2.63-2+2024b) ... Setting up libmoosex-types-perl (0.50-2) ... Setting up libmoosex-oneargnew-perl (0.007-1) ... Setting up libmoosex-lazyrequire-perl (0.11-2) ... Setting up liblog-dispatch-perl (2.71-1) ... Setting up libconfig-mvp-perl (2.200013-1) ... Setting up libdatetime-perl (2:1.65-1+b2) ... Setting up libpod-elemental-perl (0.103006-1) ... Setting up libmoosex-types-perl-perl (0.101344-1) ... Setting up libconfig-mvp-reader-ini-perl (2.101465-1) ... Setting up liblog-dispatch-array-perl (1.005-1) ... Setting up libpod-elemental-perlmunger-perl (0.200007-1) ... Setting up liblog-dispatchouli-perl (3.008-1) ... Setting up libpod-weaver-perl (4.020-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libwww-perl (6.77-1) ... Setting up libcpan-uploader-perl (0.103018-1) ... Setting up libdist-zilla-perl (6.032-1) ... Setting up libdist-zilla-plugin-podweaver-perl (4.010-1) ... Setting up libxml-parser-perl (2.47-1+b3) ... Setting up dh-dist-zilla (1.4.1) ... Setting up libgraph-readwrite-perl (2.10-1) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.36-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/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 dpkg-buildpackage: info: source package roary dpkg-buildpackage: info: source version 3.13.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with dist-zilla dh_dzil_clean dh_clean debian/rules build dh build --with dist-zilla dh_update_autotools_config dh_autoreconf debian/rules override_dh_dzil_build make[1]: Entering directory '/build/reproducible-path/roary-3.13.0+dfsg' mv bin/create_pan_genome_plots.R bin/create_pan_genome_plots dh_dzil_build -- [DZ] beginning to build Bio-Roary [DZ] writing Bio-Roary in .build/debian-build [DZ] built in .build/debian-build make[1]: Leaving directory '/build/reproducible-path/roary-3.13.0+dfsg' dh_auto_configure -D .build/debian-build cd .build/debian-build && /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/roary-3.13.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/roary-3.13.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro" Warning: prerequisite Digest::MD5::File 0 not found. Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::Roary Writing MYMETA.yml and MYMETA.json dh_auto_build -D .build/debian-build cd .build/debian-build && make -j12 make[1]: Entering directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' cp lib/Bio/Roary/AccessoryClustering.pm blib/lib/Bio/Roary/AccessoryClustering.pm cp lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm cp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm cp lib/Bio/Roary/AccessoryBinaryFasta.pm blib/lib/Bio/Roary/AccessoryBinaryFasta.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/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.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/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.pm cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.pm cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.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/AssemblyStatistics.pm blib/lib/Bio/Roary/AssemblyStatistics.pm cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm cp lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm blib/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.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/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pm cp lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pm cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.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/Prank.pm blib/lib/Bio/Roary/External/Prank.pm cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm cp lib/Bio/Roary/External/Fasttree.pm blib/lib/Bio/Roary/External/Fasttree.pm cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm cp lib/Bio/Roary/Output/EMBLHeaderCommon.pm blib/lib/Bio/Roary/Output/EMBLHeaderCommon.pm cp lib/Bio/Roary/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm cp lib/Bio/Roary/JobRunner/Parallel.pm blib/lib/Bio/Roary/JobRunner/Parallel.pm cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.pm cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm cp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.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/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm cp lib/Bio/Roary/Output/GroupMultifasta.pm blib/lib/Bio/Roary/Output/GroupMultifasta.pm cp lib/Bio/Roary/External/Mcl.pm blib/lib/Bio/Roary/External/Mcl.pm cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm cp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm cp lib/Bio/Roary/Output/QueryGroups.pm blib/lib/Bio/Roary/Output/QueryGroups.pm cp lib/Bio/Roary/SampleOrder.pm blib/lib/Bio/Roary/SampleOrder.pm cp lib/Bio/Roary/ReorderSpreadsheet.pm blib/lib/Bio/Roary/ReorderSpreadsheet.pm cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm cp lib/Bio/Roary/SequenceLengths.pm blib/lib/Bio/Roary/SequenceLengths.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/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm cp lib/Bio/Roary/PresenceAbsenceMatrix.pm blib/lib/Bio/Roary/PresenceAbsenceMatrix.pm cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm cp lib/Bio/Roary/SpreadsheetRole.pm blib/lib/Bio/Roary/SpreadsheetRole.pm cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.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 cp bin/iterative_cdhit blib/script/iterative_cdhit "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome "/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 "/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 cp bin/pan_genome_core_alignment blib/script/pan_genome_core_alignment cp bin/pan_genome_post_analysis blib/script/pan_genome_post_analysis "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_assembly_statistics "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_core_alignment 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 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_reorder_spreadsheet "/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 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/protein_alignment_from_nucleotides cp bin/roary blib/script/roary "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/query_pan_genome "/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 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-create_pan_genome_plots.R "/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 "/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 Manifying 28 pod documents Manifying 25 pod documents make[1]: Leaving directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/roary-3.13.0+dfsg' # Hmmm, seems the test is not automatically run anyway by the build system dh_auto_test || true make[1]: Leaving directory '/build/reproducible-path/roary-3.13.0+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with dist-zilla dh_testroot dh_prep dh_auto_install -D .build/debian-build --destdir=debian/roary/ cd .build/debian-build && make -j12 install DESTDIR=/build/reproducible-path/roary-3.13.0\+dfsg/debian/roary AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ChunkFastaFile.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SplitGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupStatistics.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReformatInputGFFs.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Exceptions.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CombinedProteome.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SequenceLengths.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterFullClusters.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AssemblyStatistics.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFF.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/LookupGeneFiles.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParseGFFAnnotationRole.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SampleOrder.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PostAnalysis.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/BedFromGFFRole.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PresenceAbsenceMatrix.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/UniqueGenesPerSample.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ContigsToGeneIDsFromGFF.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFFs.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PrepareInputFiles.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SortFasta.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GeneNamesFromGFF.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/IterativeCdhit.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryClustering.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryBinaryFasta.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/OrderGenes.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/InflateClusters.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParallelAllAgainstAllBlast.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnnotateGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReorderSpreadsheet.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupLabels.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterUnknownsFromFasta.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/MergeMultifastaAlignments.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ClustersRole.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnalyseGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SpreadsheetRole.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupMultifasta.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/QueryGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastas.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EmblGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaNucleotide.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/BlastIdentityFrequency.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastasNucleotide.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaProtein.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/DifferenceBetweenSets.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EMBLHeaderCommon.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/NumberOfGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/AssemblyStatistics.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryPostAnalysis.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/UniqueGenesPerSample.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Roary.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/IterativeCdhit.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryCoreAlignment.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/CreatePanGenome.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Common.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/QueryRoary.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Local.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Parallel.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Role.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Cdhit.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Fasttree.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/PostAnalysis.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/CheckTools.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Makeblastdb.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Prank.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mafft.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/IterativeCdhit.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mcl.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Blastp.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/GeneAlignmentFromNucleotides.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/QC/Report.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/protein_alignment_from_nucleotides.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_core_alignment.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-query_pan_genome.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/transfer_annotation_to_groups.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_reorder_spreadsheet.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome_plots.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/query_pan_genome.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/parallel_all_against_all_blastp.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/extract_proteome_from_gff.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/iterative_cdhit.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_assembly_statistics.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_post_analysis.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-unique_genes_per_sample.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-pan_genome_reorder_spreadsheet.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ClustersRole.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnalyseGroups.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AssemblyStatistics.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Fasttree.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::NumberOfGroups.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Cdhit.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Local.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastasNucleotide.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFF.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ChunkFastaFile.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Role.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::OrderGenes.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Common.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::LookupGeneFiles.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::DifferenceBetweenSets.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Makeblastdb.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::MergeMultifastaAlignments.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::TransferAnnotationToGroups.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::AssemblyStatistics.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Prank.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SplitGroups.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SequenceLengths.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Exceptions.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::EmblGroups.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Blastp.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaNucleotide.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ParallelAllAgainstAllBlast.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PostAnalysis.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ContigsToGeneIDsFromGFF.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupMultifasta.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Roary.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReformatInputGFFs.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryReorderSpreadsheet.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::UniqueGenesPerSample.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SampleOrder.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PresenceAbsenceMatrix.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::FilterUnknownsFromFasta.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::CheckTools.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::PostAnalysis.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::BlastIdentityFrequency.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReorderSpreadsheet.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GroupLabels.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::EMBLHeaderCommon.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::UniqueGenesPerSample.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GroupStatistics.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SortFasta.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::CreatePanGenome.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::IterativeCdhit.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFFs.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Mafft.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryPostAnalysis.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::IterativeCdhit.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::IterativeCdhit.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastas.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Parallel.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GeneNamesFromGFF.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryCoreAlignment.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Mcl.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::QueryRoary.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::BedFromGFFRole.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaProtein.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::QC::Report.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ExtractProteomeFromGff.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::QueryGroups.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ParseGFFAnnotationRole.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PrepareInputFiles.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnnotateGroups.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AccessoryClustering.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SpreadsheetRole.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::FilterFullClusters.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::GeneAlignmentFromNucleotides.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractCoreGenesFromSpreadsheet.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::GeneAlignmentFromNucleotides.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CombinedProteome.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AccessoryBinaryFasta.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::InflateClusters.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_core_alignment Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/create_pan_genome Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/create_pan_genome_plots Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/extract_proteome_from_gff Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-pan_genome_reorder_spreadsheet Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/protein_alignment_from_nucleotides Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_post_analysis Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-create_pan_genome_plots.R Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/query_pan_genome Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_assembly_statistics Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-unique_genes_per_sample Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/parallel_all_against_all_blastp Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/iterative_cdhit Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_reorder_spreadsheet Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/transfer_annotation_to_groups Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-query_pan_genome make[1]: Leaving directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'roary' in '../roary_3.13.0+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../roary_3.13.0+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../roary_3.13.0+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration 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/2221921 and its subdirectories I: Current time: Sun Dec 28 01:58:26 -12 2025 I: pbuilder-time-stamp: 1766930306 Mon Nov 25 07:35:28 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom01-amd64.debian.net. Mon Nov 25 07:35:28 UTC 2024 I: Preparing to do remote build '2' on infom01-amd64.debian.net. Mon Nov 25 07:35:28 UTC 2024 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Mon Nov 25 07:35:28 UTC 2024 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-UGCeyP' ==================================================================================== Mon Nov 25 07:35:29 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom01-amd64, called using "2 roary trixie /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ 3.13.0+dfsg-1" as arguments. Mon Nov 25 07:35:29 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-UuEA9ckM" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Nov 25 07:35:29 UTC 2024 I: Downloading source for trixie/roary=3.13.0+dfsg-1 Reading package lists... NOTICE: 'roary' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/roary.git Please use: git clone https://salsa.debian.org/med-team/roary.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 216 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main roary 3.13.0+dfsg-1 (dsc) [2501 B] Get:2 http://deb.debian.org/debian trixie/main roary 3.13.0+dfsg-1 (tar) [207 kB] Get:3 http://deb.debian.org/debian trixie/main roary 3.13.0+dfsg-1 (diff) [6612 B] Fetched 216 kB in 0s (2067 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'roary' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/roary.git Please use: git clone https://salsa.debian.org/med-team/roary.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 216 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main roary 3.13.0+dfsg-1 (dsc) [2501 B] Get:2 http://deb.debian.org/debian trixie/main roary 3.13.0+dfsg-1 (tar) [207 kB] Get:3 http://deb.debian.org/debian trixie/main roary 3.13.0+dfsg-1 (diff) [6612 B] Fetched 216 kB in 0s (2067 kB/s) Download complete and in download only mode ============================================================================= Re-Building roary in trixie on amd64 on infom01-amd64 now. Date: Mon Nov 25 07:35:30 UTC 2024 Date UTC: Mon Nov 25 07:35:30 UTC 2024 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/pbuilderrc_ybpu + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' roary = debian-installer -o roary = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' roary = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo 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.oU2ie3pZ/pbuilderrc_ybpu --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/b2 --logfile b2/build.log roary_3.13.0+dfsg-1.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Mon Nov 25 21:35:30 +14 2024 I: pbuilder-time-stamp: 1732520130 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [roary_3.13.0+dfsg-1.dsc] 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 13:51:49 2019 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 dpkg-source: info: extracting roary in roary-3.13.0+dfsg dpkg-source: info: unpacking roary_3.13.0+dfsg.orig.tar.xz dpkg-source: info: unpacking roary_3.13.0+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying rename_R_script.patch dpkg-source: info: applying use-dz-starter.patch dpkg-source: info: applying use-debian-perl-path.patch dpkg-source: info: applying new-bioperl-require.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2228133/tmp/hooks/D01_modify_environment starting debug: Running on infom01-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Nov 25 07:35 /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/2228133/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2228133/tmp/hooks/D02_print_environment starting I: set 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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=fffeff89364541e88d42ab1dae4cbd47 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2228133 PS4='+ ' 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.oU2ie3pZ/pbuilderrc_ybpu --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/b2 --logfile b2/build.log roary_3.13.0+dfsg-1.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' I: uname -a Linux i-capture-the-hostname 6.1.0-28-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2228133/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 12~), dh-dist-zilla, libdist-zilla-plugin-podweaver-perl, bioperl (>= 1.7.4), libarray-utils-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, mafft, fasttree, perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19969 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 12~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-dist-zilla; however: Package dh-dist-zilla is not installed. pbuilder-satisfydepends-dummy depends on libdist-zilla-plugin-podweaver-perl; however: Package libdist-zilla-plugin-podweaver-perl is not installed. pbuilder-satisfydepends-dummy depends on bioperl (>= 1.7.4); however: Package bioperl is not installed. pbuilder-satisfydepends-dummy depends on libarray-utils-perl; however: Package libarray-utils-perl is not installed. pbuilder-satisfydepends-dummy depends on libenv-path-perl; however: Package libenv-path-perl is not installed. pbuilder-satisfydepends-dummy depends on libexception-class-perl; however: Package libexception-class-perl is not installed. pbuilder-satisfydepends-dummy depends on libfile-find-rule-perl; however: Package libfile-find-rule-perl is not installed. pbuilder-satisfydepends-dummy depends on libfile-grep-perl; however: Package libfile-grep-perl is not installed. pbuilder-satisfydepends-dummy depends on libfile-slurper-perl; however: Package libfile-slurper-perl is not installed. pbuilder-satisfydepends-dummy depends on libfile-which-perl; however: Package libfile-which-perl is not installed. pbuilder-satisfydepends-dummy depends on libfindbin-libs-perl; however: Package libfindbin-libs-perl is not installed. pbuilder-satisfydepends-dummy depends on libgraph-perl; however: Package libgraph-perl is not installed. pbuilder-satisfydepends-dummy depends on libgraph-readwrite-perl; however: Package libgraph-readwrite-perl is not installed. pbuilder-satisfydepends-dummy depends on liblog-log4perl-perl; however: Package liblog-log4perl-perl is not installed. pbuilder-satisfydepends-dummy depends on libmoose-perl; however: Package libmoose-perl is not installed. pbuilder-satisfydepends-dummy depends on libperlio-utf8-strict-perl; however: Package libperlio-utf8-strict-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-most-perl; however: Package libtest-most-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-file-perl; however: Package libtest-file-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-files-perl; however: Package libtest-files-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-output-perl; however: Package libtest-output-perl is not installed. pbuilder-satisfydepends-dummy depends on libtext-csv-perl; however: Package libtext-csv-perl is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on cd-hit; however: Package cd-hit is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on mcl; however: Package mcl is not installed. pbuilder-satisfydepends-dummy depends on parallel; however: Package parallel is not installed. pbuilder-satisfydepends-dummy depends on prank; however: Package prank is not installed. pbuilder-satisfydepends-dummy depends on r-base-core; however: Package r-base-core is not installed. pbuilder-satisfydepends-dummy depends on mafft; however: Package mafft is not installed. pbuilder-satisfydepends-dummy depends on fasttree; however: Package fasttree is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bioperl{a} bsdextrautils{a} ca-certificates{a} cd-hit{a} debhelper{a} dh-autoreconf{a} dh-dist-zilla{a} dh-strip-nondeterminism{a} dwz{a} fasttree{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libalgorithm-c3-perl{a} libalgorithm-diff-perl{a} libaliased-perl{a} libapp-cmd-perl{a} libarchive-zip-perl{a} libarray-utils-perl{a} libautobox-perl{a} libb-hooks-endofscope-perl{a} libb-hooks-op-check-perl{a} libbio-perl-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcapture-tiny-perl{a} libcarp-clan-perl{a} libclass-c3-perl{a} libclass-data-inheritable-perl{a} libclass-inspector-perl{a} libclass-load-perl{a} libclass-load-xs-perl{a} libclass-method-modifiers-perl{a} libclass-singleton-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcom-err2{a} libconfig-ini-perl{a} libconfig-mvp-perl{a} libconfig-mvp-reader-ini-perl{a} libconst-fast-perl{a} libcpan-uploader-perl{a} libcpanel-json-xs-perl{a} libcurl4t64{a} libdata-compare-perl{a} libdata-optlist-perl{a} libdata-section-perl{a} libdata-stag-perl{a} libdatetime-locale-perl{a} libdatetime-perl{a} libdatetime-timezone-perl{a} libdatrie1{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-globaldestruction-perl{a} libdevel-overloadinfo-perl{a} libdevel-stacktrace-perl{a} libdist-checkconflicts-perl{a} libdist-zilla-perl{a} libdist-zilla-plugin-podweaver-perl{a} libdynaloader-functions-perl{a} libelf1t64{a} libencode-locale-perl{a} libenv-path-perl{a} libeval-closure-perl{a} libexception-class-perl{a} libexpat1{a} libexporter-tiny-perl{a} libfile-chdir-perl{a} libfile-copy-recursive-perl{a} libfile-find-rule-perl{a} libfile-grep-perl{a} libfile-listing-perl{a} libfile-pushd-perl{a} libfile-sharedir-install-perl{a} libfile-sharedir-perl{a} libfile-slurper-perl{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libfindbin-libs-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgetopt-long-descriptive-perl{a} libgfortran5{a} libglib2.0-0t64{a} libgraph-perl{a} libgraph-readwrite-perl{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhash-merge-simple-perl{a} libheap-perl{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libice6{a} libicu72{a} libimport-into-perl{a} libio-all-perl{a} libio-html-perl{a} libio-socket-ssl-perl{a} libio-string-perl{a} libio-stringy-perl{a} libio-tiecombine-perl{a} libjbig0{a} libjpeg62-turbo{a} libjson-maybexs-perl{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap-2.5-0{a} liblerc4{a} liblist-moreutils-perl{a} liblist-moreutils-xs-perl{a} liblmdb0{a} liblog-dispatch-array-perl{a} liblog-dispatch-perl{a} liblog-dispatchouli-perl{a} liblog-log4perl-perl{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmixin-linewise-perl{a} libmodule-implementation-perl{a} libmodule-path-perl{a} libmodule-pluggable-perl{a} libmodule-runtime-conflicts-perl{a} libmodule-runtime-perl{a} libmoo-perl{a} libmoose-autobox-perl{a} libmoose-perl{a} libmoosex-lazyrequire-perl{a} libmoosex-oneargnew-perl{a} libmoosex-role-parameterized-perl{a} libmoosex-setonce-perl{a} libmoosex-types-perl{a} libmoosex-types-perl-perl{a} libmro-compat-perl{a} libnamespace-autoclean-perl{a} libnamespace-clean-perl{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libnsl2{a} libnumber-compare-perl{a} libpackage-deprecationmanager-perl{a} libpackage-stash-perl{a} libpackage-stash-xs-perl{a} libpadwalker-perl{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libparams-classify-perl{a} libparams-util-perl{a} libparams-validate-perl{a} libparams-validationcompiler-perl{a} libparse-yapp-perl{a} libpath-tiny-perl{a} libperl-prereqscanner-perl{a} libperl-version-perl{a} libperlio-utf8-strict-perl{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpod-elemental-perl{a} libpod-elemental-perlmunger-perl{a} libpod-eventual-perl{a} libpod-weaver-perl{a} libppi-perl{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librole-hasmessage-perl{a} librole-identifiable-perl{a} librole-tiny-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libscope-guard-perl{a} libsensors-config{a} libsensors5{a} libset-object-perl{a} libsharpyuv0{a} libsm6{a} libsoftware-license-perl{a} libspecio-perl{a} libspiffy-perl{a} libssh2-1t64{a} libstring-errf-perl{a} libstring-flogger-perl{a} libstring-formatter-perl{a} libstring-rewriteprefix-perl{a} libstring-truncate-perl{a} libsub-exporter-formethods-perl{a} libsub-exporter-globexporter-perl{a} libsub-exporter-perl{a} libsub-exporter-progressive-perl{a} libsub-identify-perl{a} libsub-install-perl{a} libsub-name-perl{a} libsub-quote-perl{a} libsub-uplevel-perl{a} libsyntax-keyword-junction-perl{a} libtask-weaken-perl{a} libtcl8.6{a} libterm-encoding-perl{a} libterm-readkey-perl{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-file-perl{a} libtest-files-perl{a} libtest-most-perl{a} libtest-output-perl{a} libtest-warn-perl{a} libtest2-suite-perl{a} libtext-csv-perl{a} libtext-diff-perl{a} libtext-glob-perl{a} libtext-template-perl{a} libthai-data{a} libthai0{a} libthrowable-perl{a} libtie-ixhash-perl{a} libtiff6{a} libtimedate-perl{a} libtingea0{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtry-tiny-perl{a} libtype-tiny-perl{a} libuchardet0{a} liburi-perl{a} libuv1t64{a} libvariable-magic-perl{a} libwebp7{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml-parser-perl{a} libxml-writer-perl{a} libxml2{a} libxrender1{a} libxss1{a} libxstring-perl{a} libxt6t64{a} libyaml-tiny-perl{a} m4{a} mafft{a} man-db{a} mcl{a} media-types{a} ncbi-blast+{a} ncbi-data{a} netbase{a} openssl{a} parallel{a} perl-openssl-defaults{a} po-debconf{a} prank{a} procps{a} python3{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} r-base-core{a} readline-common{a} sensible-utils{a} sysstat{a} tzdata{a} ucf{a} unzip{a} x11-common{a} xdg-utils{a} zip{a} The following packages are RECOMMENDED but will NOT be installed: bash-completion bcron bioperl-run cpanminus cron cronie curl devscripts krb5-locales libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libarchive-tar-wrapper-perl libarray-compare-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libcache-cache-perl libclass-c3-xs-perl libconvert-binary-c-perl libdata-dump-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libdevel-lexalias-perl libdevel-partialdump-perl libfile-mimeinfo-perl libgd-perl libglib2.0-data libgraphviz-perl libhtml-form-perl libhtml-format-perl libhtml-tableextract-perl libhttp-daemon-perl libio-compress-brotli-perl libipc-shareable-perl libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libmailtools-perl libmime-lite-perl libmldbm-perl libnet-dbus-perl libpod-coverage-trustpod-perl libpostscript-perl libref-util-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl libterm-readline-gnu-perl libterm-ui-perl libtest-cpan-meta-perl libtest-pod-coverage-perl libtest-pod-perl libtext-csv-xs-perl libtype-tiny-xs-perl libunicode-utf8-perl libx11-protocol-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libyaml-perl linux-sysctl-defaults lynx perl-doc perl-tk psmisc publicsuffix r-base-dev r-doc-html r-recommended ruby shared-mime-info systemd systemd-cron wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 315 newly installed, 0 to remove and 0 not upgraded. Need to get 116 MB of archives. After unpacking 392 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libclass-data-inheritable-perl all 0.10-1 [8632 B] Get: 48 http://deb.debian.org/debian trixie/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 bioperl all 1.7.8-1 [246 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 cd-hit amd64 4.8.1-4 [522 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 67 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libparams-util-perl amd64 1.102-3+b1 [24.4 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.009-1+b1 [16.2 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.5 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libclass-load-perl all 0.25-2 [15.3 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libio-stringy-perl all 2.113-2 [48.3 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libparams-validate-perl amd64 1.31-2+b3 [63.4 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libgetopt-long-descriptive-perl all 0.115-1 [27.6 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libio-tiecombine-perl all 1.005-3 [10.8 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libmodule-pluggable-perl all 5.2-5 [23.0 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libstring-rewriteprefix-perl all 0.009-1 [7140 B] Get: 94 http://deb.debian.org/debian trixie/main amd64 libapp-cmd-perl all 0.336-1 [65.8 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libscope-guard-perl all 0.21-2 [8212 B] Get: 96 http://deb.debian.org/debian trixie/main amd64 libautobox-perl amd64 3.0.2-1+b1 [33.0 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libperlio-utf8-strict-perl amd64 0.010-1+b3 [11.4 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libmixin-linewise-perl all 0.111-1 [14.4 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libconfig-ini-perl all 1:0.029-1 [23.7 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libclass-load-xs-perl amd64 0.10-2+b4 [14.2 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get: 102 http://deb.debian.org/debian trixie/main amd64 libdevel-globaldestruction-perl all 0.14-4 [7144 B] Get: 103 http://deb.debian.org/debian trixie/main amd64 libalgorithm-c3-perl all 0.11-2 [10.8 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libclass-c3-perl all 0.35-2 [21.0 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libmro-compat-perl all 0.15-2 [11.8 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libdevel-overloadinfo-perl all 0.007-1 [7896 B] Get: 107 http://deb.debian.org/debian trixie/main amd64 libeval-closure-perl all 0.14-3 [11.2 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libdist-checkconflicts-perl all 0.11-2 [10.5 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-conflicts-perl all 0.003-2 [7356 B] Get: 110 http://deb.debian.org/debian trixie/main amd64 libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libpackage-stash-xs-perl amd64 0.30-1+b4 [20.9 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libmoose-perl amd64 2.2207-1+b2 [766 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libvariable-magic-perl amd64 0.64-1+b1 [44.9 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libsub-identify-perl amd64 0.14-3+b3 [11.3 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libsub-name-perl amd64 0.27-1+b3 [12.5 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libnamespace-autoclean-perl all 0.31-1 [13.8 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libmoosex-role-parameterized-perl all 1.11-2 [41.9 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libmoosex-oneargnew-perl all 0.007-1 [8180 B] Get: 121 http://deb.debian.org/debian trixie/main amd64 libcpanel-json-xs-perl amd64 4.38-1+b1 [129 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libjson-maybexs-perl all 1.004008-1 [12.9 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libstring-formatter-perl all 1.235-1 [22.1 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libstring-errf-perl all 0.009-1 [12.9 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 librole-hasmessage-perl all 0.007-1 [9112 B] Get: 127 http://deb.debian.org/debian trixie/main amd64 librole-identifiable-perl all 0.009-1 [10.4 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b4 [36.1 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libthrowable-perl all 1.001-2 [15.7 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libtie-ixhash-perl all 1.23-4 [11.7 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libconfig-mvp-perl all 2.200013-1 [47.1 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libconfig-mvp-reader-ini-perl all 2.101465-1 [6900 B] Get: 138 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 139 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-2 [339 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.30-1 [105 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.83-1+b1 [99.7 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.47-1+b1 [13.9 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libterm-readkey-perl amd64 2.38-2+b4 [24.6 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libcpan-uploader-perl all 0.103018-1 [16.3 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libdata-section-perl all 0.200008-1 [13.1 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libclass-inspector-perl all 1.36-3 [17.5 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libfile-sharedir-perl all 1.118-3 [16.0 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libparams-validationcompiler-perl all 0.31-1 [30.9 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libxstring-perl amd64 0.005-2+b4 [8076 B] Get: 165 http://deb.debian.org/debian trixie/main amd64 libspecio-perl all 0.48-1 [142 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libdatetime-locale-perl all 1:1.41-1 [3131 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libclass-singleton-perl all 1.6-2 [12.5 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libdatetime-timezone-perl all 1:2.63-2+2024b [261 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libdatetime-perl amd64 2:1.65-1+b2 [116 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libfile-copy-recursive-perl all 0.45-4 [20.0 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libnumber-compare-perl all 0.03-3 [6332 B] Get: 172 http://deb.debian.org/debian trixie/main amd64 libtext-glob-perl all 0.11-3 [7676 B] Get: 173 http://deb.debian.org/debian trixie/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 libfile-pushd-perl all 1.016-2 [13.5 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libfile-sharedir-install-perl all 0.14-2 [11.6 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libhash-merge-simple-perl all 0.052-1 [8232 B] Get: 177 http://deb.debian.org/debian trixie/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 liblog-dispatch-perl all 2.71-1 [75.8 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 liblog-dispatch-array-perl all 1.005-1 [6700 B] Get: 180 http://deb.debian.org/debian trixie/main amd64 libstring-flogger-perl all 1.101246-1 [7380 B] Get: 181 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-globexporter-perl all 0.006-1 [8024 B] Get: 182 http://deb.debian.org/debian trixie/main amd64 liblog-dispatchouli-perl all 3.008-1 [34.4 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libexporter-tiny-perl all 1.006002-1 [38.7 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 liblist-moreutils-xs-perl amd64 0.430-4+b2 [42.1 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libsyntax-keyword-junction-perl all 0.003009-1 [12.7 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libmoose-autobox-perl all 0.16-2 [52.8 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 libaliased-perl all 0.34-3 [13.5 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libmoosex-lazyrequire-perl all 0.11-2 [9212 B] Get: 190 http://deb.debian.org/debian trixie/main amd64 libmoosex-setonce-perl all 0.200002-2 [6632 B] Get: 191 http://deb.debian.org/debian trixie/main amd64 libcarp-clan-perl all 6.08-2 [14.1 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-formethods-perl all 0.100055-1 [8024 B] Get: 193 http://deb.debian.org/debian trixie/main amd64 libmoosex-types-perl all 0.50-2 [54.6 kB] Get: 194 http://deb.debian.org/debian trixie/main amd64 libmoosex-types-perl-perl all 0.101344-1 [8160 B] Get: 195 http://deb.debian.org/debian trixie/main amd64 libpath-tiny-perl all 0.146-1 [56.2 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 libmodule-path-perl all 0.19-3 [12.3 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 libtask-weaken-perl all 1.06-2 [9364 B] Get: 198 http://deb.debian.org/debian trixie/main amd64 libppi-perl all 1.279-1 [294 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 libtype-tiny-perl all 2.004000-1 [357 kB] Get: 200 http://deb.debian.org/debian trixie/main amd64 libperl-prereqscanner-perl all 1.100-1 [31.0 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 libperl-version-perl all 1.017-1 [29.0 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 libtext-template-perl all 1.61-1 [54.4 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 libsoftware-license-perl all 0.104006-1 [116 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 libterm-encoding-perl all 0.03-2 [4980 B] Get: 205 http://deb.debian.org/debian trixie/main amd64 libyaml-tiny-perl all 1.74-1 [30.7 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 libdist-zilla-perl all 6.032-1 [343 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 dh-dist-zilla all 1.4.1 [17.9 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get: 209 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 libarray-utils-perl all 0.5-3 [6184 B] Get: 218 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3+b1 [152 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 220 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 223 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 224 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 225 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 226 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 227 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get: 229 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 230 http://deb.debian.org/debian trixie/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get: 231 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 232 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 233 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 234 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 235 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 236 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 237 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 238 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get: 239 http://deb.debian.org/debian trixie/main amd64 libdata-compare-perl all 1.29-1 [19.6 kB] Get: 240 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 241 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 242 http://deb.debian.org/debian trixie/main amd64 libpod-eventual-perl all 0.094003-1 [14.2 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 libstring-truncate-perl all 1.100603-1 [10.2 kB] Get: 244 http://deb.debian.org/debian trixie/main amd64 libpod-elemental-perl all 0.103006-1 [67.2 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 libpod-elemental-perlmunger-perl all 0.200007-1 [10.5 kB] Get: 246 http://deb.debian.org/debian trixie/main amd64 libpod-weaver-perl all 4.020-1 [70.1 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 libdist-zilla-plugin-podweaver-perl all 4.010-1 [9580 B] Get: 248 http://deb.debian.org/debian trixie/main amd64 libenv-path-perl all 0.19-4 [19.1 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 libfile-chdir-perl all 0.1008-1.2 [11.9 kB] Get: 250 http://deb.debian.org/debian trixie/main amd64 libfile-grep-perl all 0.02-3 [8352 B] Get: 251 http://deb.debian.org/debian trixie/main amd64 libfile-slurper-perl all 0.014-1 [8560 B] Get: 252 http://deb.debian.org/debian trixie/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 253 http://deb.debian.org/debian trixie/main amd64 libfindbin-libs-perl all 3.0.2-1 [29.7 kB] Get: 254 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get: 255 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 256 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get: 257 http://deb.debian.org/debian trixie/main amd64 libheap-perl all 0.80-5 [34.3 kB] Get: 258 http://deb.debian.org/debian trixie/main amd64 libset-object-perl amd64 1.42-1+b5 [37.6 kB] Get: 259 http://deb.debian.org/debian trixie/main amd64 libgraph-perl all 1:0.9729-1 [108 kB] Get: 260 http://deb.debian.org/debian trixie/main amd64 libspiffy-perl all 0.46-1 [25.7 kB] Get: 261 http://deb.debian.org/debian trixie/main amd64 libio-all-perl all 0.87-2 [67.3 kB] Get: 262 http://deb.debian.org/debian trixie/main amd64 libparse-yapp-perl all 1.21-4 [41.5 kB] Get: 263 http://deb.debian.org/debian trixie/main amd64 libxml-parser-perl amd64 2.47-1+b3 [198 kB] Get: 264 http://deb.debian.org/debian trixie/main amd64 libxml-writer-perl all 0.900-2 [26.8 kB] Get: 265 http://deb.debian.org/debian trixie/main amd64 libgraph-readwrite-perl all 2.10-1 [45.2 kB] Get: 266 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 267 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get: 268 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 269 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 270 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 271 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 272 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3+b1 [2450 kB] Get: 273 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 274 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get: 275 http://deb.debian.org/debian trixie/main amd64 liblog-log4perl-perl all 1.57-1 [367 kB] Get: 276 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB] Get: 277 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB] Get: 278 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB] Get: 279 http://deb.debian.org/debian trixie/main amd64 libpadwalker-perl amd64 2.5-1+b6 [18.6 kB] Get: 280 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 281 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 282 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [223 kB] Get: 283 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [54.2 kB] Get: 284 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [35.2 kB] Get: 285 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b2 [12.8 kB] Get: 286 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b2 [9236 B] Get: 287 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 288 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get: 289 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 290 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 291 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get: 292 http://deb.debian.org/debian trixie/main amd64 libtest-file-perl all 1.993-1 [24.5 kB] Get: 293 http://deb.debian.org/debian trixie/main amd64 libtest2-suite-perl all 0.000163-1 [383 kB] Get: 294 http://deb.debian.org/debian trixie/main amd64 libtest-files-perl all 0.26-1 [21.6 kB] Get: 295 http://deb.debian.org/debian trixie/main amd64 libtest-output-perl all 1.034-1 [16.0 kB] Get: 296 http://deb.debian.org/debian trixie/main amd64 libtext-csv-perl all 2.04-1 [112 kB] Get: 297 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 298 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 299 http://deb.debian.org/debian trixie/main amd64 libtingea0 amd64 21-361-2+b2 [52.1 kB] Get: 300 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get: 301 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get: 302 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get: 303 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 304 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get: 305 http://deb.debian.org/debian trixie/main amd64 mafft amd64 7.505-1 [1078 kB] Get: 306 http://deb.debian.org/debian trixie/main amd64 mcl amd64 1:22-282+ds-2 [474 kB] Get: 307 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get: 308 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.16.0+ds-6+b1 [15.2 MB] Get: 309 http://deb.debian.org/debian trixie/main amd64 sysstat amd64 12.7.5-2 [623 kB] Get: 310 http://deb.debian.org/debian trixie/main amd64 parallel all 20240222+ds-2 [2163 kB] Get: 311 http://deb.debian.org/debian trixie/main amd64 prank amd64 0.0.170427+dfsg-3 [395 kB] Get: 312 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-14 [233 kB] Get: 313 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 314 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 315 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Fetched 116 MB in 2s (73.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (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 ... 19969 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_amd64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:amd64 (3.12.7-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... Selecting previously unselected package python3-minimal. (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 ... 20289 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_amd64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (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 ... 21351 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package libproc2-0:amd64. 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Selecting previously unselected package gettext. Preparing to unpack .../049-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../050-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../051-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../052-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../053-libparams-util-perl_1.102-3+b1_amd64.deb ... Unpacking libparams-util-perl (1.102-3+b1) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../054-libsub-install-perl_0.929-1_all.deb ... Unpacking libsub-install-perl (0.929-1) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../055-libdata-optlist-perl_0.114-1_all.deb ... Unpacking libdata-optlist-perl (0.114-1) ... Selecting previously unselected package libb-hooks-op-check-perl:amd64. Preparing to unpack .../056-libb-hooks-op-check-perl_0.22-3+b2_amd64.deb ... Unpacking libb-hooks-op-check-perl:amd64 (0.22-3+b2) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../057-libdynaloader-functions-perl_0.004-1_all.deb ... Unpacking libdynaloader-functions-perl (0.004-1) ... Selecting previously unselected package libdevel-callchecker-perl:amd64. Preparing to unpack .../058-libdevel-callchecker-perl_0.009-1+b1_amd64.deb ... Unpacking libdevel-callchecker-perl:amd64 (0.009-1+b1) ... Selecting previously unselected package libparams-classify-perl:amd64. Preparing to unpack .../059-libparams-classify-perl_0.015-2+b4_amd64.deb ... Unpacking libparams-classify-perl:amd64 (0.015-2+b4) ... 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Selecting previously unselected package libfile-sharedir-perl. Preparing to unpack .../140-libfile-sharedir-perl_1.118-3_all.deb ... Unpacking libfile-sharedir-perl (1.118-3) ... Selecting previously unselected package libparams-validationcompiler-perl. Preparing to unpack .../141-libparams-validationcompiler-perl_0.31-1_all.deb ... Unpacking libparams-validationcompiler-perl (0.31-1) ... Selecting previously unselected package libxstring-perl:amd64. Preparing to unpack .../142-libxstring-perl_0.005-2+b4_amd64.deb ... Unpacking libxstring-perl:amd64 (0.005-2+b4) ... Selecting previously unselected package libspecio-perl. Preparing to unpack .../143-libspecio-perl_0.48-1_all.deb ... Unpacking libspecio-perl (0.48-1) ... Selecting previously unselected package libdatetime-locale-perl. Preparing to unpack .../144-libdatetime-locale-perl_1%3a1.41-1_all.deb ... Unpacking libdatetime-locale-perl (1:1.41-1) ... Selecting previously unselected package libclass-singleton-perl. 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Selecting previously unselected package libaliased-perl. Preparing to unpack .../166-libaliased-perl_0.34-3_all.deb ... Unpacking libaliased-perl (0.34-3) ... Selecting previously unselected package libmoosex-lazyrequire-perl. Preparing to unpack .../167-libmoosex-lazyrequire-perl_0.11-2_all.deb ... Unpacking libmoosex-lazyrequire-perl (0.11-2) ... Selecting previously unselected package libmoosex-setonce-perl. Preparing to unpack .../168-libmoosex-setonce-perl_0.200002-2_all.deb ... Unpacking libmoosex-setonce-perl (0.200002-2) ... Selecting previously unselected package libcarp-clan-perl. Preparing to unpack .../169-libcarp-clan-perl_6.08-2_all.deb ... Unpacking libcarp-clan-perl (6.08-2) ... Selecting previously unselected package libsub-exporter-formethods-perl. Preparing to unpack .../170-libsub-exporter-formethods-perl_0.100055-1_all.deb ... Unpacking libsub-exporter-formethods-perl (0.100055-1) ... Selecting previously unselected package libmoosex-types-perl. 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Setting up liblog-dispatchouli-perl (3.008-1) ... Setting up libpod-weaver-perl (4.020-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libwww-perl (6.77-1) ... Setting up libcpan-uploader-perl (0.103018-1) ... Setting up libdist-zilla-perl (6.032-1) ... Setting up libdist-zilla-plugin-podweaver-perl (4.010-1) ... Setting up libxml-parser-perl (2.47-1+b3) ... Setting up dh-dist-zilla (1.4.1) ... Setting up libgraph-readwrite-perl (2.10-1) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.36-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/2228133/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2228133/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/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 dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with dist-zilla dh_dzil_clean dh_clean debian/rules build dh build --with dist-zilla dh_update_autotools_config dh_autoreconf debian/rules override_dh_dzil_build make[1]: Entering directory '/build/reproducible-path/roary-3.13.0+dfsg' mv bin/create_pan_genome_plots.R bin/create_pan_genome_plots dh_dzil_build -- [DZ] beginning to build Bio-Roary [DZ] writing Bio-Roary in .build/debian-build [DZ] built in .build/debian-build make[1]: Leaving directory '/build/reproducible-path/roary-3.13.0+dfsg' dh_auto_configure -D .build/debian-build cd .build/debian-build && /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/roary-3.13.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/roary-3.13.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro" Warning: prerequisite Digest::MD5::File 0 not found. Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::Roary Writing MYMETA.yml and MYMETA.json dh_auto_build -D .build/debian-build cd .build/debian-build && make -j12 make[1]: Entering directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' cp lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm blib/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm cp lib/Bio/Roary/AccessoryClustering.pm blib/lib/Bio/Roary/AccessoryClustering.pm cp lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm blib/lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.pm cp lib/Bio/Roary/AssemblyStatistics.pm blib/lib/Bio/Roary/AssemblyStatistics.pm cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm cp lib/Bio/Roary/CommandLine/IterativeCdhit.pm blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pm cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm cp lib/Bio/Roary/AccessoryBinaryFasta.pm blib/lib/Bio/Roary/AccessoryBinaryFasta.pm cp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm cp lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.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/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm cp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm cp lib/Bio/Roary/CommandLine/AssemblyStatistics.pm blib/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.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/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm cp lib/Bio/Roary/External/Mafft.pm blib/lib/Bio/Roary/External/Mafft.pm cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm cp lib/Bio/Roary/External/Fasttree.pm blib/lib/Bio/Roary/External/Fasttree.pm cp lib/Bio/Roary/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pm cp lib/Bio/Roary/Output/EMBLHeaderCommon.pm blib/lib/Bio/Roary/Output/EMBLHeaderCommon.pm cp lib/Bio/Roary/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm cp lib/Bio/Roary/JobRunner/Parallel.pm blib/lib/Bio/Roary/JobRunner/Parallel.pm cp lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm cp lib/Bio/Roary/Output/GroupMultifasta.pm blib/lib/Bio/Roary/Output/GroupMultifasta.pm cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm cp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.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/External/Mcl.pm blib/lib/Bio/Roary/External/Mcl.pm cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm cp lib/Bio/Roary/GeneNamesFromGFF.pm blib/lib/Bio/Roary/GeneNamesFromGFF.pm cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm cp lib/Bio/Roary/MergeMultifastaAlignments.pm blib/lib/Bio/Roary/MergeMultifastaAlignments.pm cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pm cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm cp lib/Bio/Roary/External/IterativeCdhit.pm blib/lib/Bio/Roary/External/IterativeCdhit.pm cp lib/Bio/Roary/Output/QueryGroups.pm blib/lib/Bio/Roary/Output/QueryGroups.pm cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.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/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.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/SpreadsheetRole.pm blib/lib/Bio/Roary/SpreadsheetRole.pm cp lib/Bio/Roary/SampleOrder.pm blib/lib/Bio/Roary/SampleOrder.pm cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm cp lib/Bio/Roary/UniqueGenesPerSample.pm blib/lib/Bio/Roary/UniqueGenesPerSample.pm cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm cp lib/Bio/Roary/PresenceAbsenceMatrix.pm blib/lib/Bio/Roary/PresenceAbsenceMatrix.pm cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm cp lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.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 cp bin/iterative_cdhit blib/script/iterative_cdhit "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome cp bin/pan_genome_assembly_statistics blib/script/pan_genome_assembly_statistics "/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 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/iterative_cdhit 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_assembly_statistics cp bin/pan_genome_post_analysis blib/script/pan_genome_post_analysis "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_core_alignment 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_post_analysis cp bin/parallel_all_against_all_blastp blib/script/parallel_all_against_all_blastp cp bin/protein_alignment_from_nucleotides blib/script/protein_alignment_from_nucleotides "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_reorder_spreadsheet cp bin/query_pan_genome blib/script/query_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/parallel_all_against_all_blastp "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/protein_alignment_from_nucleotides "/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 "/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 cp bin/roary-query_pan_genome blib/script/roary-query_pan_genome cp bin/roary-unique_genes_per_sample blib/script/roary-unique_genes_per_sample "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-pan_genome_reorder_spreadsheet "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-query_pan_genome "/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 Manifying 28 pod documents Manifying 25 pod documents make[1]: Leaving directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/roary-3.13.0+dfsg' # Hmmm, seems the test is not automatically run anyway by the build system dh_auto_test || true make[1]: Leaving directory '/build/reproducible-path/roary-3.13.0+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with dist-zilla dh_testroot dh_prep dh_auto_install -D .build/debian-build --destdir=debian/roary/ cd .build/debian-build && make -j12 install DESTDIR=/build/reproducible-path/roary-3.13.0\+dfsg/debian/roary AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryBinaryFasta.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnnotateGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SequenceLengths.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AssemblyStatistics.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFFs.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParseGFFAnnotationRole.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SampleOrder.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupStatistics.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ContigsToGeneIDsFromGFF.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PostAnalysis.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterUnknownsFromFasta.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ClustersRole.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/BedFromGFFRole.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/IterativeCdhit.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SpreadsheetRole.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Exceptions.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnalyseGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/OrderGenes.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SortFasta.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupLabels.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ChunkFastaFile.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/UniqueGenesPerSample.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SplitGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReformatInputGFFs.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFF.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReorderSpreadsheet.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GeneNamesFromGFF.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CombinedProteome.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PresenceAbsenceMatrix.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryClustering.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/LookupGeneFiles.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/InflateClusters.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterFullClusters.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PrepareInputFiles.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParallelAllAgainstAllBlast.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/MergeMultifastaAlignments.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/QC/Report.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mafft.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Fasttree.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Prank.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/PostAnalysis.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Cdhit.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/GeneAlignmentFromNucleotides.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/IterativeCdhit.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mcl.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Makeblastdb.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Blastp.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/CheckTools.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Parallel.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Role.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Local.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastasNucleotide.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/DifferenceBetweenSets.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/NumberOfGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastas.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaProtein.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaNucleotide.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/BlastIdentityFrequency.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EMBLHeaderCommon.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupMultifasta.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/QueryGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EmblGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/CreatePanGenome.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/AssemblyStatistics.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/QueryRoary.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryPostAnalysis.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryCoreAlignment.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/IterativeCdhit.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Roary.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/UniqueGenesPerSample.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Common.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/parallel_all_against_all_blastp.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/protein_alignment_from_nucleotides.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_post_analysis.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome_plots.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/iterative_cdhit.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-unique_genes_per_sample.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_assembly_statistics.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_reorder_spreadsheet.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-pan_genome_reorder_spreadsheet.1p Installing 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/build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::GeneAlignmentFromNucleotides.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFFs.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Roary.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ParallelAllAgainstAllBlast.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::CreatePanGenome.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::AssemblyStatistics.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnalyseGroups.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Cdhit.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CombinedProteome.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Mcl.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::IterativeCdhit.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReorderSpreadsheet.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Blastp.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/protein_alignment_from_nucleotides Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/parallel_all_against_all_blastp Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/create_pan_genome Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/extract_proteome_from_gff Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_core_alignment Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/iterative_cdhit Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/create_pan_genome_plots Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/query_pan_genome Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_assembly_statistics Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-unique_genes_per_sample Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-pan_genome_reorder_spreadsheet Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-query_pan_genome Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_reorder_spreadsheet Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/transfer_annotation_to_groups Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_post_analysis Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-create_pan_genome_plots.R make[1]: Leaving directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'roary' in '../roary_3.13.0+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../roary_3.13.0+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../roary_3.13.0+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . 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/2228133/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2228133/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/2228133 and its subdirectories I: Current time: Mon Nov 25 21:39:54 +14 2024 I: pbuilder-time-stamp: 1732520394 + false + set +x Mon Nov 25 07:39:54 UTC 2024 I: Signing ./b2/roary_3.13.0+dfsg-1_amd64.buildinfo as roary_3.13.0+dfsg-1_amd64.buildinfo.asc Mon Nov 25 07:39:54 UTC 2024 I: Signed ./b2/roary_3.13.0+dfsg-1_amd64.buildinfo as ./b2/roary_3.13.0+dfsg-1_amd64.buildinfo.asc Mon Nov 25 07:39:54 UTC 2024 - build #2 for roary/trixie/amd64 on infom01-amd64 done. Starting cleanup. All cleanup done. Mon Nov 25 07:39:54 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-UuEA9ckM, removing. /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ: total 176 drwxr-xr-x 2 jenkins jenkins 4096 Nov 25 07:35 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 25 07:39 b2 -rw------- 1 jenkins jenkins 163150 Nov 25 07:35 rbuildlog.9YsMTsD -rw-r--r-- 1 jenkins jenkins 2501 Nov 8 2019 roary_3.13.0+dfsg-1.dsc /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/b1: total 596 -rw-r--r-- 1 jenkins jenkins 159244 Nov 25 07:35 build.log -rw-r--r-- 1 jenkins jenkins 6612 Nov 25 07:35 roary_3.13.0+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2501 Nov 25 07:35 roary_3.13.0+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 172956 Nov 25 07:35 roary_3.13.0+dfsg-1_all.deb -rw-r--r-- 1 jenkins jenkins 14497 Nov 25 07:35 roary_3.13.0+dfsg-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 15379 Nov 25 07:35 roary_3.13.0+dfsg-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1145 Nov 25 07:35 roary_3.13.0+dfsg-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 1592 Nov 25 07:35 roary_3.13.0+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 207348 Nov 25 07:35 roary_3.13.0+dfsg.orig.tar.xz /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/b2: total 588 -rw-r--r-- 1 jenkins jenkins 161173 Nov 25 07:39 build.log -rw-r--r-- 1 jenkins jenkins 6612 Nov 25 07:39 roary_3.13.0+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2501 Nov 25 07:39 roary_3.13.0+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 172956 Nov 25 07:39 roary_3.13.0+dfsg-1_all.deb -rw-r--r-- 1 jenkins jenkins 14494 Nov 25 07:39 roary_3.13.0+dfsg-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 15376 Nov 25 07:39 roary_3.13.0+dfsg-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1145 Nov 25 07:39 roary_3.13.0+dfsg-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 1592 Nov 25 07:39 roary_3.13.0+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 207348 Nov 25 07:39 roary_3.13.0+dfsg.orig.tar.xz Mon Nov 25 07:39:55 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. Mon Nov 25 07:39:56 UTC 2024 I: roary_3.13.0+dfsg-1_amd64.changes: Format: 1.8 Date: Fri, 08 Nov 2019 14:37:07 +0100 Source: roary Binary: roary Architecture: all Version: 3.13.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.13.0+dfsg-1) unstable; urgency=medium . * New upstream release. * Use debhelper 12. * Bump Standards-Version. * Update source lintian override location and tags. Checksums-Sha1: d98d02d7ee7612a8d5c9f9bf8c6f0786aba8c4b3 172956 roary_3.13.0+dfsg-1_all.deb 466d96149c2992664c2a900f4a50b25117139543 14497 roary_3.13.0+dfsg-1_amd64.buildinfo Checksums-Sha256: 407c586f74905ca1cd02fa839d4f37a5975f5f0fb0e1a730dd4949f3f62a08c3 172956 roary_3.13.0+dfsg-1_all.deb a83d86733e349a14066694f75a80f4b18eb5d0186fc819f2900a10a742176924 14497 roary_3.13.0+dfsg-1_amd64.buildinfo Files: af01483d1d735e74de6bd65123abd903 172956 science optional roary_3.13.0+dfsg-1_all.deb 1caace9327fc81cb567ca92c0ab85e84 14497 science optional roary_3.13.0+dfsg-1_amd64.buildinfo removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/roary_3.13.0+dfsg-1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/roary_3.13.0+dfsg-1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/roary_3.13.0+dfsg-1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/roary_3.13.0+dfsg-1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/amd64/roary_3.13.0+dfsg-1_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/roary_3.13.0+dfsg-1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-11-25 07:35:27.807890803 +0000 +++ b2/build.log 2024-11-25 07:39:55.587791207 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Dec 28 01:56:01 -12 2025 -I: pbuilder-time-stamp: 1766930161 +I: Current time: Mon Nov 25 21:35:30 +14 2024 +I: pbuilder-time-stamp: 1732520130 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -30,51 +30,83 @@ dpkg-source: info: applying new-bioperl-require.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2221921/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2228133/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 25 07:35 /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/2228133/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2228133/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges: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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='ada19eb8f6c441e19002ecde773b8ad5' - 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='2221921' - PS1='# ' - PS2='> ' + INVOCATION_ID=fffeff89364541e88d42ab1dae4cbd47 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2228133 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.oU2ie3pZ/pbuilderrc_IGIj --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/b1 --logfile b1/build.log roary_3.13.0+dfsg-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/pbuilderrc_ybpu --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/b2 --logfile b2/build.log roary_3.13.0+dfsg-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2221921/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2228133/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -485,7 +517,7 @@ Get: 313 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 314 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 315 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] -Fetched 116 MB in 1s (83.0 MB/s) +Fetched 116 MB in 2s (73.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (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 ... 19969 files and directories currently installed.) @@ -1530,8 +1562,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Dec 28 13:57:30 UTC 2025. -Universal Time is now: Sun Dec 28 13:57:30 UTC 2025. +Local time is now: Mon Nov 25 07:39:09 UTC 2024. +Universal Time is now: Mon Nov 25 07:39:09 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libjson-maybexs-perl (1.004008-1) ... @@ -1803,7 +1835,11 @@ fakeroot is already the newest version (1.36-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/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/2228133/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2228133/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/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 @@ -1837,116 +1873,116 @@ dh_auto_build -D .build/debian-build cd .build/debian-build && make -j12 make[1]: Entering directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' -cp lib/Bio/Roary/AccessoryClustering.pm blib/lib/Bio/Roary/AccessoryClustering.pm -cp lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm -cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm +cp lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm blib/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm -cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm -cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm -cp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm -cp lib/Bio/Roary/AccessoryBinaryFasta.pm blib/lib/Bio/Roary/AccessoryBinaryFasta.pm -cp lib/Bio/Roary/AnnotateGroups.pm blib/lib/Bio/Roary/AnnotateGroups.pm +cp lib/Bio/Roary/AccessoryClustering.pm blib/lib/Bio/Roary/AccessoryClustering.pm +cp lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm blib/lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm +cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.pm +cp lib/Bio/Roary/AssemblyStatistics.pm blib/lib/Bio/Roary/AssemblyStatistics.pm +cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm -cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.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/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm +cp lib/Bio/Roary/AccessoryBinaryFasta.pm blib/lib/Bio/Roary/AccessoryBinaryFasta.pm cp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm -cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm -cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.pm -cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm -cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm +cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm +cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm +cp lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.pm -cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.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/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/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm +cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm -cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm -cp lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm blib/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.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/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pm -cp lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm -cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pm -cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm -cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm -cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm -cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm -cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.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/Prank.pm blib/lib/Bio/Roary/External/Prank.pm -cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm -cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm +cp lib/Bio/Roary/CommandLine/AssemblyStatistics.pm blib/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm +cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm +cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.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/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm +cp lib/Bio/Roary/External/Mafft.pm blib/lib/Bio/Roary/External/Mafft.pm cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm +cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm cp lib/Bio/Roary/External/Fasttree.pm blib/lib/Bio/Roary/External/Fasttree.pm -cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm +cp lib/Bio/Roary/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pm cp lib/Bio/Roary/Output/EMBLHeaderCommon.pm blib/lib/Bio/Roary/Output/EMBLHeaderCommon.pm cp lib/Bio/Roary/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm -cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm -cp lib/Bio/Roary/JobRunner/Parallel.pm blib/lib/Bio/Roary/JobRunner/Parallel.pm -cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.pm +cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm -cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm +cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm +cp lib/Bio/Roary/JobRunner/Parallel.pm blib/lib/Bio/Roary/JobRunner/Parallel.pm +cp lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm +cp lib/Bio/Roary/Output/GroupMultifasta.pm blib/lib/Bio/Roary/Output/GroupMultifasta.pm +cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm cp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm -cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm -cp lib/Bio/Roary/External/Mafft.pm blib/lib/Bio/Roary/External/Mafft.pm +cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.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/External/Mcl.pm blib/lib/Bio/Roary/External/Mcl.pm +cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm cp lib/Bio/Roary/GeneNamesFromGFF.pm blib/lib/Bio/Roary/GeneNamesFromGFF.pm +cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm +cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm +cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm +cp lib/Bio/Roary/MergeMultifastaAlignments.pm blib/lib/Bio/Roary/MergeMultifastaAlignments.pm +cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm +cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pm cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm -cp lib/Bio/Roary/Output/GroupMultifasta.pm blib/lib/Bio/Roary/Output/GroupMultifasta.pm -cp lib/Bio/Roary/External/Mcl.pm blib/lib/Bio/Roary/External/Mcl.pm +cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm +cp lib/Bio/Roary/External/IterativeCdhit.pm blib/lib/Bio/Roary/External/IterativeCdhit.pm +cp lib/Bio/Roary/Output/QueryGroups.pm blib/lib/Bio/Roary/Output/QueryGroups.pm +cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm +cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm +cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm cp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm -cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm -cp lib/Bio/Roary/Output/QueryGroups.pm blib/lib/Bio/Roary/Output/QueryGroups.pm -cp lib/Bio/Roary/SampleOrder.pm blib/lib/Bio/Roary/SampleOrder.pm +cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm cp lib/Bio/Roary/ReorderSpreadsheet.pm blib/lib/Bio/Roary/ReorderSpreadsheet.pm -cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm cp lib/Bio/Roary/SequenceLengths.pm blib/lib/Bio/Roary/SequenceLengths.pm -cp lib/Bio/Roary/UniqueGenesPerSample.pm blib/lib/Bio/Roary/UniqueGenesPerSample.pm +cp lib/Bio/Roary/SpreadsheetRole.pm blib/lib/Bio/Roary/SpreadsheetRole.pm +cp lib/Bio/Roary/SampleOrder.pm blib/lib/Bio/Roary/SampleOrder.pm cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm -cp lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm +cp lib/Bio/Roary/UniqueGenesPerSample.pm blib/lib/Bio/Roary/UniqueGenesPerSample.pm +cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm cp lib/Bio/Roary/PresenceAbsenceMatrix.pm blib/lib/Bio/Roary/PresenceAbsenceMatrix.pm cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm -cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm -cp lib/Bio/Roary/SpreadsheetRole.pm blib/lib/Bio/Roary/SpreadsheetRole.pm -cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm +cp lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm -cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm -cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm +cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.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 cp bin/iterative_cdhit blib/script/iterative_cdhit "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome +cp bin/pan_genome_assembly_statistics blib/script/pan_genome_assembly_statistics "/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 "/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 cp bin/pan_genome_core_alignment blib/script/pan_genome_core_alignment -cp bin/pan_genome_post_analysis blib/script/pan_genome_post_analysis "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_assembly_statistics +cp bin/pan_genome_post_analysis blib/script/pan_genome_post_analysis "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_core_alignment 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 -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_reorder_spreadsheet -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/parallel_all_against_all_blastp +cp bin/parallel_all_against_all_blastp blib/script/parallel_all_against_all_blastp cp bin/protein_alignment_from_nucleotides blib/script/protein_alignment_from_nucleotides +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_reorder_spreadsheet cp bin/query_pan_genome blib/script/query_pan_genome +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/parallel_all_against_all_blastp "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/protein_alignment_from_nucleotides -cp bin/roary blib/script/roary "/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 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-create_pan_genome_plots.R -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-pan_genome_reorder_spreadsheet +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-query_pan_genome cp bin/roary-unique_genes_per_sample blib/script/roary-unique_genes_per_sample +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-pan_genome_reorder_spreadsheet +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-query_pan_genome "/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 @@ -1973,196 +2009,196 @@ Manifying 28 pod documents Manifying 25 pod documents Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ChunkFastaFile.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SplitGroups.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupStatistics.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReformatInputGFFs.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Exceptions.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CombinedProteome.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryBinaryFasta.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnnotateGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SequenceLengths.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterFullClusters.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AssemblyStatistics.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFF.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/LookupGeneFiles.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFFs.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParseGFFAnnotationRole.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SampleOrder.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupStatistics.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ContigsToGeneIDsFromGFF.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PostAnalysis.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterUnknownsFromFasta.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ClustersRole.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/BedFromGFFRole.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PresenceAbsenceMatrix.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/UniqueGenesPerSample.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ContigsToGeneIDsFromGFF.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFFs.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PrepareInputFiles.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/IterativeCdhit.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SpreadsheetRole.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Exceptions.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnalyseGroups.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/OrderGenes.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SortFasta.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupLabels.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ChunkFastaFile.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/UniqueGenesPerSample.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SplitGroups.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReformatInputGFFs.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFF.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReorderSpreadsheet.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GeneNamesFromGFF.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/IterativeCdhit.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CombinedProteome.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PresenceAbsenceMatrix.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryClustering.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryBinaryFasta.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/OrderGenes.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/LookupGeneFiles.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/InflateClusters.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterFullClusters.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PrepareInputFiles.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParallelAllAgainstAllBlast.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnnotateGroups.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReorderSpreadsheet.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupLabels.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterUnknownsFromFasta.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/MergeMultifastaAlignments.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ClustersRole.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnalyseGroups.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SpreadsheetRole.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupMultifasta.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/QueryGroups.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/QC/Report.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mafft.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Fasttree.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Prank.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/PostAnalysis.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Cdhit.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/GeneAlignmentFromNucleotides.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/IterativeCdhit.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mcl.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Makeblastdb.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Blastp.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/CheckTools.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Parallel.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Role.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Local.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastasNucleotide.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/DifferenceBetweenSets.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/NumberOfGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastas.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EmblGroups.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaProtein.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaNucleotide.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/BlastIdentityFrequency.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastasNucleotide.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaProtein.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/DifferenceBetweenSets.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EMBLHeaderCommon.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/NumberOfGroups.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupMultifasta.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/QueryGroups.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EmblGroups.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/CreatePanGenome.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/AssemblyStatistics.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/QueryRoary.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryPostAnalysis.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/UniqueGenesPerSample.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Roary.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/IterativeCdhit.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryCoreAlignment.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/CreatePanGenome.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Common.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/IterativeCdhit.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Roary.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/UniqueGenesPerSample.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/QueryRoary.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Local.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Parallel.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Role.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Cdhit.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Fasttree.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/PostAnalysis.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/CheckTools.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Makeblastdb.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Prank.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mafft.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/IterativeCdhit.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mcl.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Blastp.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/GeneAlignmentFromNucleotides.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/QC/Report.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Common.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/parallel_all_against_all_blastp.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/protein_alignment_from_nucleotides.1p -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_core_alignment.1p -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-query_pan_genome.1p -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/transfer_annotation_to_groups.1p -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_reorder_spreadsheet.1p +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome.1p +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_post_analysis.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome_plots.1p -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/query_pan_genome.1p -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/parallel_all_against_all_blastp.1p -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/extract_proteome_from_gff.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/iterative_cdhit.1p +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-unique_genes_per_sample.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_assembly_statistics.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary.1p -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_post_analysis.1p -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome.1p -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-unique_genes_per_sample.1p +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_reorder_spreadsheet.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-pan_genome_reorder_spreadsheet.1p -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ClustersRole.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnalyseGroups.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AssemblyStatistics.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Fasttree.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::NumberOfGroups.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Cdhit.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Local.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastasNucleotide.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFF.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ChunkFastaFile.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Role.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_core_alignment.1p +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/transfer_annotation_to_groups.1p +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-query_pan_genome.1p +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/query_pan_genome.1p +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/extract_proteome_from_gff.1p +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::BedFromGFFRole.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SequenceLengths.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GroupLabels.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastas.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::UniqueGenesPerSample.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::OrderGenes.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Common.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Local.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::QueryRoary.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::LookupGeneFiles.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::DifferenceBetweenSets.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SpreadsheetRole.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::NumberOfGroups.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Makeblastdb.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::MergeMultifastaAlignments.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::TransferAnnotationToGroups.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::AssemblyStatistics.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Prank.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SplitGroups.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SequenceLengths.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Exceptions.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::EmblGroups.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Blastp.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaNucleotide.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ParallelAllAgainstAllBlast.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PostAnalysis.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryPostAnalysis.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AccessoryClustering.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::QC::Report.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AssemblyStatistics.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::InflateClusters.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Mafft.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Prank.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ContigsToGeneIDsFromGFF.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupMultifasta.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Roary.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReformatInputGFFs.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastasNucleotide.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnnotateGroups.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryReorderSpreadsheet.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::UniqueGenesPerSample.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SampleOrder.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PresenceAbsenceMatrix.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::FilterUnknownsFromFasta.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::CheckTools.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::PostAnalysis.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::BlastIdentityFrequency.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReorderSpreadsheet.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GroupLabels.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::EMBLHeaderCommon.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::UniqueGenesPerSample.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GroupStatistics.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SortFasta.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::CreatePanGenome.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::IterativeCdhit.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFFs.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Mafft.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryPostAnalysis.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::IterativeCdhit.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::IterativeCdhit.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastas.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::EmblGroups.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Parallel.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GeneNamesFromGFF.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::FilterFullClusters.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryCoreAlignment.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Mcl.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::QueryRoary.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::BedFromGFFRole.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaProtein.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::QC::Report.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ExtractProteomeFromGff.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::GeneAlignmentFromNucleotides.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::EMBLHeaderCommon.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::DifferenceBetweenSets.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::FilterUnknownsFromFasta.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Exceptions.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFF.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Role.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GeneNamesFromGFF.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::BlastIdentityFrequency.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ClustersRole.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractCoreGenesFromSpreadsheet.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::QueryGroups.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::MergeMultifastaAlignments.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PresenceAbsenceMatrix.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::IterativeCdhit.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::PostAnalysis.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SampleOrder.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SortFasta.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Common.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AccessoryBinaryFasta.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReformatInputGFFs.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PostAnalysis.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SplitGroups.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ChunkFastaFile.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ParseGFFAnnotationRole.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupMultifasta.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Fasttree.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::UniqueGenesPerSample.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ExtractProteomeFromGff.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PrepareInputFiles.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnnotateGroups.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AccessoryClustering.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SpreadsheetRole.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::FilterFullClusters.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::TransferAnnotationToGroups.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::CheckTools.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::IterativeCdhit.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::GeneAlignmentFromNucleotides.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractCoreGenesFromSpreadsheet.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::GeneAlignmentFromNucleotides.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFFs.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Roary.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ParallelAllAgainstAllBlast.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::CreatePanGenome.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::AssemblyStatistics.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnalyseGroups.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Cdhit.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CombinedProteome.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AccessoryBinaryFasta.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::InflateClusters.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_core_alignment +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Mcl.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::IterativeCdhit.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReorderSpreadsheet.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Blastp.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/protein_alignment_from_nucleotides +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/parallel_all_against_all_blastp Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/create_pan_genome -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/create_pan_genome_plots Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/extract_proteome_from_gff -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-pan_genome_reorder_spreadsheet -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/protein_alignment_from_nucleotides -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_post_analysis -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-create_pan_genome_plots.R +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_core_alignment +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/iterative_cdhit +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/create_pan_genome_plots Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/query_pan_genome Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_assembly_statistics Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-unique_genes_per_sample -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/parallel_all_against_all_blastp -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/iterative_cdhit +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-pan_genome_reorder_spreadsheet +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-query_pan_genome Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_reorder_spreadsheet -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/transfer_annotation_to_groups -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-query_pan_genome +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_post_analysis +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-create_pan_genome_plots.R make[1]: Leaving directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' dh_installdocs dh_installchangelogs @@ -2186,12 +2222,14 @@ 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/2228133/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2228133/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/2221921 and its subdirectories -I: Current time: Sun Dec 28 01:58:26 -12 2025 -I: pbuilder-time-stamp: 1766930306 +I: removing directory /srv/workspace/pbuilder/2228133 and its subdirectories +I: Current time: Mon Nov 25 21:39:54 +14 2024 +I: pbuilder-time-stamp: 1732520394 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/roary_3.13.0+dfsg-1.diff: 89.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/roary_3.13.0+dfsg-1.diff.gz b2/build.log: 83.3% -- replaced with stdout Compressing the 1st log... b1/build.log: 83.6% -- replaced with stdout Mon Nov 25 07:39:57 UTC 2024 I: diffoscope 283 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_roary_trixie_amd64_1732520397 + touch /var/log/reproducible-builds/diffoscope_stamp_roary_trixie_amd64_1732520397 + RESULT=0 + systemd-run '--description=diffoscope on roary/3.13.0+dfsg-1 in trixie/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_34-36868 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ --run-session -c jenkins-reproducible-trixie-diffoscope-3b46175d-9baf-4378-a11b-5d6c6c0984f9 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/dbd-tmp-D7ah9B2 ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/roary_3.13.0+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/roary_3.13.0+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/roary_3.13.0+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/b1/roary_3.13.0+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/b2/roary_3.13.0+dfsg-1_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_34-36868.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/roary_3.13.0+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/roary_3.13.0+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/roary_3.13.0+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/b1/roary_3.13.0+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.oU2ie3pZ/b2/roary_3.13.0+dfsg-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.333s) 0.333s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.016s) 0.016s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 627ms CPU time consumed: 627ms _ __ ___ __ _ _ __ _ _ | '__/ _ \ / _` | '__| | | | | | | (_) | (_| | | | |_| | |_| \___/ \__,_|_| \__, | |___/ Mon Nov 25 07:39:58 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Mon Nov 25 07:39:58 UTC 2024 I: roary from trixie built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-25 07:39:58] INFO: Starting at 2024-11-25 07:39:58.878726 [2024-11-25 07:39:58] INFO: Generating the pages of 1 package(s) [2024-11-25 07:39:59] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/amd64/roary didn't produce a buildlog, even though it has been built. [2024-11-25 07:39:59] INFO: Finished at 2024-11-25 07:39:59.500102, took: 0:00:00.621381 Mon Nov 25 07:39:59 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/amd64/roary.html Mon Nov 25 07:39:59 UTC 2024 I: Submitting .buildinfo files to external archives: Mon Nov 25 07:39:59 UTC 2024 I: Submitting 16K b1/roary_3.13.0+dfsg-1_amd64.buildinfo.asc https://buildinfo.debian.net/466d96149c2992664c2a900f4a50b25117139543/roary_3.13.0+dfsg-1_all Mon Nov 25 07:40:00 UTC 2024 I: Submitting 16K b2/roary_3.13.0+dfsg-1_amd64.buildinfo.asc https://buildinfo.debian.net/2fc1c1d2ad6ced8affb5f652f98b55c4327a8e7b/roary_3.13.0+dfsg-1_all Mon Nov 25 07:40:01 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Nov 25 07:40:01 UTC 2024 I: Done submitting .buildinfo files. Mon Nov 25 07:40:01 UTC 2024 I: Removing signed roary_3.13.0+dfsg-1_amd64.buildinfo.asc files: removed './b1/roary_3.13.0+dfsg-1_amd64.buildinfo.asc' removed './b2/roary_3.13.0+dfsg-1_amd64.buildinfo.asc' 1732520401 amd64 trixie roary Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/roary_3.13.0+dfsg-1.rbuild.log: 82.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/roary_3.13.0+dfsg-1.rbuild.log.gz [2024-11-25 07:40:01] INFO: Starting at 2024-11-25 07:40:01.521986 [2024-11-25 07:40:01] INFO: Generating the pages of 1 package(s) [2024-11-25 07:40:02] INFO: Finished at 2024-11-25 07:40:02.136436, took: 0:00:00.614459 All cleanup done. Mon Nov 25 07:40:02 UTC 2024 - total duration: 0h 7m 5s. Mon Nov 25 07:40:02 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-u22m2YjF, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 7min 9.304s CPU time consumed: 7.528s