Running as unit: rb-build-i386_9-32171.service ==================================================================================== Fri Nov 22 09:00:15 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_i386_9) on jenkins, called using "ionos2-i386 ionos6-i386" as arguments. Fri Nov 22 09:00:15 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-p3eeq3hC" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Nov 22 09:00:15 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos2-i386.debian.net is marked as down. Fri Nov 22 09:00:15 UTC 2024 - checking via ssh if ionos2-i386.debian.net is up. removed '/tmp/read-only-fs-test-1GBmNE' Fri Nov 22 09:00:15 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos6-i386.debian.net is marked as down. Fri Nov 22 09:00:15 UTC 2024 - checking via ssh if ionos6-i386.debian.net is up. removed '/tmp/read-only-fs-test-NsFCvZ' 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 i386 on jenkins now. 1st build will be done on ionos2-i386.debian.net. 2nd build will be done on ionos6-i386.debian.net. ============================================================================= Fri Nov 22 09:00:35 UTC 2024 I: starting to build roary/trixie/i386 on jenkins on '2024-11-22 09:00' Fri Nov 22 09:00:35 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_9/32171/console.log 1732266035 i386 trixie roary Fri Nov 22 09:00:35 UTC 2024 I: Downloading source for trixie/roary=3.13.0+dfsg-1 --2024-11-22 09:00:35-- 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% 389M=0s 2024-11-22 09:00:35 (389 MB/s) - ‘roary_3.13.0+dfsg-1.dsc’ saved [2501/2501] --2024-11-22 09:00:35-- 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% 389M=0s 2024-11-22 09:00:35 (389 MB/s) - ‘roary_3.13.0+dfsg-1.dsc’ saved [2501/2501] Fri Nov 22 09:00:35 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----- Fri Nov 22 09:00:35 UTC 2024 I: Checking whether the package is not for us Fri Nov 22 09:00:35 UTC 2024 I: Starting 1st build on remote node ionos2-i386.debian.net. Fri Nov 22 09:00:35 UTC 2024 I: Preparing to do remote build '1' on ionos2-i386.debian.net. Fri Nov 22 09:00:35 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos2-i386.debian.net is marked as down. Fri Nov 22 09:00:35 UTC 2024 - checking via ssh if ionos2-i386.debian.net is up. removed '/tmp/read-only-fs-test-nEg4Ld' ==================================================================================== Fri Nov 22 09:00:36 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos2-i386, called using "1 roary trixie /srv/reproducible-results/rbuild-debian/r-b-build.h5cOr7Lo 3.13.0+dfsg-1" as arguments. Fri Nov 22 09:00:36 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-BCrV4ven" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Nov 22 09:00:36 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 (3095 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 (3095 kB/s) Download complete and in download only mode ============================================================================= Building roary in trixie on i386 on ionos2-i386 now. Date: Fri Nov 22 10:00:37 CET 2024 Date UTC: Fri Nov 22 09:00:37 UTC 2024 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Nov 21 21:00:37 -12 2024 I: pbuilder-time-stamp: 1732266037 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: using eatmydata during job 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/12241/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='6109fc1478a94bd993f3546f3f99d1e2' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='12241' 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.h5cOr7Lo/pbuilderrc_z39m --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.h5cOr7Lo/b1 --logfile b1/build.log roary_3.13.0+dfsg-1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos2-i386 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) 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/12241/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: i386 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 ... 19956 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} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{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 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 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 117 MB of archives. After unpacking 397 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libpython3.12-minimal i386 3.12.7-3 [814 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 python3.12-minimal i386 3.12.7-3 [2236 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.1-1+b1 [23.4 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 12 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 libtirpc3t64 i386 1.3.4+ds-1.3+b1 [90.5 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 libnsl2 i386 1.3.0-3+b3 [42.7 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-5 [173 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libpython3.12-stdlib i386 3.12.7-3 [1964 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 python3.12 i386 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main i386 python3 i386 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 libproc2-0 i386 2:4.0.4-6 [65.7 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 procps i386 2:4.0.4-6 [876 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 openssl i386 3.3.2-2 [1387 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 ca-certificates all 20240203 [158 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-11 [95.6 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 ucf all 3.0043+nmu1 [55.2 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-2 [723 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 bedtools i386 2.31.1+dfsg-2 [745 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 libio-string-perl all 1.08-4 [12.1 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 libdata-stag-perl all 0.14-3 [448 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libclass-data-inheritable-perl all 0.10-1 [8632 B] Get: 48 http://deb.debian.org/debian trixie/main i386 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 libexception-class-perl all 1.45-1 [34.6 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 libtest-deep-perl all 1.204-1 [52.9 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 libtext-diff-perl all 1.45-2 [27.2 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 libtest-differences-perl all 0.71-1 [17.9 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 libtest-warn-perl all 0.37-2 [14.5 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 libtest-most-perl all 0.38-1 [25.1 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 bioperl all 1.7.8-1 [246 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 cd-hit i386 4.8.1-4 [524 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 67 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 libparams-util-perl i386 1.102-3+b1 [24.7 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 libsub-install-perl all 0.929-1 [10.5 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 libb-hooks-op-check-perl i386 0.22-3+b2 [10.7 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 libdevel-callchecker-perl i386 0.009-1+b1 [16.2 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 libparams-classify-perl i386 0.015-2+b4 [23.1 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 libpackage-stash-perl all 0.40-1 [22.0 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 libclass-load-perl all 0.25-2 [15.3 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 libio-stringy-perl all 2.113-2 [48.3 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 libparams-validate-perl i386 1.31-2+b3 [64.9 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 libgetopt-long-descriptive-perl all 0.115-1 [27.6 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 libio-tiecombine-perl all 1.005-3 [10.8 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 libmodule-pluggable-perl all 5.2-5 [23.0 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 libstring-rewriteprefix-perl all 0.009-1 [7140 B] Get: 94 http://deb.debian.org/debian trixie/main i386 libapp-cmd-perl all 0.336-1 [65.8 kB] Get: 95 http://deb.debian.org/debian trixie/main i386 libscope-guard-perl all 0.21-2 [8212 B] Get: 96 http://deb.debian.org/debian trixie/main i386 libautobox-perl i386 3.0.2-1+b1 [33.5 kB] Get: 97 http://deb.debian.org/debian trixie/main i386 libperlio-utf8-strict-perl i386 0.010-1+b3 [11.6 kB] Get: 98 http://deb.debian.org/debian trixie/main i386 libmixin-linewise-perl all 0.111-1 [14.4 kB] Get: 99 http://deb.debian.org/debian trixie/main i386 libconfig-ini-perl all 1:0.029-1 [23.7 kB] Get: 100 http://deb.debian.org/debian trixie/main i386 libclass-load-xs-perl i386 0.10-2+b4 [14.3 kB] Get: 101 http://deb.debian.org/debian trixie/main i386 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get: 102 http://deb.debian.org/debian trixie/main i386 libdevel-globaldestruction-perl all 0.14-4 [7144 B] Get: 103 http://deb.debian.org/debian trixie/main i386 libalgorithm-c3-perl all 0.11-2 [10.8 kB] Get: 104 http://deb.debian.org/debian trixie/main i386 libclass-c3-perl all 0.35-2 [21.0 kB] Get: 105 http://deb.debian.org/debian trixie/main i386 libmro-compat-perl all 0.15-2 [11.8 kB] Get: 106 http://deb.debian.org/debian trixie/main i386 libdevel-overloadinfo-perl all 0.007-1 [7896 B] Get: 107 http://deb.debian.org/debian trixie/main i386 libeval-closure-perl all 0.14-3 [11.2 kB] Get: 108 http://deb.debian.org/debian trixie/main i386 libdist-checkconflicts-perl all 0.11-2 [10.5 kB] Get: 109 http://deb.debian.org/debian trixie/main i386 libmodule-runtime-conflicts-perl all 0.003-2 [7356 B] Get: 110 http://deb.debian.org/debian trixie/main i386 libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB] Get: 111 http://deb.debian.org/debian trixie/main i386 libpackage-stash-xs-perl i386 0.30-1+b4 [21.2 kB] Get: 112 http://deb.debian.org/debian trixie/main i386 libmoose-perl i386 2.2207-1+b2 [767 kB] Get: 113 http://deb.debian.org/debian trixie/main i386 libvariable-magic-perl i386 0.64-1+b1 [45.8 kB] Get: 114 http://deb.debian.org/debian trixie/main i386 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB] Get: 115 http://deb.debian.org/debian trixie/main i386 libsub-identify-perl i386 0.14-3+b3 [11.2 kB] Get: 116 http://deb.debian.org/debian trixie/main i386 libsub-name-perl i386 0.27-1+b3 [12.6 kB] Get: 117 http://deb.debian.org/debian trixie/main i386 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get: 118 http://deb.debian.org/debian trixie/main i386 libnamespace-autoclean-perl all 0.31-1 [13.8 kB] Get: 119 http://deb.debian.org/debian trixie/main i386 libmoosex-role-parameterized-perl all 1.11-2 [41.9 kB] Get: 120 http://deb.debian.org/debian trixie/main i386 libmoosex-oneargnew-perl all 0.007-1 [8180 B] Get: 121 http://deb.debian.org/debian trixie/main i386 libcpanel-json-xs-perl i386 4.38-1+b1 [134 kB] Get: 122 http://deb.debian.org/debian trixie/main i386 libjson-maybexs-perl all 1.004008-1 [12.9 kB] Get: 123 http://deb.debian.org/debian trixie/main i386 libstring-formatter-perl all 1.235-1 [22.1 kB] Get: 124 http://deb.debian.org/debian trixie/main i386 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 125 http://deb.debian.org/debian trixie/main i386 libstring-errf-perl all 0.009-1 [12.9 kB] Get: 126 http://deb.debian.org/debian trixie/main i386 librole-hasmessage-perl all 0.007-1 [9112 B] Get: 127 http://deb.debian.org/debian trixie/main i386 librole-identifiable-perl all 0.009-1 [10.4 kB] Get: 128 http://deb.debian.org/debian trixie/main i386 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 129 http://deb.debian.org/debian trixie/main i386 libclass-xsaccessor-perl i386 1.19-4+b4 [37.5 kB] Get: 130 http://deb.debian.org/debian trixie/main i386 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 131 http://deb.debian.org/debian trixie/main i386 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 132 http://deb.debian.org/debian trixie/main i386 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 133 http://deb.debian.org/debian trixie/main i386 libmoo-perl all 2.005005-1 [58.0 kB] Get: 134 http://deb.debian.org/debian trixie/main i386 libthrowable-perl all 1.001-2 [15.7 kB] Get: 135 http://deb.debian.org/debian trixie/main i386 libtie-ixhash-perl all 1.23-4 [11.7 kB] Get: 136 http://deb.debian.org/debian trixie/main i386 libconfig-mvp-perl all 2.200013-1 [47.1 kB] Get: 137 http://deb.debian.org/debian trixie/main i386 libconfig-mvp-reader-ini-perl all 2.101465-1 [6900 B] Get: 138 http://deb.debian.org/debian trixie/main i386 perl-openssl-defaults i386 7+b2 [6720 B] Get: 139 http://deb.debian.org/debian trixie/main i386 libnet-ssleay-perl i386 1.94-2 [340 kB] Get: 140 http://deb.debian.org/debian trixie/main i386 libio-socket-ssl-perl all 2.089-1 [223 kB] Get: 141 http://deb.debian.org/debian trixie/main i386 liburi-perl all 5.30-1 [105 kB] Get: 142 http://deb.debian.org/debian trixie/main i386 libnet-http-perl all 6.23-1 [23.9 kB] Get: 143 http://deb.debian.org/debian trixie/main i386 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 144 http://deb.debian.org/debian trixie/main i386 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 145 http://deb.debian.org/debian trixie/main i386 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 146 http://deb.debian.org/debian trixie/main i386 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 147 http://deb.debian.org/debian trixie/main i386 libhtml-parser-perl i386 3.83-1+b1 [101 kB] Get: 148 http://deb.debian.org/debian trixie/main i386 libhtml-tree-perl all 5.07-3 [211 kB] Get: 149 http://deb.debian.org/debian trixie/main i386 libclone-perl i386 0.47-1+b1 [14.0 kB] Get: 150 http://deb.debian.org/debian trixie/main i386 libio-html-perl all 1.004-3 [16.2 kB] Get: 151 http://deb.debian.org/debian trixie/main i386 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 152 http://deb.debian.org/debian trixie/main i386 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 153 http://deb.debian.org/debian trixie/main i386 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 154 http://deb.debian.org/debian trixie/main i386 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 155 http://deb.debian.org/debian trixie/main i386 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 156 http://deb.debian.org/debian trixie/main i386 libwww-perl all 6.77-1 [183 kB] Get: 157 http://deb.debian.org/debian trixie/main i386 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 158 http://deb.debian.org/debian trixie/main i386 libterm-readkey-perl i386 2.38-2+b4 [25.4 kB] Get: 159 http://deb.debian.org/debian trixie/main i386 libcpan-uploader-perl all 0.103018-1 [16.3 kB] Get: 160 http://deb.debian.org/debian trixie/main i386 libdata-section-perl all 0.200008-1 [13.1 kB] Get: 161 http://deb.debian.org/debian trixie/main i386 libclass-inspector-perl all 1.36-3 [17.5 kB] Get: 162 http://deb.debian.org/debian trixie/main i386 libfile-sharedir-perl all 1.118-3 [16.0 kB] Get: 163 http://deb.debian.org/debian trixie/main i386 libparams-validationcompiler-perl all 0.31-1 [30.9 kB] Get: 164 http://deb.debian.org/debian trixie/main i386 libxstring-perl i386 0.005-2+b4 [8212 B] Get: 165 http://deb.debian.org/debian trixie/main i386 libspecio-perl all 0.48-1 [142 kB] Get: 166 http://deb.debian.org/debian trixie/main i386 libdatetime-locale-perl all 1:1.41-1 [3131 kB] Get: 167 http://deb.debian.org/debian trixie/main i386 libclass-singleton-perl all 1.6-2 [12.5 kB] Get: 168 http://deb.debian.org/debian trixie/main i386 libdatetime-timezone-perl all 1:2.63-2+2024b [261 kB] Get: 169 http://deb.debian.org/debian trixie/main i386 libdatetime-perl i386 2:1.65-1+b2 [119 kB] Get: 170 http://deb.debian.org/debian trixie/main i386 libfile-copy-recursive-perl all 0.45-4 [20.0 kB] Get: 171 http://deb.debian.org/debian trixie/main i386 libnumber-compare-perl all 0.03-3 [6332 B] Get: 172 http://deb.debian.org/debian trixie/main i386 libtext-glob-perl all 0.11-3 [7676 B] Get: 173 http://deb.debian.org/debian trixie/main i386 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get: 174 http://deb.debian.org/debian trixie/main i386 libfile-pushd-perl all 1.016-2 [13.5 kB] Get: 175 http://deb.debian.org/debian trixie/main i386 libfile-sharedir-install-perl all 0.14-2 [11.6 kB] Get: 176 http://deb.debian.org/debian trixie/main i386 libhash-merge-simple-perl all 0.052-1 [8232 B] Get: 177 http://deb.debian.org/debian trixie/main i386 libjson-perl all 4.10000-1 [87.5 kB] Get: 178 http://deb.debian.org/debian trixie/main i386 liblog-dispatch-perl all 2.71-1 [75.8 kB] Get: 179 http://deb.debian.org/debian trixie/main i386 liblog-dispatch-array-perl all 1.005-1 [6700 B] Get: 180 http://deb.debian.org/debian trixie/main i386 libstring-flogger-perl all 1.101246-1 [7380 B] Get: 181 http://deb.debian.org/debian trixie/main i386 libsub-exporter-globexporter-perl all 0.006-1 [8024 B] Get: 182 http://deb.debian.org/debian trixie/main i386 liblog-dispatchouli-perl all 3.008-1 [34.4 kB] Get: 183 http://deb.debian.org/debian trixie/main i386 libexporter-tiny-perl all 1.006002-1 [38.7 kB] Get: 184 http://deb.debian.org/debian trixie/main i386 liblist-moreutils-xs-perl i386 0.430-4+b2 [45.1 kB] Get: 185 http://deb.debian.org/debian trixie/main i386 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get: 186 http://deb.debian.org/debian trixie/main i386 libsyntax-keyword-junction-perl all 0.003009-1 [12.7 kB] Get: 187 http://deb.debian.org/debian trixie/main i386 libmoose-autobox-perl all 0.16-2 [52.8 kB] Get: 188 http://deb.debian.org/debian trixie/main i386 libaliased-perl all 0.34-3 [13.5 kB] Get: 189 http://deb.debian.org/debian trixie/main i386 libmoosex-lazyrequire-perl all 0.11-2 [9212 B] Get: 190 http://deb.debian.org/debian trixie/main i386 libmoosex-setonce-perl all 0.200002-2 [6632 B] Get: 191 http://deb.debian.org/debian trixie/main i386 libcarp-clan-perl all 6.08-2 [14.1 kB] Get: 192 http://deb.debian.org/debian trixie/main i386 libsub-exporter-formethods-perl all 0.100055-1 [8024 B] Get: 193 http://deb.debian.org/debian trixie/main i386 libmoosex-types-perl all 0.50-2 [54.6 kB] Get: 194 http://deb.debian.org/debian trixie/main i386 libmoosex-types-perl-perl all 0.101344-1 [8160 B] Get: 195 http://deb.debian.org/debian trixie/main i386 libpath-tiny-perl all 0.146-1 [56.2 kB] Get: 196 http://deb.debian.org/debian trixie/main i386 libmodule-path-perl all 0.19-3 [12.3 kB] Get: 197 http://deb.debian.org/debian trixie/main i386 libtask-weaken-perl all 1.06-2 [9364 B] Get: 198 http://deb.debian.org/debian trixie/main i386 libppi-perl all 1.279-1 [294 kB] Get: 199 http://deb.debian.org/debian trixie/main i386 libtype-tiny-perl all 2.004000-1 [357 kB] Get: 200 http://deb.debian.org/debian trixie/main i386 libperl-prereqscanner-perl all 1.100-1 [31.0 kB] Get: 201 http://deb.debian.org/debian trixie/main i386 libperl-version-perl all 1.017-1 [29.0 kB] Get: 202 http://deb.debian.org/debian trixie/main i386 libtext-template-perl all 1.61-1 [54.4 kB] Get: 203 http://deb.debian.org/debian trixie/main i386 libsoftware-license-perl all 0.104006-1 [116 kB] Get: 204 http://deb.debian.org/debian trixie/main i386 libterm-encoding-perl all 0.03-2 [4980 B] Get: 205 http://deb.debian.org/debian trixie/main i386 libyaml-tiny-perl all 1.74-1 [30.7 kB] Get: 206 http://deb.debian.org/debian trixie/main i386 libdist-zilla-perl all 6.032-1 [343 kB] Get: 207 http://deb.debian.org/debian trixie/main i386 dh-dist-zilla all 1.4.1 [17.9 kB] Get: 208 http://deb.debian.org/debian trixie/main i386 fasttree i386 2.1.11-2 [183 kB] Get: 209 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB] Get: 210 http://deb.debian.org/debian trixie/main i386 libpng16-16t64 i386 1.6.44-2 [288 kB] Get: 211 http://deb.debian.org/debian trixie/main i386 libfreetype6 i386 2.13.3+dfsg-1 [464 kB] Get: 212 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 213 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 214 http://deb.debian.org/debian trixie/main i386 fontconfig-config i386 2.15.0-1.1+b1 [318 kB] Get: 215 http://deb.debian.org/debian trixie/main i386 libfontconfig1 i386 2.15.0-1.1+b1 [402 kB] Get: 216 http://deb.debian.org/debian trixie/main i386 fontconfig i386 2.15.0-1.1+b1 [463 kB] Get: 217 http://deb.debian.org/debian trixie/main i386 libarray-utils-perl all 0.5-3 [6184 B] Get: 218 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-3+b1 [143 kB] Get: 219 http://deb.debian.org/debian trixie/main i386 libpixman-1-0 i386 0.44.0-3 [246 kB] Get: 220 http://deb.debian.org/debian trixie/main i386 libxau6 i386 1:1.0.11-1 [20.7 kB] Get: 221 http://deb.debian.org/debian trixie/main i386 libxdmcp6 i386 1:1.1.2-3+b2 [24.9 kB] Get: 222 http://deb.debian.org/debian trixie/main i386 libxcb1 i386 1.17.0-2+b1 [148 kB] Get: 223 http://deb.debian.org/debian trixie/main i386 libx11-data all 2:1.8.10-2 [337 kB] Get: 224 http://deb.debian.org/debian trixie/main i386 libx11-6 i386 2:1.8.10-2 [834 kB] Get: 225 http://deb.debian.org/debian trixie/main i386 libxcb-render0 i386 1.17.0-2+b1 [116 kB] Get: 226 http://deb.debian.org/debian trixie/main i386 libxcb-shm0 i386 1.17.0-2+b1 [105 kB] Get: 227 http://deb.debian.org/debian trixie/main i386 libxext6 i386 2:1.3.4-1+b2 [52.6 kB] Get: 228 http://deb.debian.org/debian trixie/main i386 libxrender1 i386 1:0.9.10-1.1+b2 [28.9 kB] Get: 229 http://deb.debian.org/debian trixie/main i386 libcairo2 i386 1.18.2-2 [591 kB] Get: 230 http://deb.debian.org/debian trixie/main i386 libconst-fast-perl all 0.014-2 [8792 B] Get: 231 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB] Get: 232 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB] Get: 233 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.18+dfsg-3+b1 [200 kB] Get: 234 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB] Get: 235 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB] Get: 236 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB] Get: 237 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB] Get: 238 http://deb.debian.org/debian trixie/main i386 libcurl4t64 i386 8.11.0-1 [392 kB] Get: 239 http://deb.debian.org/debian trixie/main i386 libdata-compare-perl all 1.29-1 [19.6 kB] Get: 240 http://deb.debian.org/debian trixie/main i386 libdatrie1 i386 0.2.13-3+b1 [39.9 kB] Get: 241 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.22-1 [48.1 kB] Get: 242 http://deb.debian.org/debian trixie/main i386 libpod-eventual-perl all 0.094003-1 [14.2 kB] Get: 243 http://deb.debian.org/debian trixie/main i386 libstring-truncate-perl all 1.100603-1 [10.2 kB] Get: 244 http://deb.debian.org/debian trixie/main i386 libpod-elemental-perl all 0.103006-1 [67.2 kB] Get: 245 http://deb.debian.org/debian trixie/main i386 libpod-elemental-perlmunger-perl all 0.200007-1 [10.5 kB] Get: 246 http://deb.debian.org/debian trixie/main i386 libpod-weaver-perl all 4.020-1 [70.1 kB] Get: 247 http://deb.debian.org/debian trixie/main i386 libdist-zilla-plugin-podweaver-perl all 4.010-1 [9580 B] Get: 248 http://deb.debian.org/debian trixie/main i386 libenv-path-perl all 0.19-4 [19.1 kB] Get: 249 http://deb.debian.org/debian trixie/main i386 libfile-chdir-perl all 0.1008-1.2 [11.9 kB] Get: 250 http://deb.debian.org/debian trixie/main i386 libfile-grep-perl all 0.02-3 [8352 B] Get: 251 http://deb.debian.org/debian trixie/main i386 libfile-slurper-perl all 0.014-1 [8560 B] Get: 252 http://deb.debian.org/debian trixie/main i386 libfile-which-perl all 1.27-2 [15.1 kB] Get: 253 http://deb.debian.org/debian trixie/main i386 libfindbin-libs-perl all 3.0.2-1 [29.7 kB] Get: 254 http://deb.debian.org/debian trixie/main i386 libfribidi0 i386 1.0.15-1 [72.4 kB] Get: 255 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14.2.0-8 [735 kB] Get: 256 http://deb.debian.org/debian trixie/main i386 libglib2.0-0t64 i386 2.82.2-2 [1570 kB] Get: 257 http://deb.debian.org/debian trixie/main i386 libheap-perl all 0.80-5 [34.3 kB] Get: 258 http://deb.debian.org/debian trixie/main i386 libset-object-perl i386 1.42-1+b5 [38.3 kB] Get: 259 http://deb.debian.org/debian trixie/main i386 libgraph-perl all 1:0.9729-1 [108 kB] Get: 260 http://deb.debian.org/debian trixie/main i386 libspiffy-perl all 0.46-1 [25.7 kB] Get: 261 http://deb.debian.org/debian trixie/main i386 libio-all-perl all 0.87-2 [67.3 kB] Get: 262 http://deb.debian.org/debian trixie/main i386 libparse-yapp-perl all 1.21-4 [41.5 kB] Get: 263 http://deb.debian.org/debian trixie/main i386 libxml-parser-perl i386 2.47-1+b3 [200 kB] Get: 264 http://deb.debian.org/debian trixie/main i386 libxml-writer-perl all 0.900-2 [26.8 kB] Get: 265 http://deb.debian.org/debian trixie/main i386 libgraph-readwrite-perl all 2.10-1 [45.2 kB] Get: 266 http://deb.debian.org/debian trixie/main i386 libgraphite2-3 i386 1.3.14-2+b1 [77.8 kB] Get: 267 http://deb.debian.org/debian trixie/main i386 libharfbuzz0b i386 10.0.1-1 [503 kB] Get: 268 http://deb.debian.org/debian trixie/main i386 x11-common all 1:7.7+23.1 [216 kB] Get: 269 http://deb.debian.org/debian trixie/main i386 libice6 i386 2:1.1.1-1 [67.8 kB] Get: 270 http://deb.debian.org/debian trixie/main i386 libjbig0 i386 2.1-6.1+b2 [32.2 kB] Get: 271 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-3+b1 [171 kB] Get: 272 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.0-3+b1 [2196 kB] Get: 273 http://deb.debian.org/debian trixie/main i386 liblerc4 i386 4.0.0+ds-5 [191 kB] Get: 274 http://deb.debian.org/debian trixie/main i386 liblmdb0 i386 0.9.31-1+b2 [46.9 kB] Get: 275 http://deb.debian.org/debian trixie/main i386 liblog-log4perl-perl all 1.57-1 [367 kB] Get: 276 http://deb.debian.org/debian trixie/main i386 libmbedcrypto7t64 i386 2.28.8-1 [299 kB] Get: 277 http://deb.debian.org/debian trixie/main i386 libmbedx509-1t64 i386 2.28.8-1 [133 kB] Get: 278 http://deb.debian.org/debian trixie/main i386 libmbedtls14t64 i386 2.28.8-1 [171 kB] Get: 279 http://deb.debian.org/debian trixie/main i386 libpadwalker-perl i386 2.5-1+b6 [19.1 kB] Get: 280 http://deb.debian.org/debian trixie/main i386 libthai-data all 0.1.29-2 [168 kB] Get: 281 http://deb.debian.org/debian trixie/main i386 libthai0 i386 0.1.29-2+b1 [50.3 kB] Get: 282 http://deb.debian.org/debian trixie/main i386 libpango-1.0-0 i386 1.54.0+ds-3 [230 kB] Get: 283 http://deb.debian.org/debian trixie/main i386 libpangoft2-1.0-0 i386 1.54.0+ds-3 [58.1 kB] Get: 284 http://deb.debian.org/debian trixie/main i386 libpangocairo-1.0-0 i386 1.54.0+ds-3 [36.1 kB] Get: 285 http://deb.debian.org/debian trixie/main i386 libpaper1 i386 1.1.29+b2 [13.0 kB] Get: 286 http://deb.debian.org/debian trixie/main i386 libpaper-utils i386 1.1.29+b2 [9304 B] Get: 287 http://deb.debian.org/debian trixie/main i386 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 288 http://deb.debian.org/debian trixie/main i386 libsensors5 i386 1:3.6.0-10+b1 [35.8 kB] Get: 289 http://deb.debian.org/debian trixie/main i386 libsharpyuv0 i386 1.4.0-0.1+b1 [113 kB] Get: 290 http://deb.debian.org/debian trixie/main i386 libsm6 i386 2:1.2.4-1 [35.9 kB] Get: 291 http://deb.debian.org/debian trixie/main i386 libtcl8.6 i386 8.6.15+dfsg-2 [1103 kB] Get: 292 http://deb.debian.org/debian trixie/main i386 libtest-file-perl all 1.993-1 [24.5 kB] Get: 293 http://deb.debian.org/debian trixie/main i386 libtest2-suite-perl all 0.000163-1 [383 kB] Get: 294 http://deb.debian.org/debian trixie/main i386 libtest-files-perl all 0.26-1 [21.6 kB] Get: 295 http://deb.debian.org/debian trixie/main i386 libtest-output-perl all 1.034-1 [16.0 kB] Get: 296 http://deb.debian.org/debian trixie/main i386 libtext-csv-perl all 2.04-1 [112 kB] Get: 297 http://deb.debian.org/debian trixie/main i386 libwebp7 i386 1.4.0-0.1+b1 [322 kB] Get: 298 http://deb.debian.org/debian trixie/main i386 libtiff6 i386 4.5.1+git230720-5 [339 kB] Get: 299 http://deb.debian.org/debian trixie/main i386 libtingea0 i386 21-361-2+b2 [54.8 kB] Get: 300 http://deb.debian.org/debian trixie/main i386 libxft2 i386 2.3.6-1+b2 [55.3 kB] Get: 301 http://deb.debian.org/debian trixie/main i386 libxss1 i386 1:1.2.3-1+b2 [17.3 kB] Get: 302 http://deb.debian.org/debian trixie/main i386 libtk8.6 i386 8.6.15-1 [833 kB] Get: 303 http://deb.debian.org/debian trixie/main i386 libuv1t64 i386 1.48.0-7 [157 kB] Get: 304 http://deb.debian.org/debian trixie/main i386 libxt6t64 i386 1:1.2.1-1.2+b1 [193 kB] Get: 305 http://deb.debian.org/debian trixie/main i386 mafft i386 7.505-1 [1007 kB] Get: 306 http://deb.debian.org/debian trixie/main i386 mcl i386 1:22-282+ds-2 [480 kB] Get: 307 http://deb.debian.org/debian trixie/main i386 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get: 308 http://deb.debian.org/debian trixie/main i386 ncbi-blast+ i386 2.16.0+ds-6 [16.6 MB] Get: 309 http://deb.debian.org/debian trixie/main i386 sysstat i386 12.7.5-2 [626 kB] Get: 310 http://deb.debian.org/debian trixie/main i386 parallel all 20240222+ds-2 [2163 kB] Get: 311 http://deb.debian.org/debian trixie/main i386 prank i386 0.0.170427+dfsg-3 [405 kB] Get: 312 http://deb.debian.org/debian trixie/main i386 zip i386 3.0-14 [239 kB] Get: 313 http://deb.debian.org/debian trixie/main i386 unzip i386 6.0-28 [166 kB] Get: 314 http://deb.debian.org/debian trixie/main i386 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 315 http://deb.debian.org/debian trixie/main i386 r-base-core i386 4.4.2-1 [28.3 MB] Fetched 117 MB in 2s (52.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:i386. (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 ... 19956 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.7-3) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.4-1_i386.deb ... Unpacking libexpat1:i386 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_i386.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:i386 (3.12.7-3) ... Setting up libexpat1:i386 (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 ... 20276 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_i386.deb ... 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Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3 to /lib/i386-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3.0.0 to /lib/i386-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:i386 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:i386. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_i386.deb ... Unpacking libnsl2:i386 (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:i386. Preparing to unpack .../14-libreadline8t64_8.2-5_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:i386. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_i386.deb ... Unpacking libpython3.12-stdlib:i386 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_i386.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_i386.deb ... Unpacking libpython3-stdlib:i386 (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 ... 21338 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_i386.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package libproc2-0:i386. 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Setting up libicu72:i386 (72.1-5+b1) ... Setting up liblerc4:i386 (4.0.0+ds-5) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libparse-yapp-perl (1.21-4) ... Setting up libmbedcrypto7t64:i386 (2.28.8-1) ... Setting up libclass-inspector-perl (1.36-3) ... Setting up libdynaloader-functions-perl (0.004-1) ... Setting up libdatrie1:i386 (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:i386 (1.17.0-2+b1) ... Setting up mafft (7.505-1) ... Setting up libclone-perl:i386 (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:i386 (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:i386 (1.1.0-2+b6) ... Setting up libheap-perl (0.80-5) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libuv1t64:i386 (1.48.0-7) ... Setting up libmagic1t64:i386 (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:i386 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:i386 (1.64.0-1) ... Setting up libdeflate0:i386 (1.22-1) ... Setting up perl-openssl-defaults:i386 (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:i386 (1.17.0-2+b1) ... Setting up libfindbin-libs-perl (3.0.2-1) ... Setting up libcom-err2:i386 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libxstring-perl:i386 (0.005-2+b4) ... Setting up libyaml-tiny-perl (1.74-1) ... Setting up libjbig0:i386 (2.1-6.1+b2) ... Setting up libsub-install-perl (0.929-1) ... Setting up libelf1t64:i386 (0.192-4) ... Setting up libtest2-suite-perl (0.000163-1) ... Setting up libkrb5support0:i386 (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:i386 (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: Fri Nov 22 09:01:18 UTC 2024. Universal Time is now: Fri Nov 22 09:01:18 UTC 2024. 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:i386 (0.30-1+b4) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:i386 (2.82.2-2) ... No schema files found: doing nothing. Setting up libblas3:i386 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-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:i386 (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:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... 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Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libtest-exception-perl (0.43-3) ... Setting up libfreetype6:i386 (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:i386 (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 libreadline8t64:i386 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libmbedtls14t64:i386 (2.28.8-1) ... Setting up groff-base (1.23.0-5) ... Setting up libhtml-parser-perl:i386 (3.83-1+b1) ... Setting up libharfbuzz0b:i386 (10.0.1-1) ... Setting up libxss1:i386 (1:1.2.3-1+b2) ... Setting up libfontconfig1:i386 (2.15.0-1.1+b1) ... Setting up libmro-compat-perl (0.15-2) ... Setting up libsm6:i386 (2:1.2.4-1) ... 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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 i386 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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/roary-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -j11 make[1]: Entering directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm cp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm cp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm cp lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.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/AccessoryBinaryFasta.pm blib/lib/Bio/Roary/AccessoryBinaryFasta.pm cp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm cp lib/Bio/Roary/CommandLine/IterativeCdhit.pm blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pm cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.pm cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.pm cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm cp lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm cp lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm cp lib/Bio/Roary/AssemblyStatistics.pm blib/lib/Bio/Roary/AssemblyStatistics.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/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/AnnotateGroups.pm blib/lib/Bio/Roary/AnnotateGroups.pm cp lib/Bio/Roary/AccessoryClustering.pm blib/lib/Bio/Roary/AccessoryClustering.pm cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm cp lib/Bio/Roary/External/Mafft.pm blib/lib/Bio/Roary/External/Mafft.pm cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.pm cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm cp lib/Bio/Roary/External/Fasttree.pm blib/lib/Bio/Roary/External/Fasttree.pm cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.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/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/GeneNamesFromGFF.pm blib/lib/Bio/Roary/GeneNamesFromGFF.pm cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.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/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/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm cp lib/Bio/Roary/ReorderSpreadsheet.pm blib/lib/Bio/Roary/ReorderSpreadsheet.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/Output/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.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/PresenceAbsenceMatrix.pm blib/lib/Bio/Roary/PresenceAbsenceMatrix.pm cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm cp lib/Bio/Roary/SequenceLengths.pm blib/lib/Bio/Roary/SequenceLengths.pm cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm cp lib/Bio/Roary/UniqueGenesPerSample.pm blib/lib/Bio/Roary/UniqueGenesPerSample.pm cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm cp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm cp bin/create_pan_genome blib/script/create_pan_genome cp bin/extract_proteome_from_gff blib/script/extract_proteome_from_gff cp bin/create_pan_genome_plots blib/script/create_pan_genome_plots "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome cp bin/iterative_cdhit blib/script/iterative_cdhit cp bin/pan_genome_assembly_statistics blib/script/pan_genome_assembly_statistics "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/extract_proteome_from_gff "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome_plots cp bin/pan_genome_core_alignment blib/script/pan_genome_core_alignment "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/iterative_cdhit "/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 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_reorder_spreadsheet cp bin/parallel_all_against_all_blastp blib/script/parallel_all_against_all_blastp 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/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 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 -j11 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/MergeMultifastaAlignments.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/ReformatInputGFFs.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/ExtractCoreGenesFromSpreadsheet.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/LookupGeneFiles.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/ContigsToGeneIDsFromGFF.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/SplitGroups.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/AnalyseGroups.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/UniqueGenesPerSample.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/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/SequenceLengths.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/SampleOrder.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/SortFasta.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/PostAnalysis.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/ExtractProteomeFromGFF.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/PresenceAbsenceMatrix.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/ParseGFFAnnotationRole.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/GroupLabels.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/BedFromGFFRole.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/Output/GroupsMultifastasNucleotide.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/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/GroupsMultifastaNucleotide.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/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/DifferenceBetweenSets.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/CommandLine/IterativeCdhit.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/TransferAnnotationToGroups.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/RoaryCoreAlignment.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/AssemblyStatistics.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/Roary.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/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/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/Role.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/QC/Report.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/IterativeCdhit.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/Mafft.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/CheckTools.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/PostAnalysis.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/Cdhit.pm 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/parallel_all_against_all_blastp.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/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/man1/roary.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/create_pan_genome.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/pan_genome_post_analysis.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/pan_genome_reorder_spreadsheet.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/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/protein_alignment_from_nucleotides.1p 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::AnnotateGroups.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::ClustersRole.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::MergeMultifastaAlignments.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::NumberOfGroups.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::EmblGroups.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::CommandLine::QueryRoary.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::External::Cdhit.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::CommandLine::AssemblyStatistics.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::PrepareInputFiles.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::Exceptions.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::PostAnalysis.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::Output::EMBLHeaderCommon.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::LookupGeneFiles.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::PresenceAbsenceMatrix.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::CombinedProteome.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::External::Blastp.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::CommandLine::TransferAnnotationToGroups.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::Output::GroupsMultifastaProtein.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::CommandLine::UniqueGenesPerSample.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::CommandLine::Roary.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::External::Mafft.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::External::CheckTools.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::ExtractCoreGenesFromSpreadsheet.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::GroupsMultifastas.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::Output::GroupsMultifastasNucleotide.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::ReorderSpreadsheet.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::GroupStatistics.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::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::CommandLine::RoaryReorderSpreadsheet.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::InflateClusters.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::AccessoryClustering.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::External::Fasttree.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::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::ContigsToGeneIDsFromGFF.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::FilterFullClusters.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::UniqueGenesPerSample.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::CommandLine::RoaryPostAnalysis.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::JobRunner::Role.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::SequenceLengths.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/bin/roary-unique_genes_per_sample 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/iterative_cdhit 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/create_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/pan_genome_assembly_statistics 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/transfer_annotation_to_groups 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/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/protein_alignment_from_nucleotides 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/create_pan_genome_plots Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/parallel_all_against_all_blastp 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_i386.buildinfo dpkg-genchanges --build=binary -O../roary_3.13.0+dfsg-1_i386.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/12241 and its subdirectories I: Current time: Thu Nov 21 21:02:15 -12 2024 I: pbuilder-time-stamp: 1732266135 Fri Nov 22 09:02:15 UTC 2024 I: Signing ./b1/roary_3.13.0+dfsg-1_i386.buildinfo as roary_3.13.0+dfsg-1_i386.buildinfo.asc Fri Nov 22 09:02:16 UTC 2024 I: Signed ./b1/roary_3.13.0+dfsg-1_i386.buildinfo as ./b1/roary_3.13.0+dfsg-1_i386.buildinfo.asc Fri Nov 22 09:02:16 UTC 2024 - build #1 for roary/trixie/i386 on ionos2-i386 done. Starting cleanup. All cleanup done. Fri Nov 22 09:02:16 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-BCrV4ven, removing. /srv/reproducible-results/rbuild-debian/r-b-build.h5cOr7Lo: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 09:02 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 09:00 b2 -rw------- 1 jenkins jenkins 3610 Nov 22 09:00 rbuildlog.bS1XI9v -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.h5cOr7Lo/b1: total 584 -rw-r--r-- 1 jenkins jenkins 158424 Nov 22 09:02 build.log -rw-r--r-- 1 jenkins jenkins 6612 Nov 22 09:02 roary_3.13.0+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2501 Nov 22 09:02 roary_3.13.0+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 172956 Nov 22 09:02 roary_3.13.0+dfsg-1_all.deb -rw-r--r-- 1 jenkins jenkins 14471 Nov 22 09:02 roary_3.13.0+dfsg-1_i386.buildinfo -rw-r--r-- 1 jenkins jenkins 15353 Nov 22 09:02 roary_3.13.0+dfsg-1_i386.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1142 Nov 22 09:02 roary_3.13.0+dfsg-1_i386.changes -rw-r--r-- 1 jenkins jenkins 1589 Nov 22 09:02 roary_3.13.0+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 207348 Nov 22 09:02 roary_3.13.0+dfsg.orig.tar.xz /srv/reproducible-results/rbuild-debian/r-b-build.h5cOr7Lo/b2: total 0 Fri Nov 22 09:02:16 UTC 2024 I: Deleting $TMPDIR on ionos2-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Nov 21 21:00:37 -12 2024 I: pbuilder-time-stamp: 1732266037 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: using eatmydata during job 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/12241/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='6109fc1478a94bd993f3546f3f99d1e2' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='12241' 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.h5cOr7Lo/pbuilderrc_z39m --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.h5cOr7Lo/b1 --logfile b1/build.log roary_3.13.0+dfsg-1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos2-i386 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) 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/12241/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: i386 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 ... 19956 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} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{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 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 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 117 MB of archives. After unpacking 397 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libpython3.12-minimal i386 3.12.7-3 [814 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 python3.12-minimal i386 3.12.7-3 [2236 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.1-1+b1 [23.4 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 12 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 libtirpc3t64 i386 1.3.4+ds-1.3+b1 [90.5 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 libnsl2 i386 1.3.0-3+b3 [42.7 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-5 [173 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libpython3.12-stdlib i386 3.12.7-3 [1964 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 python3.12 i386 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main i386 python3 i386 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 libproc2-0 i386 2:4.0.4-6 [65.7 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 procps i386 2:4.0.4-6 [876 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 openssl i386 3.3.2-2 [1387 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 ca-certificates all 20240203 [158 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-11 [95.6 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 ucf all 3.0043+nmu1 [55.2 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-2 [723 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 bedtools i386 2.31.1+dfsg-2 [745 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 libio-string-perl all 1.08-4 [12.1 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 libdata-stag-perl all 0.14-3 [448 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libclass-data-inheritable-perl all 0.10-1 [8632 B] Get: 48 http://deb.debian.org/debian trixie/main i386 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 libexception-class-perl all 1.45-1 [34.6 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 libtest-deep-perl all 1.204-1 [52.9 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 libtext-diff-perl all 1.45-2 [27.2 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 libtest-differences-perl all 0.71-1 [17.9 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 libtest-warn-perl all 0.37-2 [14.5 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 libtest-most-perl all 0.38-1 [25.1 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 bioperl all 1.7.8-1 [246 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 cd-hit i386 4.8.1-4 [524 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 67 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 libparams-util-perl i386 1.102-3+b1 [24.7 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 libsub-install-perl all 0.929-1 [10.5 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 libb-hooks-op-check-perl i386 0.22-3+b2 [10.7 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 libdevel-callchecker-perl i386 0.009-1+b1 [16.2 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 libparams-classify-perl i386 0.015-2+b4 [23.1 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 libpackage-stash-perl all 0.40-1 [22.0 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 libclass-load-perl all 0.25-2 [15.3 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 libio-stringy-perl all 2.113-2 [48.3 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 libparams-validate-perl i386 1.31-2+b3 [64.9 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 libgetopt-long-descriptive-perl all 0.115-1 [27.6 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 libio-tiecombine-perl all 1.005-3 [10.8 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 libmodule-pluggable-perl all 5.2-5 [23.0 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 libstring-rewriteprefix-perl all 0.009-1 [7140 B] Get: 94 http://deb.debian.org/debian trixie/main i386 libapp-cmd-perl all 0.336-1 [65.8 kB] Get: 95 http://deb.debian.org/debian trixie/main i386 libscope-guard-perl all 0.21-2 [8212 B] Get: 96 http://deb.debian.org/debian trixie/main i386 libautobox-perl i386 3.0.2-1+b1 [33.5 kB] Get: 97 http://deb.debian.org/debian trixie/main i386 libperlio-utf8-strict-perl i386 0.010-1+b3 [11.6 kB] Get: 98 http://deb.debian.org/debian trixie/main i386 libmixin-linewise-perl all 0.111-1 [14.4 kB] Get: 99 http://deb.debian.org/debian trixie/main i386 libconfig-ini-perl all 1:0.029-1 [23.7 kB] Get: 100 http://deb.debian.org/debian trixie/main i386 libclass-load-xs-perl i386 0.10-2+b4 [14.3 kB] Get: 101 http://deb.debian.org/debian trixie/main i386 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get: 102 http://deb.debian.org/debian trixie/main i386 libdevel-globaldestruction-perl all 0.14-4 [7144 B] Get: 103 http://deb.debian.org/debian trixie/main i386 libalgorithm-c3-perl all 0.11-2 [10.8 kB] Get: 104 http://deb.debian.org/debian trixie/main i386 libclass-c3-perl all 0.35-2 [21.0 kB] Get: 105 http://deb.debian.org/debian trixie/main i386 libmro-compat-perl all 0.15-2 [11.8 kB] Get: 106 http://deb.debian.org/debian trixie/main i386 libdevel-overloadinfo-perl all 0.007-1 [7896 B] Get: 107 http://deb.debian.org/debian trixie/main i386 libeval-closure-perl all 0.14-3 [11.2 kB] Get: 108 http://deb.debian.org/debian trixie/main i386 libdist-checkconflicts-perl all 0.11-2 [10.5 kB] Get: 109 http://deb.debian.org/debian trixie/main i386 libmodule-runtime-conflicts-perl all 0.003-2 [7356 B] Get: 110 http://deb.debian.org/debian trixie/main i386 libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB] Get: 111 http://deb.debian.org/debian trixie/main i386 libpackage-stash-xs-perl i386 0.30-1+b4 [21.2 kB] Get: 112 http://deb.debian.org/debian trixie/main i386 libmoose-perl i386 2.2207-1+b2 [767 kB] Get: 113 http://deb.debian.org/debian trixie/main i386 libvariable-magic-perl i386 0.64-1+b1 [45.8 kB] Get: 114 http://deb.debian.org/debian trixie/main i386 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB] Get: 115 http://deb.debian.org/debian trixie/main i386 libsub-identify-perl i386 0.14-3+b3 [11.2 kB] Get: 116 http://deb.debian.org/debian trixie/main i386 libsub-name-perl i386 0.27-1+b3 [12.6 kB] Get: 117 http://deb.debian.org/debian trixie/main i386 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get: 118 http://deb.debian.org/debian trixie/main i386 libnamespace-autoclean-perl all 0.31-1 [13.8 kB] Get: 119 http://deb.debian.org/debian trixie/main i386 libmoosex-role-parameterized-perl all 1.11-2 [41.9 kB] Get: 120 http://deb.debian.org/debian trixie/main i386 libmoosex-oneargnew-perl all 0.007-1 [8180 B] Get: 121 http://deb.debian.org/debian trixie/main i386 libcpanel-json-xs-perl i386 4.38-1+b1 [134 kB] Get: 122 http://deb.debian.org/debian trixie/main i386 libjson-maybexs-perl all 1.004008-1 [12.9 kB] Get: 123 http://deb.debian.org/debian trixie/main i386 libstring-formatter-perl all 1.235-1 [22.1 kB] Get: 124 http://deb.debian.org/debian trixie/main i386 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 125 http://deb.debian.org/debian trixie/main i386 libstring-errf-perl all 0.009-1 [12.9 kB] Get: 126 http://deb.debian.org/debian trixie/main i386 librole-hasmessage-perl all 0.007-1 [9112 B] Get: 127 http://deb.debian.org/debian trixie/main i386 librole-identifiable-perl all 0.009-1 [10.4 kB] Get: 128 http://deb.debian.org/debian trixie/main i386 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 129 http://deb.debian.org/debian trixie/main i386 libclass-xsaccessor-perl i386 1.19-4+b4 [37.5 kB] Get: 130 http://deb.debian.org/debian trixie/main i386 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 131 http://deb.debian.org/debian trixie/main i386 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 132 http://deb.debian.org/debian trixie/main i386 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 133 http://deb.debian.org/debian trixie/main i386 libmoo-perl all 2.005005-1 [58.0 kB] Get: 134 http://deb.debian.org/debian trixie/main i386 libthrowable-perl all 1.001-2 [15.7 kB] Get: 135 http://deb.debian.org/debian trixie/main i386 libtie-ixhash-perl all 1.23-4 [11.7 kB] Get: 136 http://deb.debian.org/debian trixie/main i386 libconfig-mvp-perl all 2.200013-1 [47.1 kB] Get: 137 http://deb.debian.org/debian trixie/main i386 libconfig-mvp-reader-ini-perl all 2.101465-1 [6900 B] Get: 138 http://deb.debian.org/debian trixie/main i386 perl-openssl-defaults i386 7+b2 [6720 B] Get: 139 http://deb.debian.org/debian trixie/main i386 libnet-ssleay-perl i386 1.94-2 [340 kB] Get: 140 http://deb.debian.org/debian trixie/main i386 libio-socket-ssl-perl all 2.089-1 [223 kB] Get: 141 http://deb.debian.org/debian trixie/main i386 liburi-perl all 5.30-1 [105 kB] Get: 142 http://deb.debian.org/debian trixie/main i386 libnet-http-perl all 6.23-1 [23.9 kB] Get: 143 http://deb.debian.org/debian trixie/main i386 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 144 http://deb.debian.org/debian trixie/main i386 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 145 http://deb.debian.org/debian trixie/main i386 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 146 http://deb.debian.org/debian trixie/main i386 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 147 http://deb.debian.org/debian trixie/main i386 libhtml-parser-perl i386 3.83-1+b1 [101 kB] Get: 148 http://deb.debian.org/debian trixie/main i386 libhtml-tree-perl all 5.07-3 [211 kB] Get: 149 http://deb.debian.org/debian trixie/main i386 libclone-perl i386 0.47-1+b1 [14.0 kB] Get: 150 http://deb.debian.org/debian trixie/main i386 libio-html-perl all 1.004-3 [16.2 kB] Get: 151 http://deb.debian.org/debian trixie/main i386 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 152 http://deb.debian.org/debian trixie/main i386 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 153 http://deb.debian.org/debian trixie/main i386 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 154 http://deb.debian.org/debian trixie/main i386 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 155 http://deb.debian.org/debian trixie/main i386 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 156 http://deb.debian.org/debian trixie/main i386 libwww-perl all 6.77-1 [183 kB] Get: 157 http://deb.debian.org/debian trixie/main i386 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 158 http://deb.debian.org/debian trixie/main i386 libterm-readkey-perl i386 2.38-2+b4 [25.4 kB] Get: 159 http://deb.debian.org/debian trixie/main i386 libcpan-uploader-perl all 0.103018-1 [16.3 kB] Get: 160 http://deb.debian.org/debian trixie/main i386 libdata-section-perl all 0.200008-1 [13.1 kB] Get: 161 http://deb.debian.org/debian trixie/main i386 libclass-inspector-perl all 1.36-3 [17.5 kB] Get: 162 http://deb.debian.org/debian trixie/main i386 libfile-sharedir-perl all 1.118-3 [16.0 kB] Get: 163 http://deb.debian.org/debian trixie/main i386 libparams-validationcompiler-perl all 0.31-1 [30.9 kB] Get: 164 http://deb.debian.org/debian trixie/main i386 libxstring-perl i386 0.005-2+b4 [8212 B] Get: 165 http://deb.debian.org/debian trixie/main i386 libspecio-perl all 0.48-1 [142 kB] Get: 166 http://deb.debian.org/debian trixie/main i386 libdatetime-locale-perl all 1:1.41-1 [3131 kB] Get: 167 http://deb.debian.org/debian trixie/main i386 libclass-singleton-perl all 1.6-2 [12.5 kB] Get: 168 http://deb.debian.org/debian trixie/main i386 libdatetime-timezone-perl all 1:2.63-2+2024b [261 kB] Get: 169 http://deb.debian.org/debian trixie/main i386 libdatetime-perl i386 2:1.65-1+b2 [119 kB] Get: 170 http://deb.debian.org/debian trixie/main i386 libfile-copy-recursive-perl all 0.45-4 [20.0 kB] Get: 171 http://deb.debian.org/debian trixie/main i386 libnumber-compare-perl all 0.03-3 [6332 B] Get: 172 http://deb.debian.org/debian trixie/main i386 libtext-glob-perl all 0.11-3 [7676 B] Get: 173 http://deb.debian.org/debian trixie/main i386 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get: 174 http://deb.debian.org/debian trixie/main i386 libfile-pushd-perl all 1.016-2 [13.5 kB] Get: 175 http://deb.debian.org/debian trixie/main i386 libfile-sharedir-install-perl all 0.14-2 [11.6 kB] Get: 176 http://deb.debian.org/debian trixie/main i386 libhash-merge-simple-perl all 0.052-1 [8232 B] Get: 177 http://deb.debian.org/debian trixie/main i386 libjson-perl all 4.10000-1 [87.5 kB] Get: 178 http://deb.debian.org/debian trixie/main i386 liblog-dispatch-perl all 2.71-1 [75.8 kB] Get: 179 http://deb.debian.org/debian trixie/main i386 liblog-dispatch-array-perl all 1.005-1 [6700 B] Get: 180 http://deb.debian.org/debian trixie/main i386 libstring-flogger-perl all 1.101246-1 [7380 B] Get: 181 http://deb.debian.org/debian trixie/main i386 libsub-exporter-globexporter-perl all 0.006-1 [8024 B] Get: 182 http://deb.debian.org/debian trixie/main i386 liblog-dispatchouli-perl all 3.008-1 [34.4 kB] Get: 183 http://deb.debian.org/debian trixie/main i386 libexporter-tiny-perl all 1.006002-1 [38.7 kB] Get: 184 http://deb.debian.org/debian trixie/main i386 liblist-moreutils-xs-perl i386 0.430-4+b2 [45.1 kB] Get: 185 http://deb.debian.org/debian trixie/main i386 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get: 186 http://deb.debian.org/debian trixie/main i386 libsyntax-keyword-junction-perl all 0.003009-1 [12.7 kB] Get: 187 http://deb.debian.org/debian trixie/main i386 libmoose-autobox-perl all 0.16-2 [52.8 kB] Get: 188 http://deb.debian.org/debian trixie/main i386 libaliased-perl all 0.34-3 [13.5 kB] Get: 189 http://deb.debian.org/debian trixie/main i386 libmoosex-lazyrequire-perl all 0.11-2 [9212 B] Get: 190 http://deb.debian.org/debian trixie/main i386 libmoosex-setonce-perl all 0.200002-2 [6632 B] Get: 191 http://deb.debian.org/debian trixie/main i386 libcarp-clan-perl all 6.08-2 [14.1 kB] Get: 192 http://deb.debian.org/debian trixie/main i386 libsub-exporter-formethods-perl all 0.100055-1 [8024 B] Get: 193 http://deb.debian.org/debian trixie/main i386 libmoosex-types-perl all 0.50-2 [54.6 kB] Get: 194 http://deb.debian.org/debian trixie/main i386 libmoosex-types-perl-perl all 0.101344-1 [8160 B] Get: 195 http://deb.debian.org/debian trixie/main i386 libpath-tiny-perl all 0.146-1 [56.2 kB] Get: 196 http://deb.debian.org/debian trixie/main i386 libmodule-path-perl all 0.19-3 [12.3 kB] Get: 197 http://deb.debian.org/debian trixie/main i386 libtask-weaken-perl all 1.06-2 [9364 B] Get: 198 http://deb.debian.org/debian trixie/main i386 libppi-perl all 1.279-1 [294 kB] Get: 199 http://deb.debian.org/debian trixie/main i386 libtype-tiny-perl all 2.004000-1 [357 kB] Get: 200 http://deb.debian.org/debian trixie/main i386 libperl-prereqscanner-perl all 1.100-1 [31.0 kB] Get: 201 http://deb.debian.org/debian trixie/main i386 libperl-version-perl all 1.017-1 [29.0 kB] Get: 202 http://deb.debian.org/debian trixie/main i386 libtext-template-perl all 1.61-1 [54.4 kB] Get: 203 http://deb.debian.org/debian trixie/main i386 libsoftware-license-perl all 0.104006-1 [116 kB] Get: 204 http://deb.debian.org/debian trixie/main i386 libterm-encoding-perl all 0.03-2 [4980 B] Get: 205 http://deb.debian.org/debian trixie/main i386 libyaml-tiny-perl all 1.74-1 [30.7 kB] Get: 206 http://deb.debian.org/debian trixie/main i386 libdist-zilla-perl all 6.032-1 [343 kB] Get: 207 http://deb.debian.org/debian trixie/main i386 dh-dist-zilla all 1.4.1 [17.9 kB] Get: 208 http://deb.debian.org/debian trixie/main i386 fasttree i386 2.1.11-2 [183 kB] Get: 209 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB] Get: 210 http://deb.debian.org/debian trixie/main i386 libpng16-16t64 i386 1.6.44-2 [288 kB] Get: 211 http://deb.debian.org/debian trixie/main i386 libfreetype6 i386 2.13.3+dfsg-1 [464 kB] Get: 212 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 213 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 214 http://deb.debian.org/debian trixie/main i386 fontconfig-config i386 2.15.0-1.1+b1 [318 kB] Get: 215 http://deb.debian.org/debian trixie/main i386 libfontconfig1 i386 2.15.0-1.1+b1 [402 kB] Get: 216 http://deb.debian.org/debian trixie/main i386 fontconfig i386 2.15.0-1.1+b1 [463 kB] Get: 217 http://deb.debian.org/debian trixie/main i386 libarray-utils-perl all 0.5-3 [6184 B] Get: 218 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-3+b1 [143 kB] Get: 219 http://deb.debian.org/debian trixie/main i386 libpixman-1-0 i386 0.44.0-3 [246 kB] Get: 220 http://deb.debian.org/debian trixie/main i386 libxau6 i386 1:1.0.11-1 [20.7 kB] Get: 221 http://deb.debian.org/debian trixie/main i386 libxdmcp6 i386 1:1.1.2-3+b2 [24.9 kB] Get: 222 http://deb.debian.org/debian trixie/main i386 libxcb1 i386 1.17.0-2+b1 [148 kB] Get: 223 http://deb.debian.org/debian trixie/main i386 libx11-data all 2:1.8.10-2 [337 kB] Get: 224 http://deb.debian.org/debian trixie/main i386 libx11-6 i386 2:1.8.10-2 [834 kB] Get: 225 http://deb.debian.org/debian trixie/main i386 libxcb-render0 i386 1.17.0-2+b1 [116 kB] Get: 226 http://deb.debian.org/debian trixie/main i386 libxcb-shm0 i386 1.17.0-2+b1 [105 kB] Get: 227 http://deb.debian.org/debian trixie/main i386 libxext6 i386 2:1.3.4-1+b2 [52.6 kB] Get: 228 http://deb.debian.org/debian trixie/main i386 libxrender1 i386 1:0.9.10-1.1+b2 [28.9 kB] Get: 229 http://deb.debian.org/debian trixie/main i386 libcairo2 i386 1.18.2-2 [591 kB] Get: 230 http://deb.debian.org/debian trixie/main i386 libconst-fast-perl all 0.014-2 [8792 B] Get: 231 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB] Get: 232 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB] Get: 233 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.18+dfsg-3+b1 [200 kB] Get: 234 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB] Get: 235 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB] Get: 236 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB] Get: 237 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB] Get: 238 http://deb.debian.org/debian trixie/main i386 libcurl4t64 i386 8.11.0-1 [392 kB] Get: 239 http://deb.debian.org/debian trixie/main i386 libdata-compare-perl all 1.29-1 [19.6 kB] Get: 240 http://deb.debian.org/debian trixie/main i386 libdatrie1 i386 0.2.13-3+b1 [39.9 kB] Get: 241 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.22-1 [48.1 kB] Get: 242 http://deb.debian.org/debian trixie/main i386 libpod-eventual-perl all 0.094003-1 [14.2 kB] Get: 243 http://deb.debian.org/debian trixie/main i386 libstring-truncate-perl all 1.100603-1 [10.2 kB] Get: 244 http://deb.debian.org/debian trixie/main i386 libpod-elemental-perl all 0.103006-1 [67.2 kB] Get: 245 http://deb.debian.org/debian trixie/main i386 libpod-elemental-perlmunger-perl all 0.200007-1 [10.5 kB] Get: 246 http://deb.debian.org/debian trixie/main i386 libpod-weaver-perl all 4.020-1 [70.1 kB] Get: 247 http://deb.debian.org/debian trixie/main i386 libdist-zilla-plugin-podweaver-perl all 4.010-1 [9580 B] Get: 248 http://deb.debian.org/debian trixie/main i386 libenv-path-perl all 0.19-4 [19.1 kB] Get: 249 http://deb.debian.org/debian trixie/main i386 libfile-chdir-perl all 0.1008-1.2 [11.9 kB] Get: 250 http://deb.debian.org/debian trixie/main i386 libfile-grep-perl all 0.02-3 [8352 B] Get: 251 http://deb.debian.org/debian trixie/main i386 libfile-slurper-perl all 0.014-1 [8560 B] Get: 252 http://deb.debian.org/debian trixie/main i386 libfile-which-perl all 1.27-2 [15.1 kB] Get: 253 http://deb.debian.org/debian trixie/main i386 libfindbin-libs-perl all 3.0.2-1 [29.7 kB] Get: 254 http://deb.debian.org/debian trixie/main i386 libfribidi0 i386 1.0.15-1 [72.4 kB] Get: 255 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14.2.0-8 [735 kB] Get: 256 http://deb.debian.org/debian trixie/main i386 libglib2.0-0t64 i386 2.82.2-2 [1570 kB] Get: 257 http://deb.debian.org/debian trixie/main i386 libheap-perl all 0.80-5 [34.3 kB] Get: 258 http://deb.debian.org/debian trixie/main i386 libset-object-perl i386 1.42-1+b5 [38.3 kB] Get: 259 http://deb.debian.org/debian trixie/main i386 libgraph-perl all 1:0.9729-1 [108 kB] Get: 260 http://deb.debian.org/debian trixie/main i386 libspiffy-perl all 0.46-1 [25.7 kB] Get: 261 http://deb.debian.org/debian trixie/main i386 libio-all-perl all 0.87-2 [67.3 kB] Get: 262 http://deb.debian.org/debian trixie/main i386 libparse-yapp-perl all 1.21-4 [41.5 kB] Get: 263 http://deb.debian.org/debian trixie/main i386 libxml-parser-perl i386 2.47-1+b3 [200 kB] Get: 264 http://deb.debian.org/debian trixie/main i386 libxml-writer-perl all 0.900-2 [26.8 kB] Get: 265 http://deb.debian.org/debian trixie/main i386 libgraph-readwrite-perl all 2.10-1 [45.2 kB] Get: 266 http://deb.debian.org/debian trixie/main i386 libgraphite2-3 i386 1.3.14-2+b1 [77.8 kB] Get: 267 http://deb.debian.org/debian trixie/main i386 libharfbuzz0b i386 10.0.1-1 [503 kB] Get: 268 http://deb.debian.org/debian trixie/main i386 x11-common all 1:7.7+23.1 [216 kB] Get: 269 http://deb.debian.org/debian trixie/main i386 libice6 i386 2:1.1.1-1 [67.8 kB] Get: 270 http://deb.debian.org/debian trixie/main i386 libjbig0 i386 2.1-6.1+b2 [32.2 kB] Get: 271 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-3+b1 [171 kB] Get: 272 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.0-3+b1 [2196 kB] Get: 273 http://deb.debian.org/debian trixie/main i386 liblerc4 i386 4.0.0+ds-5 [191 kB] Get: 274 http://deb.debian.org/debian trixie/main i386 liblmdb0 i386 0.9.31-1+b2 [46.9 kB] Get: 275 http://deb.debian.org/debian trixie/main i386 liblog-log4perl-perl all 1.57-1 [367 kB] Get: 276 http://deb.debian.org/debian trixie/main i386 libmbedcrypto7t64 i386 2.28.8-1 [299 kB] Get: 277 http://deb.debian.org/debian trixie/main i386 libmbedx509-1t64 i386 2.28.8-1 [133 kB] Get: 278 http://deb.debian.org/debian trixie/main i386 libmbedtls14t64 i386 2.28.8-1 [171 kB] Get: 279 http://deb.debian.org/debian trixie/main i386 libpadwalker-perl i386 2.5-1+b6 [19.1 kB] Get: 280 http://deb.debian.org/debian trixie/main i386 libthai-data all 0.1.29-2 [168 kB] Get: 281 http://deb.debian.org/debian trixie/main i386 libthai0 i386 0.1.29-2+b1 [50.3 kB] Get: 282 http://deb.debian.org/debian trixie/main i386 libpango-1.0-0 i386 1.54.0+ds-3 [230 kB] Get: 283 http://deb.debian.org/debian trixie/main i386 libpangoft2-1.0-0 i386 1.54.0+ds-3 [58.1 kB] Get: 284 http://deb.debian.org/debian trixie/main i386 libpangocairo-1.0-0 i386 1.54.0+ds-3 [36.1 kB] Get: 285 http://deb.debian.org/debian trixie/main i386 libpaper1 i386 1.1.29+b2 [13.0 kB] Get: 286 http://deb.debian.org/debian trixie/main i386 libpaper-utils i386 1.1.29+b2 [9304 B] Get: 287 http://deb.debian.org/debian trixie/main i386 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 288 http://deb.debian.org/debian trixie/main i386 libsensors5 i386 1:3.6.0-10+b1 [35.8 kB] Get: 289 http://deb.debian.org/debian trixie/main i386 libsharpyuv0 i386 1.4.0-0.1+b1 [113 kB] Get: 290 http://deb.debian.org/debian trixie/main i386 libsm6 i386 2:1.2.4-1 [35.9 kB] Get: 291 http://deb.debian.org/debian trixie/main i386 libtcl8.6 i386 8.6.15+dfsg-2 [1103 kB] Get: 292 http://deb.debian.org/debian trixie/main i386 libtest-file-perl all 1.993-1 [24.5 kB] Get: 293 http://deb.debian.org/debian trixie/main i386 libtest2-suite-perl all 0.000163-1 [383 kB] Get: 294 http://deb.debian.org/debian trixie/main i386 libtest-files-perl all 0.26-1 [21.6 kB] Get: 295 http://deb.debian.org/debian trixie/main i386 libtest-output-perl all 1.034-1 [16.0 kB] Get: 296 http://deb.debian.org/debian trixie/main i386 libtext-csv-perl all 2.04-1 [112 kB] Get: 297 http://deb.debian.org/debian trixie/main i386 libwebp7 i386 1.4.0-0.1+b1 [322 kB] Get: 298 http://deb.debian.org/debian trixie/main i386 libtiff6 i386 4.5.1+git230720-5 [339 kB] Get: 299 http://deb.debian.org/debian trixie/main i386 libtingea0 i386 21-361-2+b2 [54.8 kB] Get: 300 http://deb.debian.org/debian trixie/main i386 libxft2 i386 2.3.6-1+b2 [55.3 kB] Get: 301 http://deb.debian.org/debian trixie/main i386 libxss1 i386 1:1.2.3-1+b2 [17.3 kB] Get: 302 http://deb.debian.org/debian trixie/main i386 libtk8.6 i386 8.6.15-1 [833 kB] Get: 303 http://deb.debian.org/debian trixie/main i386 libuv1t64 i386 1.48.0-7 [157 kB] Get: 304 http://deb.debian.org/debian trixie/main i386 libxt6t64 i386 1:1.2.1-1.2+b1 [193 kB] Get: 305 http://deb.debian.org/debian trixie/main i386 mafft i386 7.505-1 [1007 kB] Get: 306 http://deb.debian.org/debian trixie/main i386 mcl i386 1:22-282+ds-2 [480 kB] Get: 307 http://deb.debian.org/debian trixie/main i386 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get: 308 http://deb.debian.org/debian trixie/main i386 ncbi-blast+ i386 2.16.0+ds-6 [16.6 MB] Get: 309 http://deb.debian.org/debian trixie/main i386 sysstat i386 12.7.5-2 [626 kB] Get: 310 http://deb.debian.org/debian trixie/main i386 parallel all 20240222+ds-2 [2163 kB] Get: 311 http://deb.debian.org/debian trixie/main i386 prank i386 0.0.170427+dfsg-3 [405 kB] Get: 312 http://deb.debian.org/debian trixie/main i386 zip i386 3.0-14 [239 kB] Get: 313 http://deb.debian.org/debian trixie/main i386 unzip i386 6.0-28 [166 kB] Get: 314 http://deb.debian.org/debian trixie/main i386 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 315 http://deb.debian.org/debian trixie/main i386 r-base-core i386 4.4.2-1 [28.3 MB] Fetched 117 MB in 2s (52.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:i386. (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 ... 19956 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.7-3) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.4-1_i386.deb ... Unpacking libexpat1:i386 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_i386.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:i386 (3.12.7-3) ... Setting up libexpat1:i386 (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 ... 20276 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_i386.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:i386. Preparing to unpack .../04-libkrb5support0_1.21.3-3_i386.deb ... Unpacking libkrb5support0:i386 (1.21.3-3) ... Selecting previously unselected package libcom-err2:i386. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_i386.deb ... Unpacking libcom-err2:i386 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:i386. Preparing to unpack .../06-libk5crypto3_1.21.3-3_i386.deb ... Unpacking libk5crypto3:i386 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:i386. Preparing to unpack .../07-libkeyutils1_1.6.3-4_i386.deb ... Unpacking libkeyutils1:i386 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:i386. Preparing to unpack .../08-libkrb5-3_1.21.3-3_i386.deb ... Unpacking libkrb5-3:i386 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:i386. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_i386.deb ... Unpacking libgssapi-krb5-2:i386 (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:i386. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3 to /lib/i386-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3.0.0 to /lib/i386-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:i386 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:i386. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_i386.deb ... Unpacking libnsl2:i386 (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:i386. Preparing to unpack .../14-libreadline8t64_8.2-5_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:i386. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_i386.deb ... Unpacking libpython3.12-stdlib:i386 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_i386.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_i386.deb ... Unpacking libpython3-stdlib:i386 (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 ... 21338 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_i386.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package libproc2-0:i386. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-6_i386.deb ... Unpacking libproc2-0:i386 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-6_i386.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.3.2-2_i386.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../007-libmagic1t64_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.45-3+b1_i386.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.22.5-2_i386.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../010-libuchardet0_0.0.8-1+b2_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.23.0-5_i386.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../012-bsdextrautils_2.40.2-11_i386.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../013-libpipeline1_1.5.8-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../014-man-db_2.13.0-1_i386.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package ucf. Preparing to unpack .../015-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package m4. Preparing to unpack .../016-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../017-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../018-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../019-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../020-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package bedtools. Preparing to unpack .../021-bedtools_2.31.1+dfsg-2_i386.deb ... Unpacking bedtools (2.31.1+dfsg-2) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../022-libio-string-perl_1.08-4_all.deb ... Unpacking libio-string-perl (1.08-4) ... Selecting previously unselected package libdata-stag-perl. Preparing to unpack .../023-libdata-stag-perl_0.14-3_all.deb ... Unpacking libdata-stag-perl (0.14-3) ... Selecting previously unselected package libbio-perl-perl. Preparing to unpack .../024-libbio-perl-perl_1.7.8-1_all.deb ... Unpacking libbio-perl-perl (1.7.8-1) ... Selecting previously unselected package libclass-data-inheritable-perl. Preparing to unpack .../025-libclass-data-inheritable-perl_0.10-1_all.deb ... Unpacking libclass-data-inheritable-perl (0.10-1) ... Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../026-libdevel-stacktrace-perl_2.0500-1_all.deb ... Unpacking libdevel-stacktrace-perl (2.0500-1) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../027-libexception-class-perl_1.45-1_all.deb ... Unpacking libexception-class-perl (1.45-1) ... Selecting previously unselected package libtest-deep-perl. Preparing to unpack .../028-libtest-deep-perl_1.204-1_all.deb ... Unpacking libtest-deep-perl (1.204-1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../029-libcapture-tiny-perl_0.48-2_all.deb ... Unpacking libcapture-tiny-perl (0.48-2) ... Selecting previously unselected package libalgorithm-diff-perl. Preparing to unpack .../030-libalgorithm-diff-perl_1.201-1_all.deb ... Unpacking libalgorithm-diff-perl (1.201-1) ... Selecting previously unselected package libtext-diff-perl. Preparing to unpack .../031-libtext-diff-perl_1.45-2_all.deb ... Unpacking libtext-diff-perl (1.45-2) ... Selecting previously unselected package libtest-differences-perl. Preparing to unpack .../032-libtest-differences-perl_0.71-1_all.deb ... Unpacking libtest-differences-perl (0.71-1) ... Selecting previously unselected package libsub-uplevel-perl. Preparing to unpack .../033-libsub-uplevel-perl_0.2800-3_all.deb ... Unpacking libsub-uplevel-perl (0.2800-3) ... Selecting previously unselected package libtest-exception-perl. Preparing to unpack .../034-libtest-exception-perl_0.43-3_all.deb ... Unpacking libtest-exception-perl (0.43-3) ... Selecting previously unselected package libtest-warn-perl. Preparing to unpack .../035-libtest-warn-perl_0.37-2_all.deb ... Unpacking libtest-warn-perl (0.37-2) ... Selecting previously unselected package libtest-most-perl. Preparing to unpack .../036-libtest-most-perl_0.38-1_all.deb ... Unpacking libtest-most-perl (0.38-1) ... Selecting previously unselected package bioperl. Preparing to unpack .../037-bioperl_1.7.8-1_all.deb ... Unpacking bioperl (1.7.8-1) ... Selecting previously unselected package cd-hit. Preparing to unpack .../038-cd-hit_4.8.1-4_i386.deb ... Unpacking cd-hit (4.8.1-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../039-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../040-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../041-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../042-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../043-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../044-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:i386. Preparing to unpack .../045-libelf1t64_0.192-4_i386.deb ... Unpacking libelf1t64:i386 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../046-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../047-libicu72_72.1-5+b1_i386.deb ... Unpacking libicu72:i386 (72.1-5+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../048-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_i386.deb ... Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../049-gettext_0.22.5-2_i386.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_i386.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 ... 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Selecting previously unselected package libmoosex-role-parameterized-perl. Preparing to unpack .../097-libmoosex-role-parameterized-perl_1.11-2_all.deb ... Unpacking libmoosex-role-parameterized-perl (1.11-2) ... Selecting previously unselected package libmoosex-oneargnew-perl. Preparing to unpack .../098-libmoosex-oneargnew-perl_0.007-1_all.deb ... Unpacking libmoosex-oneargnew-perl (0.007-1) ... Selecting previously unselected package libcpanel-json-xs-perl:i386. Preparing to unpack .../099-libcpanel-json-xs-perl_4.38-1+b1_i386.deb ... Unpacking libcpanel-json-xs-perl:i386 (4.38-1+b1) ... Selecting previously unselected package libjson-maybexs-perl. Preparing to unpack .../100-libjson-maybexs-perl_1.004008-1_all.deb ... Unpacking libjson-maybexs-perl (1.004008-1) ... Selecting previously unselected package libstring-formatter-perl. Preparing to unpack .../101-libstring-formatter-perl_1.235-1_all.deb ... Unpacking libstring-formatter-perl (1.235-1) ... 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Preparing to unpack .../135-liblwp-protocol-https-perl_6.14-1_all.deb ... Unpacking liblwp-protocol-https-perl (6.14-1) ... Selecting previously unselected package libterm-readkey-perl. Preparing to unpack .../136-libterm-readkey-perl_2.38-2+b4_i386.deb ... Unpacking libterm-readkey-perl (2.38-2+b4) ... Selecting previously unselected package libcpan-uploader-perl. Preparing to unpack .../137-libcpan-uploader-perl_0.103018-1_all.deb ... Unpacking libcpan-uploader-perl (0.103018-1) ... Selecting previously unselected package libdata-section-perl. Preparing to unpack .../138-libdata-section-perl_0.200008-1_all.deb ... Unpacking libdata-section-perl (0.200008-1) ... Selecting previously unselected package libclass-inspector-perl. Preparing to unpack .../139-libclass-inspector-perl_1.36-3_all.deb ... Unpacking libclass-inspector-perl (1.36-3) ... Selecting previously unselected package libfile-sharedir-perl. Preparing to unpack .../140-libfile-sharedir-perl_1.118-3_all.deb ... 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Selecting previously unselected package libdatetime-timezone-perl. Preparing to unpack .../146-libdatetime-timezone-perl_1%3a2.63-2+2024b_all.deb ... Unpacking libdatetime-timezone-perl (1:2.63-2+2024b) ... Selecting previously unselected package libdatetime-perl. Preparing to unpack .../147-libdatetime-perl_2%3a1.65-1+b2_i386.deb ... Unpacking libdatetime-perl (2:1.65-1+b2) ... Selecting previously unselected package libfile-copy-recursive-perl. Preparing to unpack .../148-libfile-copy-recursive-perl_0.45-4_all.deb ... Unpacking libfile-copy-recursive-perl (0.45-4) ... Selecting previously unselected package libnumber-compare-perl. Preparing to unpack .../149-libnumber-compare-perl_0.03-3_all.deb ... Unpacking libnumber-compare-perl (0.03-3) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../150-libtext-glob-perl_0.11-3_all.deb ... Unpacking libtext-glob-perl (0.11-3) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../151-libfile-find-rule-perl_0.34-3_all.deb ... Unpacking libfile-find-rule-perl (0.34-3) ... Selecting previously unselected package libfile-pushd-perl. Preparing to unpack .../152-libfile-pushd-perl_1.016-2_all.deb ... Unpacking libfile-pushd-perl (1.016-2) ... Selecting previously unselected package libfile-sharedir-install-perl. Preparing to unpack .../153-libfile-sharedir-install-perl_0.14-2_all.deb ... Unpacking libfile-sharedir-install-perl (0.14-2) ... Selecting previously unselected package libhash-merge-simple-perl. Preparing to unpack .../154-libhash-merge-simple-perl_0.052-1_all.deb ... Unpacking libhash-merge-simple-perl (0.052-1) ... Selecting previously unselected package libjson-perl. Preparing to unpack .../155-libjson-perl_4.10000-1_all.deb ... Unpacking libjson-perl (4.10000-1) ... Selecting previously unselected package liblog-dispatch-perl. Preparing to unpack .../156-liblog-dispatch-perl_2.71-1_all.deb ... 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Unpacking libexporter-tiny-perl (1.006002-1) ... Selecting previously unselected package liblist-moreutils-xs-perl. Preparing to unpack .../162-liblist-moreutils-xs-perl_0.430-4+b2_i386.deb ... Unpacking liblist-moreutils-xs-perl (0.430-4+b2) ... Selecting previously unselected package liblist-moreutils-perl. Preparing to unpack .../163-liblist-moreutils-perl_0.430-2_all.deb ... Unpacking liblist-moreutils-perl (0.430-2) ... Selecting previously unselected package libsyntax-keyword-junction-perl. Preparing to unpack .../164-libsyntax-keyword-junction-perl_0.003009-1_all.deb ... Unpacking libsyntax-keyword-junction-perl (0.003009-1) ... Selecting previously unselected package libmoose-autobox-perl. Preparing to unpack .../165-libmoose-autobox-perl_0.16-2_all.deb ... Unpacking libmoose-autobox-perl (0.16-2) ... Selecting previously unselected package libaliased-perl. Preparing to unpack .../166-libaliased-perl_0.34-3_all.deb ... Unpacking libaliased-perl (0.34-3) ... 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Selecting previously unselected package libuv1t64:i386. Preparing to unpack .../281-libuv1t64_1.48.0-7_i386.deb ... Unpacking libuv1t64:i386 (1.48.0-7) ... Selecting previously unselected package libxt6t64:i386. Preparing to unpack .../282-libxt6t64_1%3a1.2.1-1.2+b1_i386.deb ... Unpacking libxt6t64:i386 (1:1.2.1-1.2+b1) ... Selecting previously unselected package mafft. Preparing to unpack .../283-mafft_7.505-1_i386.deb ... Unpacking mafft (7.505-1) ... Selecting previously unselected package mcl. Preparing to unpack .../284-mcl_1%3a22-282+ds-2_i386.deb ... Unpacking mcl (1:22-282+ds-2) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../285-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... Selecting previously unselected package ncbi-blast+. Preparing to unpack .../286-ncbi-blast+_2.16.0+ds-6_i386.deb ... Unpacking ncbi-blast+ (2.16.0+ds-6) ... Selecting previously unselected package sysstat. 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Selecting previously unselected package r-base-core. Preparing to unpack .../293-r-base-core_4.4.2-1_i386.deb ... Unpacking r-base-core (4.4.2-1) ... Setting up cd-hit (4.8.1-4) ... Setting up libarray-utils-perl (0.5-3) ... Setting up media-types (10.1.0) ... Setting up libmodule-pluggable-perl (5.2-5) ... Setting up libpipeline1:i386 (1.5.8-1) ... Setting up liblmdb0:i386 (0.9.31-1+b2) ... Setting up libgraphite2-3:i386 (1.3.14-2+b1) ... Setting up libfile-sharedir-install-perl (0.14-2) ... Setting up ncbi-data (6.1.20170106+dfsg2-5) ... Setting up libpixman-1-0:i386 (0.44.0-3) ... Setting up libsharpyuv0:i386 (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:i386 (1:1.0.11-1) ... Setting up libxdmcp6:i386 (1:1.1.2-3+b2) ... Setting up libkeyutils1:i386 (1.6.3-4) ... Setting up libxcb1:i386 (1.17.0-2+b1) ... Setting up libtie-ixhash-perl (1.23-4) ... Setting up libtask-weaken-perl (1.06-2) ... Setting up libicu72:i386 (72.1-5+b1) ... Setting up liblerc4:i386 (4.0.0+ds-5) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libparse-yapp-perl (1.21-4) ... Setting up libmbedcrypto7t64:i386 (2.28.8-1) ... Setting up libclass-inspector-perl (1.36-3) ... Setting up libdynaloader-functions-perl (0.004-1) ... Setting up libdatrie1:i386 (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:i386 (1.17.0-2+b1) ... Setting up mafft (7.505-1) ... Setting up libclone-perl:i386 (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:i386 (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:i386 (1.1.0-2+b6) ... Setting up libheap-perl (0.80-5) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libuv1t64:i386 (1.48.0-7) ... Setting up libmagic1t64:i386 (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:i386 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:i386 (1.64.0-1) ... Setting up libdeflate0:i386 (1.22-1) ... Setting up perl-openssl-defaults:i386 (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:i386 (1.17.0-2+b1) ... Setting up libfindbin-libs-perl (3.0.2-1) ... Setting up libcom-err2:i386 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libxstring-perl:i386 (0.005-2+b4) ... Setting up libyaml-tiny-perl (1.74-1) ... Setting up libjbig0:i386 (2.1-6.1+b2) ... Setting up libsub-install-perl (0.929-1) ... Setting up libelf1t64:i386 (0.192-4) ... Setting up libtest2-suite-perl (0.000163-1) ... Setting up libkrb5support0:i386 (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:i386 (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: Fri Nov 22 09:01:18 UTC 2024. Universal Time is now: Fri Nov 22 09:01:18 UTC 2024. 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:i386 (0.30-1+b4) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:i386 (2.82.2-2) ... No schema files found: doing nothing. Setting up libblas3:i386 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-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:i386 (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:i386 (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:i386 (1.0.15-1) ... Setting up libproc2-0:i386 (2:4.0.4-6) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:i386 (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:i386 (8.6.15+dfsg-2) ... Setting up autopoint (0.22.5-2) ... Setting up libb-hooks-op-check-perl:i386 (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:i386 (1:3.6.0-10+b1) ... Setting up libk5crypto3:i386 (1.21.3-3) ... Setting up libparams-util-perl (1.102-3+b1) ... Setting up libspiffy-perl (0.46-1) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-8) ... Setting up libgfortran5:i386 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libwebp7:i386 (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:i386 (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:i386 (4.5.1+git230720-5) ... Setting up libpath-tiny-perl (0.146-1) ... Setting up libuchardet0:i386 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up libjson-perl (4.10000-1) ... Setting up libtingea0:i386 (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:i386 (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:i386 (1.21.3-3) ... Setting up libmodule-path-perl (0.19-3) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libssh2-1t64:i386 (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:i386 (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:i386 (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:i386 (2:1.1.1-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up liblapack3:i386 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libmbedx509-1t64:i386 (2.28.8-1) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libhash-merge-simple-perl (0.052-1) ... Setting up libxrender1:i386 (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:i386 (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:i386 (0.009-1+b1) ... Setting up libldap-2.5-0:i386 (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:i386 (0.1.29-2+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libtest-exception-perl (0.43-3) ... Setting up libfreetype6:i386 (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:i386 (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 libreadline8t64:i386 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libmbedtls14t64:i386 (2.28.8-1) ... Setting up groff-base (1.23.0-5) ... Setting up libhtml-parser-perl:i386 (3.83-1+b1) ... Setting up libharfbuzz0b:i386 (10.0.1-1) ... Setting up libxss1:i386 (1:1.2.3-1+b2) ... Setting up libfontconfig1:i386 (2.15.0-1.1+b1) ... Setting up libmro-compat-perl (0.15-2) ... Setting up libsm6:i386 (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:i386 (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:i386 (2.3.6-1+b2) ... Setting up libcurl4t64:i386 (8.11.0-1) ... Setting up libtirpc3t64:i386 (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:i386 (8.6.15-1) ... Setting up libparams-classify-perl:i386 (0.015-2+b4) ... Setting up libpango-1.0-0:i386 (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:i386 (1.18.2-2) ... Setting up libconfig-ini-perl (1:0.029-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libxt6t64:i386 (1:1.2.1-1.2+b1) ... Setting up libdist-checkconflicts-perl (0.11-2) ... Setting up libstring-formatter-perl (1.235-1) ... Setting up parallel (20240222+ds-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-section-perl (0.200008-1) ... Setting up libnsl2:i386 (1.3.0-3+b3) ... Setting up libpangoft2-1.0-0:i386 (1.54.0+ds-3) ... Setting up libsub-exporter-globexporter-perl (0.006-1) ... Setting up libstring-rewriteprefix-perl (0.009-1) ... Setting up libpangocairo-1.0-0:i386 (1.54.0+ds-3) ... Setting up bioperl (1.7.8-1) ... Setting up libpython3.12-stdlib:i386 (3.12.7-3) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up libpod-eventual-perl (0.094003-1) ... Setting up libmodule-runtime-conflicts-perl (0.003-2) ... Setting up libtest-files-perl (0.26-1) ... 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:i386 (1.31-2+b3) ... Setting up libb-hooks-endofscope-perl (0.28-1) ... Setting up libpython3-stdlib:i386 (3.12.6-1) ... Setting up libthrowable-perl (1.001-2) ... Setting up libmoose-perl:i386 (2.2207-1+b2) ... Setting up python3 (3.12.6-1) ... Setting up ncbi-blast+ (2.16.0+ds-6) ... 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 i386 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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/roary-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -j11 make[1]: Entering directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm cp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm cp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm cp lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.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/AccessoryBinaryFasta.pm blib/lib/Bio/Roary/AccessoryBinaryFasta.pm cp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm cp lib/Bio/Roary/CommandLine/IterativeCdhit.pm blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pm cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.pm cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.pm cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm cp lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm cp lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm cp lib/Bio/Roary/AssemblyStatistics.pm blib/lib/Bio/Roary/AssemblyStatistics.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/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/AnnotateGroups.pm blib/lib/Bio/Roary/AnnotateGroups.pm cp lib/Bio/Roary/AccessoryClustering.pm blib/lib/Bio/Roary/AccessoryClustering.pm cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm cp lib/Bio/Roary/External/Mafft.pm blib/lib/Bio/Roary/External/Mafft.pm cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.pm cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm cp lib/Bio/Roary/External/Fasttree.pm blib/lib/Bio/Roary/External/Fasttree.pm cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.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/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/GeneNamesFromGFF.pm blib/lib/Bio/Roary/GeneNamesFromGFF.pm cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.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/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/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm cp lib/Bio/Roary/ReorderSpreadsheet.pm blib/lib/Bio/Roary/ReorderSpreadsheet.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/Output/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.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/PresenceAbsenceMatrix.pm blib/lib/Bio/Roary/PresenceAbsenceMatrix.pm cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm cp lib/Bio/Roary/SequenceLengths.pm blib/lib/Bio/Roary/SequenceLengths.pm cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm cp lib/Bio/Roary/UniqueGenesPerSample.pm blib/lib/Bio/Roary/UniqueGenesPerSample.pm cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm cp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm cp bin/create_pan_genome blib/script/create_pan_genome cp bin/extract_proteome_from_gff blib/script/extract_proteome_from_gff cp bin/create_pan_genome_plots blib/script/create_pan_genome_plots "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome cp bin/iterative_cdhit blib/script/iterative_cdhit cp bin/pan_genome_assembly_statistics blib/script/pan_genome_assembly_statistics "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/extract_proteome_from_gff "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome_plots cp bin/pan_genome_core_alignment blib/script/pan_genome_core_alignment "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/iterative_cdhit "/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 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_reorder_spreadsheet cp bin/parallel_all_against_all_blastp blib/script/parallel_all_against_all_blastp 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/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 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 -j11 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/MergeMultifastaAlignments.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/ReformatInputGFFs.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/ExtractCoreGenesFromSpreadsheet.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/LookupGeneFiles.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/ContigsToGeneIDsFromGFF.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/SplitGroups.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/AnalyseGroups.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/UniqueGenesPerSample.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/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/SequenceLengths.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/SampleOrder.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/SortFasta.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/PostAnalysis.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/ExtractProteomeFromGFF.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/PresenceAbsenceMatrix.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/ParseGFFAnnotationRole.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/GroupLabels.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/BedFromGFFRole.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/Output/GroupsMultifastasNucleotide.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/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/GroupsMultifastaNucleotide.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/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/DifferenceBetweenSets.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/CommandLine/IterativeCdhit.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/TransferAnnotationToGroups.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/RoaryCoreAlignment.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/AssemblyStatistics.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/Roary.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/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/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/Role.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/QC/Report.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/IterativeCdhit.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/Mafft.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/CheckTools.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/PostAnalysis.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/Cdhit.pm 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/parallel_all_against_all_blastp.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/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/man1/roary.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/create_pan_genome.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/pan_genome_post_analysis.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/pan_genome_reorder_spreadsheet.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/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/protein_alignment_from_nucleotides.1p 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::AnnotateGroups.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::ClustersRole.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::MergeMultifastaAlignments.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::NumberOfGroups.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::EmblGroups.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::CommandLine::QueryRoary.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::External::Cdhit.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::CommandLine::AssemblyStatistics.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::PrepareInputFiles.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::Exceptions.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::PostAnalysis.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::Output::EMBLHeaderCommon.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::LookupGeneFiles.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::PresenceAbsenceMatrix.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::CombinedProteome.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::External::Blastp.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::CommandLine::TransferAnnotationToGroups.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::Output::GroupsMultifastaProtein.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::CommandLine::UniqueGenesPerSample.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::CommandLine::Roary.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::External::Mafft.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::External::CheckTools.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::ExtractCoreGenesFromSpreadsheet.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::GroupsMultifastas.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::Output::GroupsMultifastasNucleotide.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::ReorderSpreadsheet.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::GroupStatistics.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::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::CommandLine::RoaryReorderSpreadsheet.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::InflateClusters.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::AccessoryClustering.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::External::Fasttree.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::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::ContigsToGeneIDsFromGFF.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::FilterFullClusters.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::UniqueGenesPerSample.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::CommandLine::RoaryPostAnalysis.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::JobRunner::Role.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::SequenceLengths.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/bin/roary-unique_genes_per_sample 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/iterative_cdhit 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/create_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/pan_genome_assembly_statistics 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/transfer_annotation_to_groups 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/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/protein_alignment_from_nucleotides 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/create_pan_genome_plots Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/parallel_all_against_all_blastp 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_i386.buildinfo dpkg-genchanges --build=binary -O../roary_3.13.0+dfsg-1_i386.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/12241 and its subdirectories I: Current time: Thu Nov 21 21:02:15 -12 2024 I: pbuilder-time-stamp: 1732266135 Fri Nov 22 09:02:17 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net. Fri Nov 22 09:02:17 UTC 2024 I: Preparing to do remote build '2' on ionos6-i386.debian.net. Fri Nov 22 09:02:17 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos6-i386.debian.net is marked as down. Fri Nov 22 09:02:17 UTC 2024 - checking via ssh if ionos6-i386.debian.net is up. removed '/tmp/read-only-fs-test-x4HZB6' ==================================================================================== Thu Dec 25 15:25:17 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos6-i386, called using "2 roary trixie /srv/reproducible-results/rbuild-debian/r-b-build.h5cOr7Lo 3.13.0+dfsg-1" as arguments. Thu Dec 25 15:25:17 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-30i8Ki9a" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Dec 25 15:25:17 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 (7406 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 (7406 kB/s) Download complete and in download only mode ============================================================================= Re-Building roary in trixie on i386 on ionos6-i386 now. Date: Thu Dec 25 16:25:18 CET 2025 Date UTC: Thu Dec 25 15:25:18 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.h5cOr7Lo + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.h5cOr7Lo/pbuilderrc_gVsO + case ${ARCH} in + let NUM_CPU-=3 + case $ARCH in + locale=de_CH + language=de + case "${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.h5cOr7Lo/pbuilderrc_gVsO --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.h5cOr7Lo/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: Fri Dec 26 05:25:18 +14 2025 I: pbuilder-time-stamp: 1766676318 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: using eatmydata during job 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/29825/tmp/hooks/D01_modify_environment starting debug: Running on ionos6-i386. 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 Dec 25 15:25 /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/29825/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/29825/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]="i686-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=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=a93c8bf7010a4134bd587822d568e4ec LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-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=29825 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.h5cOr7Lo/pbuilderrc_gVsO --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.h5cOr7Lo/b2 --logfile b2/build.log roary_3.13.0+dfsg-1.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) 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/29825/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: i386 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 ... 19956 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} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{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 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 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 117 MB of archives. After unpacking 397 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libpython3.12-minimal i386 3.12.7-3 [814 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 python3.12-minimal i386 3.12.7-3 [2236 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.1-1+b1 [23.4 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 12 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 libtirpc3t64 i386 1.3.4+ds-1.3+b1 [90.5 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 libnsl2 i386 1.3.0-3+b3 [42.7 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-5 [173 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libpython3.12-stdlib i386 3.12.7-3 [1964 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 python3.12 i386 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main i386 python3 i386 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 libproc2-0 i386 2:4.0.4-6 [65.7 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 procps i386 2:4.0.4-6 [876 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 openssl i386 3.3.2-2 [1387 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 ca-certificates all 20240203 [158 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-11 [95.6 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 ucf all 3.0043+nmu1 [55.2 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-2 [723 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 bedtools i386 2.31.1+dfsg-2 [745 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 libio-string-perl all 1.08-4 [12.1 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 libdata-stag-perl all 0.14-3 [448 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libclass-data-inheritable-perl all 0.10-1 [8632 B] Get: 48 http://deb.debian.org/debian trixie/main i386 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 libexception-class-perl all 1.45-1 [34.6 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 libtest-deep-perl all 1.204-1 [52.9 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 libtext-diff-perl all 1.45-2 [27.2 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 libtest-differences-perl all 0.71-1 [17.9 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 libtest-warn-perl all 0.37-2 [14.5 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 libtest-most-perl all 0.38-1 [25.1 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 bioperl all 1.7.8-1 [246 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 cd-hit i386 4.8.1-4 [524 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 67 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 libparams-util-perl i386 1.102-3+b1 [24.7 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 libsub-install-perl all 0.929-1 [10.5 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 libb-hooks-op-check-perl i386 0.22-3+b2 [10.7 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 libdevel-callchecker-perl i386 0.009-1+b1 [16.2 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 libparams-classify-perl i386 0.015-2+b4 [23.1 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 libpackage-stash-perl all 0.40-1 [22.0 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 libclass-load-perl all 0.25-2 [15.3 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 libio-stringy-perl all 2.113-2 [48.3 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 libparams-validate-perl i386 1.31-2+b3 [64.9 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 libgetopt-long-descriptive-perl all 0.115-1 [27.6 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 libio-tiecombine-perl all 1.005-3 [10.8 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 libmodule-pluggable-perl all 5.2-5 [23.0 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 libstring-rewriteprefix-perl all 0.009-1 [7140 B] Get: 94 http://deb.debian.org/debian trixie/main i386 libapp-cmd-perl all 0.336-1 [65.8 kB] Get: 95 http://deb.debian.org/debian trixie/main i386 libscope-guard-perl all 0.21-2 [8212 B] Get: 96 http://deb.debian.org/debian trixie/main i386 libautobox-perl i386 3.0.2-1+b1 [33.5 kB] Get: 97 http://deb.debian.org/debian trixie/main i386 libperlio-utf8-strict-perl i386 0.010-1+b3 [11.6 kB] Get: 98 http://deb.debian.org/debian trixie/main i386 libmixin-linewise-perl all 0.111-1 [14.4 kB] Get: 99 http://deb.debian.org/debian trixie/main i386 libconfig-ini-perl all 1:0.029-1 [23.7 kB] Get: 100 http://deb.debian.org/debian trixie/main i386 libclass-load-xs-perl i386 0.10-2+b4 [14.3 kB] Get: 101 http://deb.debian.org/debian trixie/main i386 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get: 102 http://deb.debian.org/debian trixie/main i386 libdevel-globaldestruction-perl all 0.14-4 [7144 B] Get: 103 http://deb.debian.org/debian trixie/main i386 libalgorithm-c3-perl all 0.11-2 [10.8 kB] Get: 104 http://deb.debian.org/debian trixie/main i386 libclass-c3-perl all 0.35-2 [21.0 kB] Get: 105 http://deb.debian.org/debian trixie/main i386 libmro-compat-perl all 0.15-2 [11.8 kB] Get: 106 http://deb.debian.org/debian trixie/main i386 libdevel-overloadinfo-perl all 0.007-1 [7896 B] Get: 107 http://deb.debian.org/debian trixie/main i386 libeval-closure-perl all 0.14-3 [11.2 kB] Get: 108 http://deb.debian.org/debian trixie/main i386 libdist-checkconflicts-perl all 0.11-2 [10.5 kB] Get: 109 http://deb.debian.org/debian trixie/main i386 libmodule-runtime-conflicts-perl all 0.003-2 [7356 B] Get: 110 http://deb.debian.org/debian trixie/main i386 libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB] Get: 111 http://deb.debian.org/debian trixie/main i386 libpackage-stash-xs-perl i386 0.30-1+b4 [21.2 kB] Get: 112 http://deb.debian.org/debian trixie/main i386 libmoose-perl i386 2.2207-1+b2 [767 kB] Get: 113 http://deb.debian.org/debian trixie/main i386 libvariable-magic-perl i386 0.64-1+b1 [45.8 kB] Get: 114 http://deb.debian.org/debian trixie/main i386 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB] Get: 115 http://deb.debian.org/debian trixie/main i386 libsub-identify-perl i386 0.14-3+b3 [11.2 kB] Get: 116 http://deb.debian.org/debian trixie/main i386 libsub-name-perl i386 0.27-1+b3 [12.6 kB] Get: 117 http://deb.debian.org/debian trixie/main i386 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get: 118 http://deb.debian.org/debian trixie/main i386 libnamespace-autoclean-perl all 0.31-1 [13.8 kB] Get: 119 http://deb.debian.org/debian trixie/main i386 libmoosex-role-parameterized-perl all 1.11-2 [41.9 kB] Get: 120 http://deb.debian.org/debian trixie/main i386 libmoosex-oneargnew-perl all 0.007-1 [8180 B] Get: 121 http://deb.debian.org/debian trixie/main i386 libcpanel-json-xs-perl i386 4.38-1+b1 [134 kB] Get: 122 http://deb.debian.org/debian trixie/main i386 libjson-maybexs-perl all 1.004008-1 [12.9 kB] Get: 123 http://deb.debian.org/debian trixie/main i386 libstring-formatter-perl all 1.235-1 [22.1 kB] Get: 124 http://deb.debian.org/debian trixie/main i386 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 125 http://deb.debian.org/debian trixie/main i386 libstring-errf-perl all 0.009-1 [12.9 kB] Get: 126 http://deb.debian.org/debian trixie/main i386 librole-hasmessage-perl all 0.007-1 [9112 B] Get: 127 http://deb.debian.org/debian trixie/main i386 librole-identifiable-perl all 0.009-1 [10.4 kB] Get: 128 http://deb.debian.org/debian trixie/main i386 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 129 http://deb.debian.org/debian trixie/main i386 libclass-xsaccessor-perl i386 1.19-4+b4 [37.5 kB] Get: 130 http://deb.debian.org/debian trixie/main i386 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 131 http://deb.debian.org/debian trixie/main i386 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 132 http://deb.debian.org/debian trixie/main i386 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 133 http://deb.debian.org/debian trixie/main i386 libmoo-perl all 2.005005-1 [58.0 kB] Get: 134 http://deb.debian.org/debian trixie/main i386 libthrowable-perl all 1.001-2 [15.7 kB] Get: 135 http://deb.debian.org/debian trixie/main i386 libtie-ixhash-perl all 1.23-4 [11.7 kB] Get: 136 http://deb.debian.org/debian trixie/main i386 libconfig-mvp-perl all 2.200013-1 [47.1 kB] Get: 137 http://deb.debian.org/debian trixie/main i386 libconfig-mvp-reader-ini-perl all 2.101465-1 [6900 B] Get: 138 http://deb.debian.org/debian trixie/main i386 perl-openssl-defaults i386 7+b2 [6720 B] Get: 139 http://deb.debian.org/debian trixie/main i386 libnet-ssleay-perl i386 1.94-2 [340 kB] Get: 140 http://deb.debian.org/debian trixie/main i386 libio-socket-ssl-perl all 2.089-1 [223 kB] Get: 141 http://deb.debian.org/debian trixie/main i386 liburi-perl all 5.30-1 [105 kB] Get: 142 http://deb.debian.org/debian trixie/main i386 libnet-http-perl all 6.23-1 [23.9 kB] Get: 143 http://deb.debian.org/debian trixie/main i386 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 144 http://deb.debian.org/debian trixie/main i386 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 145 http://deb.debian.org/debian trixie/main i386 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 146 http://deb.debian.org/debian trixie/main i386 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 147 http://deb.debian.org/debian trixie/main i386 libhtml-parser-perl i386 3.83-1+b1 [101 kB] Get: 148 http://deb.debian.org/debian trixie/main i386 libhtml-tree-perl all 5.07-3 [211 kB] Get: 149 http://deb.debian.org/debian trixie/main i386 libclone-perl i386 0.47-1+b1 [14.0 kB] Get: 150 http://deb.debian.org/debian trixie/main i386 libio-html-perl all 1.004-3 [16.2 kB] Get: 151 http://deb.debian.org/debian trixie/main i386 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 152 http://deb.debian.org/debian trixie/main i386 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 153 http://deb.debian.org/debian trixie/main i386 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 154 http://deb.debian.org/debian trixie/main i386 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 155 http://deb.debian.org/debian trixie/main i386 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 156 http://deb.debian.org/debian trixie/main i386 libwww-perl all 6.77-1 [183 kB] Get: 157 http://deb.debian.org/debian trixie/main i386 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 158 http://deb.debian.org/debian trixie/main i386 libterm-readkey-perl i386 2.38-2+b4 [25.4 kB] Get: 159 http://deb.debian.org/debian trixie/main i386 libcpan-uploader-perl all 0.103018-1 [16.3 kB] Get: 160 http://deb.debian.org/debian trixie/main i386 libdata-section-perl all 0.200008-1 [13.1 kB] Get: 161 http://deb.debian.org/debian trixie/main i386 libclass-inspector-perl all 1.36-3 [17.5 kB] Get: 162 http://deb.debian.org/debian trixie/main i386 libfile-sharedir-perl all 1.118-3 [16.0 kB] Get: 163 http://deb.debian.org/debian trixie/main i386 libparams-validationcompiler-perl all 0.31-1 [30.9 kB] Get: 164 http://deb.debian.org/debian trixie/main i386 libxstring-perl i386 0.005-2+b4 [8212 B] Get: 165 http://deb.debian.org/debian trixie/main i386 libspecio-perl all 0.48-1 [142 kB] Get: 166 http://deb.debian.org/debian trixie/main i386 libdatetime-locale-perl all 1:1.41-1 [3131 kB] Get: 167 http://deb.debian.org/debian trixie/main i386 libclass-singleton-perl all 1.6-2 [12.5 kB] Get: 168 http://deb.debian.org/debian trixie/main i386 libdatetime-timezone-perl all 1:2.63-2+2024b [261 kB] Get: 169 http://deb.debian.org/debian trixie/main i386 libdatetime-perl i386 2:1.65-1+b2 [119 kB] Get: 170 http://deb.debian.org/debian trixie/main i386 libfile-copy-recursive-perl all 0.45-4 [20.0 kB] Get: 171 http://deb.debian.org/debian trixie/main i386 libnumber-compare-perl all 0.03-3 [6332 B] Get: 172 http://deb.debian.org/debian trixie/main i386 libtext-glob-perl all 0.11-3 [7676 B] Get: 173 http://deb.debian.org/debian trixie/main i386 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get: 174 http://deb.debian.org/debian trixie/main i386 libfile-pushd-perl all 1.016-2 [13.5 kB] Get: 175 http://deb.debian.org/debian trixie/main i386 libfile-sharedir-install-perl all 0.14-2 [11.6 kB] Get: 176 http://deb.debian.org/debian trixie/main i386 libhash-merge-simple-perl all 0.052-1 [8232 B] Get: 177 http://deb.debian.org/debian trixie/main i386 libjson-perl all 4.10000-1 [87.5 kB] Get: 178 http://deb.debian.org/debian trixie/main i386 liblog-dispatch-perl all 2.71-1 [75.8 kB] Get: 179 http://deb.debian.org/debian trixie/main i386 liblog-dispatch-array-perl all 1.005-1 [6700 B] Get: 180 http://deb.debian.org/debian trixie/main i386 libstring-flogger-perl all 1.101246-1 [7380 B] Get: 181 http://deb.debian.org/debian trixie/main i386 libsub-exporter-globexporter-perl all 0.006-1 [8024 B] Get: 182 http://deb.debian.org/debian trixie/main i386 liblog-dispatchouli-perl all 3.008-1 [34.4 kB] Get: 183 http://deb.debian.org/debian trixie/main i386 libexporter-tiny-perl all 1.006002-1 [38.7 kB] Get: 184 http://deb.debian.org/debian trixie/main i386 liblist-moreutils-xs-perl i386 0.430-4+b2 [45.1 kB] Get: 185 http://deb.debian.org/debian trixie/main i386 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get: 186 http://deb.debian.org/debian trixie/main i386 libsyntax-keyword-junction-perl all 0.003009-1 [12.7 kB] Get: 187 http://deb.debian.org/debian trixie/main i386 libmoose-autobox-perl all 0.16-2 [52.8 kB] Get: 188 http://deb.debian.org/debian trixie/main i386 libaliased-perl all 0.34-3 [13.5 kB] Get: 189 http://deb.debian.org/debian trixie/main i386 libmoosex-lazyrequire-perl all 0.11-2 [9212 B] Get: 190 http://deb.debian.org/debian trixie/main i386 libmoosex-setonce-perl all 0.200002-2 [6632 B] Get: 191 http://deb.debian.org/debian trixie/main i386 libcarp-clan-perl all 6.08-2 [14.1 kB] Get: 192 http://deb.debian.org/debian trixie/main i386 libsub-exporter-formethods-perl all 0.100055-1 [8024 B] Get: 193 http://deb.debian.org/debian trixie/main i386 libmoosex-types-perl all 0.50-2 [54.6 kB] Get: 194 http://deb.debian.org/debian trixie/main i386 libmoosex-types-perl-perl all 0.101344-1 [8160 B] Get: 195 http://deb.debian.org/debian trixie/main i386 libpath-tiny-perl all 0.146-1 [56.2 kB] Get: 196 http://deb.debian.org/debian trixie/main i386 libmodule-path-perl all 0.19-3 [12.3 kB] Get: 197 http://deb.debian.org/debian trixie/main i386 libtask-weaken-perl all 1.06-2 [9364 B] Get: 198 http://deb.debian.org/debian trixie/main i386 libppi-perl all 1.279-1 [294 kB] Get: 199 http://deb.debian.org/debian trixie/main i386 libtype-tiny-perl all 2.004000-1 [357 kB] Get: 200 http://deb.debian.org/debian trixie/main i386 libperl-prereqscanner-perl all 1.100-1 [31.0 kB] Get: 201 http://deb.debian.org/debian trixie/main i386 libperl-version-perl all 1.017-1 [29.0 kB] Get: 202 http://deb.debian.org/debian trixie/main i386 libtext-template-perl all 1.61-1 [54.4 kB] Get: 203 http://deb.debian.org/debian trixie/main i386 libsoftware-license-perl all 0.104006-1 [116 kB] Get: 204 http://deb.debian.org/debian trixie/main i386 libterm-encoding-perl all 0.03-2 [4980 B] Get: 205 http://deb.debian.org/debian trixie/main i386 libyaml-tiny-perl all 1.74-1 [30.7 kB] Get: 206 http://deb.debian.org/debian trixie/main i386 libdist-zilla-perl all 6.032-1 [343 kB] Get: 207 http://deb.debian.org/debian trixie/main i386 dh-dist-zilla all 1.4.1 [17.9 kB] Get: 208 http://deb.debian.org/debian trixie/main i386 fasttree i386 2.1.11-2 [183 kB] Get: 209 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB] Get: 210 http://deb.debian.org/debian trixie/main i386 libpng16-16t64 i386 1.6.44-2 [288 kB] Get: 211 http://deb.debian.org/debian trixie/main i386 libfreetype6 i386 2.13.3+dfsg-1 [464 kB] Get: 212 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 213 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 214 http://deb.debian.org/debian trixie/main i386 fontconfig-config i386 2.15.0-1.1+b1 [318 kB] Get: 215 http://deb.debian.org/debian trixie/main i386 libfontconfig1 i386 2.15.0-1.1+b1 [402 kB] Get: 216 http://deb.debian.org/debian trixie/main i386 fontconfig i386 2.15.0-1.1+b1 [463 kB] Get: 217 http://deb.debian.org/debian trixie/main i386 libarray-utils-perl all 0.5-3 [6184 B] Get: 218 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-3+b1 [143 kB] Get: 219 http://deb.debian.org/debian trixie/main i386 libpixman-1-0 i386 0.44.0-3 [246 kB] Get: 220 http://deb.debian.org/debian trixie/main i386 libxau6 i386 1:1.0.11-1 [20.7 kB] Get: 221 http://deb.debian.org/debian trixie/main i386 libxdmcp6 i386 1:1.1.2-3+b2 [24.9 kB] Get: 222 http://deb.debian.org/debian trixie/main i386 libxcb1 i386 1.17.0-2+b1 [148 kB] Get: 223 http://deb.debian.org/debian trixie/main i386 libx11-data all 2:1.8.10-2 [337 kB] Get: 224 http://deb.debian.org/debian trixie/main i386 libx11-6 i386 2:1.8.10-2 [834 kB] Get: 225 http://deb.debian.org/debian trixie/main i386 libxcb-render0 i386 1.17.0-2+b1 [116 kB] Get: 226 http://deb.debian.org/debian trixie/main i386 libxcb-shm0 i386 1.17.0-2+b1 [105 kB] Get: 227 http://deb.debian.org/debian trixie/main i386 libxext6 i386 2:1.3.4-1+b2 [52.6 kB] Get: 228 http://deb.debian.org/debian trixie/main i386 libxrender1 i386 1:0.9.10-1.1+b2 [28.9 kB] Get: 229 http://deb.debian.org/debian trixie/main i386 libcairo2 i386 1.18.2-2 [591 kB] Get: 230 http://deb.debian.org/debian trixie/main i386 libconst-fast-perl all 0.014-2 [8792 B] Get: 231 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB] Get: 232 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB] Get: 233 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.18+dfsg-3+b1 [200 kB] Get: 234 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB] Get: 235 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB] Get: 236 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB] Get: 237 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB] Get: 238 http://deb.debian.org/debian trixie/main i386 libcurl4t64 i386 8.11.0-1 [392 kB] Get: 239 http://deb.debian.org/debian trixie/main i386 libdata-compare-perl all 1.29-1 [19.6 kB] Get: 240 http://deb.debian.org/debian trixie/main i386 libdatrie1 i386 0.2.13-3+b1 [39.9 kB] Get: 241 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.22-1 [48.1 kB] Get: 242 http://deb.debian.org/debian trixie/main i386 libpod-eventual-perl all 0.094003-1 [14.2 kB] Get: 243 http://deb.debian.org/debian trixie/main i386 libstring-truncate-perl all 1.100603-1 [10.2 kB] Get: 244 http://deb.debian.org/debian trixie/main i386 libpod-elemental-perl all 0.103006-1 [67.2 kB] Get: 245 http://deb.debian.org/debian trixie/main i386 libpod-elemental-perlmunger-perl all 0.200007-1 [10.5 kB] Get: 246 http://deb.debian.org/debian trixie/main i386 libpod-weaver-perl all 4.020-1 [70.1 kB] Get: 247 http://deb.debian.org/debian trixie/main i386 libdist-zilla-plugin-podweaver-perl all 4.010-1 [9580 B] Get: 248 http://deb.debian.org/debian trixie/main i386 libenv-path-perl all 0.19-4 [19.1 kB] Get: 249 http://deb.debian.org/debian trixie/main i386 libfile-chdir-perl all 0.1008-1.2 [11.9 kB] Get: 250 http://deb.debian.org/debian trixie/main i386 libfile-grep-perl all 0.02-3 [8352 B] Get: 251 http://deb.debian.org/debian trixie/main i386 libfile-slurper-perl all 0.014-1 [8560 B] Get: 252 http://deb.debian.org/debian trixie/main i386 libfile-which-perl all 1.27-2 [15.1 kB] Get: 253 http://deb.debian.org/debian trixie/main i386 libfindbin-libs-perl all 3.0.2-1 [29.7 kB] Get: 254 http://deb.debian.org/debian trixie/main i386 libfribidi0 i386 1.0.15-1 [72.4 kB] Get: 255 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14.2.0-8 [735 kB] Get: 256 http://deb.debian.org/debian trixie/main i386 libglib2.0-0t64 i386 2.82.2-2 [1570 kB] Get: 257 http://deb.debian.org/debian trixie/main i386 libheap-perl all 0.80-5 [34.3 kB] Get: 258 http://deb.debian.org/debian trixie/main i386 libset-object-perl i386 1.42-1+b5 [38.3 kB] Get: 259 http://deb.debian.org/debian trixie/main i386 libgraph-perl all 1:0.9729-1 [108 kB] Get: 260 http://deb.debian.org/debian trixie/main i386 libspiffy-perl all 0.46-1 [25.7 kB] Get: 261 http://deb.debian.org/debian trixie/main i386 libio-all-perl all 0.87-2 [67.3 kB] Get: 262 http://deb.debian.org/debian trixie/main i386 libparse-yapp-perl all 1.21-4 [41.5 kB] Get: 263 http://deb.debian.org/debian trixie/main i386 libxml-parser-perl i386 2.47-1+b3 [200 kB] Get: 264 http://deb.debian.org/debian trixie/main i386 libxml-writer-perl all 0.900-2 [26.8 kB] Get: 265 http://deb.debian.org/debian trixie/main i386 libgraph-readwrite-perl all 2.10-1 [45.2 kB] Get: 266 http://deb.debian.org/debian trixie/main i386 libgraphite2-3 i386 1.3.14-2+b1 [77.8 kB] Get: 267 http://deb.debian.org/debian trixie/main i386 libharfbuzz0b i386 10.0.1-1 [503 kB] Get: 268 http://deb.debian.org/debian trixie/main i386 x11-common all 1:7.7+23.1 [216 kB] Get: 269 http://deb.debian.org/debian trixie/main i386 libice6 i386 2:1.1.1-1 [67.8 kB] Get: 270 http://deb.debian.org/debian trixie/main i386 libjbig0 i386 2.1-6.1+b2 [32.2 kB] Get: 271 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-3+b1 [171 kB] Get: 272 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.0-3+b1 [2196 kB] Get: 273 http://deb.debian.org/debian trixie/main i386 liblerc4 i386 4.0.0+ds-5 [191 kB] Get: 274 http://deb.debian.org/debian trixie/main i386 liblmdb0 i386 0.9.31-1+b2 [46.9 kB] Get: 275 http://deb.debian.org/debian trixie/main i386 liblog-log4perl-perl all 1.57-1 [367 kB] Get: 276 http://deb.debian.org/debian trixie/main i386 libmbedcrypto7t64 i386 2.28.8-1 [299 kB] Get: 277 http://deb.debian.org/debian trixie/main i386 libmbedx509-1t64 i386 2.28.8-1 [133 kB] Get: 278 http://deb.debian.org/debian trixie/main i386 libmbedtls14t64 i386 2.28.8-1 [171 kB] Get: 279 http://deb.debian.org/debian trixie/main i386 libpadwalker-perl i386 2.5-1+b6 [19.1 kB] Get: 280 http://deb.debian.org/debian trixie/main i386 libthai-data all 0.1.29-2 [168 kB] Get: 281 http://deb.debian.org/debian trixie/main i386 libthai0 i386 0.1.29-2+b1 [50.3 kB] Get: 282 http://deb.debian.org/debian trixie/main i386 libpango-1.0-0 i386 1.54.0+ds-3 [230 kB] Get: 283 http://deb.debian.org/debian trixie/main i386 libpangoft2-1.0-0 i386 1.54.0+ds-3 [58.1 kB] Get: 284 http://deb.debian.org/debian trixie/main i386 libpangocairo-1.0-0 i386 1.54.0+ds-3 [36.1 kB] Get: 285 http://deb.debian.org/debian trixie/main i386 libpaper1 i386 1.1.29+b2 [13.0 kB] Get: 286 http://deb.debian.org/debian trixie/main i386 libpaper-utils i386 1.1.29+b2 [9304 B] Get: 287 http://deb.debian.org/debian trixie/main i386 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 288 http://deb.debian.org/debian trixie/main i386 libsensors5 i386 1:3.6.0-10+b1 [35.8 kB] Get: 289 http://deb.debian.org/debian trixie/main i386 libsharpyuv0 i386 1.4.0-0.1+b1 [113 kB] Get: 290 http://deb.debian.org/debian trixie/main i386 libsm6 i386 2:1.2.4-1 [35.9 kB] Get: 291 http://deb.debian.org/debian trixie/main i386 libtcl8.6 i386 8.6.15+dfsg-2 [1103 kB] Get: 292 http://deb.debian.org/debian trixie/main i386 libtest-file-perl all 1.993-1 [24.5 kB] Get: 293 http://deb.debian.org/debian trixie/main i386 libtest2-suite-perl all 0.000163-1 [383 kB] Get: 294 http://deb.debian.org/debian trixie/main i386 libtest-files-perl all 0.26-1 [21.6 kB] Get: 295 http://deb.debian.org/debian trixie/main i386 libtest-output-perl all 1.034-1 [16.0 kB] Get: 296 http://deb.debian.org/debian trixie/main i386 libtext-csv-perl all 2.04-1 [112 kB] Get: 297 http://deb.debian.org/debian trixie/main i386 libwebp7 i386 1.4.0-0.1+b1 [322 kB] Get: 298 http://deb.debian.org/debian trixie/main i386 libtiff6 i386 4.5.1+git230720-5 [339 kB] Get: 299 http://deb.debian.org/debian trixie/main i386 libtingea0 i386 21-361-2+b2 [54.8 kB] Get: 300 http://deb.debian.org/debian trixie/main i386 libxft2 i386 2.3.6-1+b2 [55.3 kB] Get: 301 http://deb.debian.org/debian trixie/main i386 libxss1 i386 1:1.2.3-1+b2 [17.3 kB] Get: 302 http://deb.debian.org/debian trixie/main i386 libtk8.6 i386 8.6.15-1 [833 kB] Get: 303 http://deb.debian.org/debian trixie/main i386 libuv1t64 i386 1.48.0-7 [157 kB] Get: 304 http://deb.debian.org/debian trixie/main i386 libxt6t64 i386 1:1.2.1-1.2+b1 [193 kB] Get: 305 http://deb.debian.org/debian trixie/main i386 mafft i386 7.505-1 [1007 kB] Get: 306 http://deb.debian.org/debian trixie/main i386 mcl i386 1:22-282+ds-2 [480 kB] Get: 307 http://deb.debian.org/debian trixie/main i386 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get: 308 http://deb.debian.org/debian trixie/main i386 ncbi-blast+ i386 2.16.0+ds-6 [16.6 MB] Get: 309 http://deb.debian.org/debian trixie/main i386 sysstat i386 12.7.5-2 [626 kB] Get: 310 http://deb.debian.org/debian trixie/main i386 parallel all 20240222+ds-2 [2163 kB] Get: 311 http://deb.debian.org/debian trixie/main i386 prank i386 0.0.170427+dfsg-3 [405 kB] Get: 312 http://deb.debian.org/debian trixie/main i386 zip i386 3.0-14 [239 kB] Get: 313 http://deb.debian.org/debian trixie/main i386 unzip i386 6.0-28 [166 kB] Get: 314 http://deb.debian.org/debian trixie/main i386 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 315 http://deb.debian.org/debian trixie/main i386 r-base-core i386 4.4.2-1 [28.3 MB] Fetched 117 MB in 2s (49.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:i386. (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 ... 19956 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.7-3) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.4-1_i386.deb ... Unpacking libexpat1:i386 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_i386.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:i386 (3.12.7-3) ... Setting up libexpat1:i386 (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 ... 20276 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_i386.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:i386. Preparing to unpack .../04-libkrb5support0_1.21.3-3_i386.deb ... Unpacking libkrb5support0:i386 (1.21.3-3) ... Selecting previously unselected package libcom-err2:i386. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_i386.deb ... Unpacking libcom-err2:i386 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:i386. Preparing to unpack .../06-libk5crypto3_1.21.3-3_i386.deb ... Unpacking libk5crypto3:i386 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:i386. Preparing to unpack .../07-libkeyutils1_1.6.3-4_i386.deb ... Unpacking libkeyutils1:i386 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:i386. Preparing to unpack .../08-libkrb5-3_1.21.3-3_i386.deb ... Unpacking libkrb5-3:i386 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:i386. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_i386.deb ... Unpacking libgssapi-krb5-2:i386 (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:i386. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3 to /lib/i386-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3.0.0 to /lib/i386-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:i386 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:i386. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_i386.deb ... Unpacking libnsl2:i386 (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:i386. Preparing to unpack .../14-libreadline8t64_8.2-5_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:i386. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_i386.deb ... Unpacking libpython3.12-stdlib:i386 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_i386.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_i386.deb ... Unpacking libpython3-stdlib:i386 (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 ... 21338 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_i386.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package libproc2-0:i386. 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Selecting previously unselected package libuv1t64:i386. Preparing to unpack .../281-libuv1t64_1.48.0-7_i386.deb ... Unpacking libuv1t64:i386 (1.48.0-7) ... Selecting previously unselected package libxt6t64:i386. Preparing to unpack .../282-libxt6t64_1%3a1.2.1-1.2+b1_i386.deb ... Unpacking libxt6t64:i386 (1:1.2.1-1.2+b1) ... Selecting previously unselected package mafft. Preparing to unpack .../283-mafft_7.505-1_i386.deb ... Unpacking mafft (7.505-1) ... Selecting previously unselected package mcl. Preparing to unpack .../284-mcl_1%3a22-282+ds-2_i386.deb ... Unpacking mcl (1:22-282+ds-2) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../285-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... Selecting previously unselected package ncbi-blast+. Preparing to unpack .../286-ncbi-blast+_2.16.0+ds-6_i386.deb ... Unpacking ncbi-blast+ (2.16.0+ds-6) ... Selecting previously unselected package sysstat. Preparing to unpack .../287-sysstat_12.7.5-2_i386.deb ... Unpacking sysstat (12.7.5-2) ... Selecting previously unselected package parallel. Preparing to unpack .../288-parallel_20240222+ds-2_all.deb ... Adding 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel' Adding 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel' Unpacking parallel (20240222+ds-2) ... Selecting previously unselected package prank. Preparing to unpack .../289-prank_0.0.170427+dfsg-3_i386.deb ... Unpacking prank (0.0.170427+dfsg-3) ... Selecting previously unselected package zip. Preparing to unpack .../290-zip_3.0-14_i386.deb ... Unpacking zip (3.0-14) ... Selecting previously unselected package unzip. Preparing to unpack .../291-unzip_6.0-28_i386.deb ... Unpacking unzip (6.0-28) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../292-xdg-utils_1.1.3-4.1_all.deb ... Unpacking xdg-utils (1.1.3-4.1) ... Selecting previously unselected package r-base-core. Preparing to unpack .../293-r-base-core_4.4.2-1_i386.deb ... Unpacking r-base-core (4.4.2-1) ... Setting up cd-hit (4.8.1-4) ... Setting up libarray-utils-perl (0.5-3) ... Setting up media-types (10.1.0) ... Setting up libmodule-pluggable-perl (5.2-5) ... Setting up libpipeline1:i386 (1.5.8-1) ... Setting up liblmdb0:i386 (0.9.31-1+b2) ... Setting up libgraphite2-3:i386 (1.3.14-2+b1) ... Setting up libfile-sharedir-install-perl (0.14-2) ... Setting up ncbi-data (6.1.20170106+dfsg2-5) ... Setting up libpixman-1-0:i386 (0.44.0-3) ... Setting up libsharpyuv0:i386 (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:i386 (1:1.0.11-1) ... Setting up libxdmcp6:i386 (1:1.1.2-3+b2) ... Setting up libkeyutils1:i386 (1.6.3-4) ... Setting up libxcb1:i386 (1.17.0-2+b1) ... Setting up libtie-ixhash-perl (1.23-4) ... Setting up libtask-weaken-perl (1.06-2) ... Setting up libicu72:i386 (72.1-5+b1) ... Setting up liblerc4:i386 (4.0.0+ds-5) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libparse-yapp-perl (1.21-4) ... Setting up libmbedcrypto7t64:i386 (2.28.8-1) ... Setting up libclass-inspector-perl (1.36-3) ... Setting up libdynaloader-functions-perl (0.004-1) ... Setting up libdatrie1:i386 (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:i386 (1.17.0-2+b1) ... Setting up mafft (7.505-1) ... Setting up libclone-perl:i386 (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:i386 (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:i386 (1.1.0-2+b6) ... Setting up libheap-perl (0.80-5) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libuv1t64:i386 (1.48.0-7) ... Setting up libmagic1t64:i386 (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:i386 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:i386 (1.64.0-1) ... Setting up libdeflate0:i386 (1.22-1) ... Setting up perl-openssl-defaults:i386 (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:i386 (1.17.0-2+b1) ... Setting up libfindbin-libs-perl (3.0.2-1) ... Setting up libcom-err2:i386 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libxstring-perl:i386 (0.005-2+b4) ... Setting up libyaml-tiny-perl (1.74-1) ... Setting up libjbig0:i386 (2.1-6.1+b2) ... Setting up libsub-install-perl (0.929-1) ... Setting up libelf1t64:i386 (0.192-4) ... Setting up libtest2-suite-perl (0.000163-1) ... Setting up libkrb5support0:i386 (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:i386 (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: Thu Dec 25 15:25:49 UTC 2025. Universal Time is now: Thu Dec 25 15:25:49 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:i386 (0.30-1+b4) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:i386 (2.82.2-2) ... No schema files found: doing nothing. Setting up libblas3:i386 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-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:i386 (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:i386 (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:i386 (1.0.15-1) ... Setting up libproc2-0:i386 (2:4.0.4-6) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:i386 (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:i386 (8.6.15+dfsg-2) ... Setting up autopoint (0.22.5-2) ... Setting up libb-hooks-op-check-perl:i386 (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:i386 (1:3.6.0-10+b1) ... Setting up libk5crypto3:i386 (1.21.3-3) ... Setting up libparams-util-perl (1.102-3+b1) ... Setting up libspiffy-perl (0.46-1) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-8) ... Setting up libgfortran5:i386 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libwebp7:i386 (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:i386 (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:i386 (4.5.1+git230720-5) ... Setting up libpath-tiny-perl (0.146-1) ... Setting up libuchardet0:i386 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up libjson-perl (4.10000-1) ... Setting up libtingea0:i386 (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:i386 (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:i386 (1.21.3-3) ... Setting up libmodule-path-perl (0.19-3) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libssh2-1t64:i386 (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:i386 (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:i386 (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:i386 (2:1.1.1-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up liblapack3:i386 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libmbedx509-1t64:i386 (2.28.8-1) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libhash-merge-simple-perl (0.052-1) ... Setting up libxrender1:i386 (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:i386 (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:i386 (0.009-1+b1) ... Setting up libldap-2.5-0:i386 (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:i386 (0.1.29-2+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libtest-exception-perl (0.43-3) ... Setting up libfreetype6:i386 (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:i386 (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 libreadline8t64:i386 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libmbedtls14t64:i386 (2.28.8-1) ... Setting up groff-base (1.23.0-5) ... Setting up libhtml-parser-perl:i386 (3.83-1+b1) ... Setting up libharfbuzz0b:i386 (10.0.1-1) ... Setting up libxss1:i386 (1:1.2.3-1+b2) ... Setting up libfontconfig1:i386 (2.15.0-1.1+b1) ... Setting up libmro-compat-perl (0.15-2) ... Setting up libsm6:i386 (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:i386 (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:i386 (2.3.6-1+b2) ... Setting up libcurl4t64:i386 (8.11.0-1) ... Setting up libtirpc3t64:i386 (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:i386 (8.6.15-1) ... Setting up libparams-classify-perl:i386 (0.015-2+b4) ... Setting up libpango-1.0-0:i386 (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:i386 (1.18.2-2) ... Setting up libconfig-ini-perl (1:0.029-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libxt6t64:i386 (1:1.2.1-1.2+b1) ... Setting up libdist-checkconflicts-perl (0.11-2) ... Setting up libstring-formatter-perl (1.235-1) ... Setting up parallel (20240222+ds-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-section-perl (0.200008-1) ... Setting up libnsl2:i386 (1.3.0-3+b3) ... Setting up libpangoft2-1.0-0:i386 (1.54.0+ds-3) ... Setting up libsub-exporter-globexporter-perl (0.006-1) ... Setting up libstring-rewriteprefix-perl (0.009-1) ... Setting up libpangocairo-1.0-0:i386 (1.54.0+ds-3) ... Setting up bioperl (1.7.8-1) ... Setting up libpython3.12-stdlib:i386 (3.12.7-3) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up libpod-eventual-perl (0.094003-1) ... Setting up libmodule-runtime-conflicts-perl (0.003-2) ... Setting up libtest-files-perl (0.26-1) ... 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:i386 (1.31-2+b3) ... Setting up libb-hooks-endofscope-perl (0.28-1) ... Setting up libpython3-stdlib:i386 (3.12.6-1) ... Setting up libthrowable-perl (1.001-2) ... Setting up libmoose-perl:i386 (2.2207-1+b2) ... Setting up python3 (3.12.6-1) ... Setting up ncbi-blast+ (2.16.0+ds-6) ... 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: user script /srv/workspace/pbuilder/29825/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/29825/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 i386 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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/roary-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -j21 make[1]: Entering directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' cp lib/Bio/Roary/AccessoryBinaryFasta.pm blib/lib/Bio/Roary/AccessoryBinaryFasta.pm cp lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm cp lib/Bio/Roary/AssemblyStatistics.pm blib/lib/Bio/Roary/AssemblyStatistics.pm cp lib/Bio/Roary/CommandLine/IterativeCdhit.pm blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pm cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm cp lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm blib/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm cp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm cp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.pm cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm cp lib/Bio/Roary/CommandLine/AssemblyStatistics.pm blib/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm cp lib/Bio/Roary/AnnotateGroups.pm blib/lib/Bio/Roary/AnnotateGroups.pm cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.pm cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm cp lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm blib/lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm 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/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm cp lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm cp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.pm cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.pm cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm cp lib/Bio/Roary/External/Fasttree.pm blib/lib/Bio/Roary/External/Fasttree.pm cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm cp lib/Bio/Roary/MergeMultifastaAlignments.pm blib/lib/Bio/Roary/MergeMultifastaAlignments.pm cp lib/Bio/Roary/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pm cp lib/Bio/Roary/JobRunner/Parallel.pm blib/lib/Bio/Roary/JobRunner/Parallel.pm cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.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/External/Mcl.pm blib/lib/Bio/Roary/External/Mcl.pm cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.pm cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.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/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.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/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm cp lib/Bio/Roary/Output/EMBLHeaderCommon.pm blib/lib/Bio/Roary/Output/EMBLHeaderCommon.pm cp lib/Bio/Roary/External/Mafft.pm blib/lib/Bio/Roary/External/Mafft.pm cp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm cp lib/Bio/Roary/External/IterativeCdhit.pm blib/lib/Bio/Roary/External/IterativeCdhit.pm cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.pm cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.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/PresenceAbsenceMatrix.pm blib/lib/Bio/Roary/PresenceAbsenceMatrix.pm cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm cp lib/Bio/Roary/Output/QueryGroups.pm blib/lib/Bio/Roary/Output/QueryGroups.pm cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm cp lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm cp lib/Bio/Roary/SpreadsheetRole.pm blib/lib/Bio/Roary/SpreadsheetRole.pm cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.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/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm cp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.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 cp bin/pan_genome_assembly_statistics blib/script/pan_genome_assembly_statistics "/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 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 cp bin/protein_alignment_from_nucleotides blib/script/protein_alignment_from_nucleotides "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/parallel_all_against_all_blastp 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 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/query_pan_genome cp bin/roary 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 cp bin/roary-pan_genome_reorder_spreadsheet blib/script/roary-pan_genome_reorder_spreadsheet cp bin/roary-query_pan_genome blib/script/roary-query_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-create_pan_genome_plots.R "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-pan_genome_reorder_spreadsheet 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-query_pan_genome cp bin/transfer_annotation_to_groups blib/script/transfer_annotation_to_groups "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-unique_genes_per_sample "/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 -j21 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/GroupLabels.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/SampleOrder.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/SplitGroups.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/ReformatInputGFFs.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/UniqueGenesPerSample.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/Exceptions.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/SpreadsheetRole.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/ParseGFFAnnotationRole.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/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/ClustersRole.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/PrepareInputFiles.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/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/FilterUnknownsFromFasta.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/ExtractCoreGenesFromSpreadsheet.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/SequenceLengths.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/IterativeCdhit.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/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/LookupGeneFiles.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/DifferenceBetweenSets.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/GroupsMultifastasNucleotide.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/EmblGroups.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/NumberOfGroups.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/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/QueryRoary.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/CreatePanGenome.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/RoaryPostAnalysis.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/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/perl5/Bio/Roary/CommandLine/TransferAnnotationToGroups.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/AssemblyStatistics.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/External/PostAnalysis.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/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/GeneAlignmentFromNucleotides.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/Cdhit.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/IterativeCdhit.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/Blastp.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/JobRunner/Role.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/Local.pm 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/man1/pan_genome_post_analysis.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/pan_genome_assembly_statistics.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/roary.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/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/transfer_annotation_to_groups.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-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/create_pan_genome_plots.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/create_pan_genome.1p 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::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::Exceptions.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::FilterFullClusters.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::Makeblastdb.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::JobRunner::Local.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::External::Prank.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::External::PostAnalysis.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::FilterUnknownsFromFasta.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::External::Mafft.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::JobRunner::Parallel.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::ReorderSpreadsheet.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::AccessoryBinaryFasta.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::QC::Report.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::External::Blastp.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::CommandLine::RoaryReorderSpreadsheet.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::AssemblyStatistics.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::BedFromGFFRole.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::MergeMultifastaAlignments.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::LookupGeneFiles.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::PrepareInputFiles.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::InflateClusters.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::GroupLabels.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::CommandLine::IterativeCdhit.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::Output::EmblGroups.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.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::IterativeCdhit.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::ChunkFastaFile.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::AnnotateGroups.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::CommandLine::ExtractProteomeFromGff.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::ExtractProteomeFromGFFs.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::TransferAnnotationToGroups.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::PostAnalysis.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::Output::DifferenceBetweenSets.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::External::Cdhit.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::ExtractCoreGenesFromSpreadsheet.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::CommandLine::RoaryPostAnalysis.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::QueryGroups.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::AccessoryClustering.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::UniqueGenesPerSample.3pm 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/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/protein_alignment_from_nucleotides 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/parallel_all_against_all_blastp 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/pan_genome_post_analysis 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_assembly_statistics 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/roary-create_pan_genome_plots.R 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/transfer_annotation_to_groups 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/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_i386.buildinfo dpkg-genchanges --build=binary -O../roary_3.13.0+dfsg-1_i386.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/29825/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/29825/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/29825 and its subdirectories I: Current time: Fri Dec 26 05:26:22 +14 2025 I: pbuilder-time-stamp: 1766676382 + false + set +x Thu Dec 25 15:26:22 UTC 2025 I: Signing ./b2/roary_3.13.0+dfsg-1_i386.buildinfo as roary_3.13.0+dfsg-1_i386.buildinfo.asc Thu Dec 25 15:26:22 UTC 2025 I: Signed ./b2/roary_3.13.0+dfsg-1_i386.buildinfo as ./b2/roary_3.13.0+dfsg-1_i386.buildinfo.asc Thu Dec 25 15:26:22 UTC 2025 - build #2 for roary/trixie/i386 on ionos6-i386 done. Starting cleanup. All cleanup done. Thu Dec 25 15:26:22 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-30i8Ki9a, removing. /srv/reproducible-results/rbuild-debian/r-b-build.h5cOr7Lo: total 176 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 09:02 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 09:03 b2 -rw------- 1 jenkins jenkins 162317 Nov 22 09:02 rbuildlog.bS1XI9v -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.h5cOr7Lo/b1: total 596 -rw-r--r-- 1 jenkins jenkins 158424 Nov 22 09:02 build.log -rw-r--r-- 1 jenkins jenkins 6612 Nov 22 09:02 roary_3.13.0+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2501 Nov 22 09:02 roary_3.13.0+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 172956 Nov 22 09:02 roary_3.13.0+dfsg-1_all.deb -rw-r--r-- 1 jenkins jenkins 14471 Nov 22 09:02 roary_3.13.0+dfsg-1_i386.buildinfo -rw-r--r-- 1 jenkins jenkins 15353 Nov 22 09:02 roary_3.13.0+dfsg-1_i386.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1142 Nov 22 09:02 roary_3.13.0+dfsg-1_i386.changes -rw-r--r-- 1 jenkins jenkins 1589 Nov 22 09:02 roary_3.13.0+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 207348 Nov 22 09:02 roary_3.13.0+dfsg.orig.tar.xz /srv/reproducible-results/rbuild-debian/r-b-build.h5cOr7Lo/b2: total 588 -rw-r--r-- 1 jenkins jenkins 160334 Nov 22 09:03 build.log -rw-r--r-- 1 jenkins jenkins 6612 Nov 22 09:03 roary_3.13.0+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2501 Nov 22 09:03 roary_3.13.0+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 172956 Nov 22 09:03 roary_3.13.0+dfsg-1_all.deb -rw-r--r-- 1 jenkins jenkins 14471 Nov 22 09:03 roary_3.13.0+dfsg-1_i386.buildinfo -rw-r--r-- 1 jenkins jenkins 15353 Nov 22 09:03 roary_3.13.0+dfsg-1_i386.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1142 Nov 22 09:03 roary_3.13.0+dfsg-1_i386.changes -rw-r--r-- 1 jenkins jenkins 1589 Nov 22 09:03 roary_3.13.0+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 207348 Nov 22 09:03 roary_3.13.0+dfsg.orig.tar.xz Fri Nov 22 09:03:23 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. Fri Nov 22 09:03:23 UTC 2024 I: roary_3.13.0+dfsg-1_i386.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 48ecc2f35142a2833948d6c00429297f754bba6e 14471 roary_3.13.0+dfsg-1_i386.buildinfo Checksums-Sha256: 407c586f74905ca1cd02fa839d4f37a5975f5f0fb0e1a730dd4949f3f62a08c3 172956 roary_3.13.0+dfsg-1_all.deb 52c4141969d4e3cebb645f9c33bc2095194c57124bd9d9bc5d46bbc1ff4c4b24 14471 roary_3.13.0+dfsg-1_i386.buildinfo Files: af01483d1d735e74de6bd65123abd903 172956 science optional roary_3.13.0+dfsg-1_all.deb 127c91839dd0c9e3fa5b8d6676ce0c21 14471 science optional roary_3.13.0+dfsg-1_i386.buildinfo removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/i386/roary_3.13.0+dfsg-1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/i386/roary_3.13.0+dfsg-1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/roary_3.13.0+dfsg-1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/roary_3.13.0+dfsg-1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/i386/roary_3.13.0+dfsg-1_i386.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/roary_3.13.0+dfsg-1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-11-22 09:02:16.527677619 +0000 +++ b2/build.log 2024-11-22 09:03:23.340669128 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Nov 21 21:00:37 -12 2024 -I: pbuilder-time-stamp: 1732266037 +I: Current time: Fri Dec 26 05:25:18 +14 2025 +I: pbuilder-time-stamp: 1766676318 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,54 +31,86 @@ dpkg-source: info: applying new-bioperl-require.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/12241/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/29825/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-i386. +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 Dec 25 15:25 /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/29825/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/29825/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='6109fc1478a94bd993f3546f3f99d1e2' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='12241' - PS1='# ' - PS2='> ' + INVOCATION_ID=a93c8bf7010a4134bd587822d568e4ec + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=29825 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.h5cOr7Lo/pbuilderrc_z39m --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.h5cOr7Lo/b1 --logfile b1/build.log roary_3.13.0+dfsg-1.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.h5cOr7Lo/pbuilderrc_gVsO --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.h5cOr7Lo/b2 --logfile b2/build.log roary_3.13.0+dfsg-1.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos2-i386 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) 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/12241/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/29825/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -489,7 +521,7 @@ Get: 313 http://deb.debian.org/debian trixie/main i386 unzip i386 6.0-28 [166 kB] Get: 314 http://deb.debian.org/debian trixie/main i386 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 315 http://deb.debian.org/debian trixie/main i386 r-base-core i386 4.4.2-1 [28.3 MB] -Fetched 117 MB in 2s (52.1 MB/s) +Fetched 117 MB in 2s (49.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:i386. (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 ... 19956 files and directories currently installed.) @@ -1535,8 +1567,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Nov 22 09:01:18 UTC 2024. -Universal Time is now: Fri Nov 22 09:01:18 UTC 2024. +Local time is now: Thu Dec 25 15:25:49 UTC 2025. +Universal Time is now: Thu Dec 25 15:25:49 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libjson-maybexs-perl (1.004008-1) ... @@ -1807,7 +1839,11 @@ 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/29825/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/29825/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 @@ -1839,120 +1875,120 @@ Writing Makefile for Bio::Roary Writing MYMETA.yml and MYMETA.json dh_auto_build -D .build/debian-build - cd .build/debian-build && make -j11 + cd .build/debian-build && make -j21 make[1]: Entering directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' -cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm -cp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm -cp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm -cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm -cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm -cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm -cp lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm -cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.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/AccessoryBinaryFasta.pm blib/lib/Bio/Roary/AccessoryBinaryFasta.pm -cp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm -cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm -cp lib/Bio/Roary/CommandLine/IterativeCdhit.pm blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pm -cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.pm -cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.pm -cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm -cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm -cp lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm -cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm cp lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm +cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm cp lib/Bio/Roary/AssemblyStatistics.pm blib/lib/Bio/Roary/AssemblyStatistics.pm +cp lib/Bio/Roary/CommandLine/IterativeCdhit.pm blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pm +cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.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.pm blib/lib/Bio/Roary.pm +cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.pm +cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm cp lib/Bio/Roary/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/AnnotateGroups.pm blib/lib/Bio/Roary/AnnotateGroups.pm +cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.pm +cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm +cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm +cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm +cp lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm blib/lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm 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/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm -cp lib/Bio/Roary/External/Mafft.pm blib/lib/Bio/Roary/External/Mafft.pm -cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm -cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.pm -cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm +cp lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm +cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm +cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm +cp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm +cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm +cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.pm +cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.pm cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm -cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm -cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm -cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm cp lib/Bio/Roary/External/Fasttree.pm blib/lib/Bio/Roary/External/Fasttree.pm -cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pm +cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.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/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/JobRunner/Parallel.pm blib/lib/Bio/Roary/JobRunner/Parallel.pm +cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.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/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm -cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm -cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm -cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.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/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/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm cp lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm -cp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm +cp lib/Bio/Roary/Output/GroupMultifasta.pm blib/lib/Bio/Roary/Output/GroupMultifasta.pm +cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm +cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm -cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm -cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm -cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm -cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm -cp lib/Bio/Roary/ReorderSpreadsheet.pm blib/lib/Bio/Roary/ReorderSpreadsheet.pm -cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm +cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm +cp lib/Bio/Roary/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm +cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm +cp lib/Bio/Roary/Output/EMBLHeaderCommon.pm blib/lib/Bio/Roary/Output/EMBLHeaderCommon.pm +cp lib/Bio/Roary/External/Mafft.pm blib/lib/Bio/Roary/External/Mafft.pm +cp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm +cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm +cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm +cp lib/Bio/Roary/External/IterativeCdhit.pm blib/lib/Bio/Roary/External/IterativeCdhit.pm +cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.pm +cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm +cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.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/PresenceAbsenceMatrix.pm blib/lib/Bio/Roary/PresenceAbsenceMatrix.pm +cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm +cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm cp lib/Bio/Roary/Output/QueryGroups.pm blib/lib/Bio/Roary/Output/QueryGroups.pm +cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm +cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm cp lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm +cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm +cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm +cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm cp lib/Bio/Roary/SpreadsheetRole.pm blib/lib/Bio/Roary/SpreadsheetRole.pm -cp lib/Bio/Roary/SampleOrder.pm blib/lib/Bio/Roary/SampleOrder.pm -cp lib/Bio/Roary/PresenceAbsenceMatrix.pm blib/lib/Bio/Roary/PresenceAbsenceMatrix.pm cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm -cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm -cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm -cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm -cp lib/Bio/Roary/SequenceLengths.pm blib/lib/Bio/Roary/SequenceLengths.pm -cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm -cp lib/Bio/Roary/UniqueGenesPerSample.pm blib/lib/Bio/Roary/UniqueGenesPerSample.pm +cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.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/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm -cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm -cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm -cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm cp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm +cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm cp bin/create_pan_genome blib/script/create_pan_genome -cp bin/extract_proteome_from_gff blib/script/extract_proteome_from_gff cp bin/create_pan_genome_plots blib/script/create_pan_genome_plots -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome +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 cp bin/pan_genome_assembly_statistics blib/script/pan_genome_assembly_statistics "/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/create_pan_genome_plots -cp bin/pan_genome_core_alignment blib/script/pan_genome_core_alignment "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/iterative_cdhit +cp bin/pan_genome_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 +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 -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 -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 +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 "/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 cp bin/roary-pan_genome_reorder_spreadsheet blib/script/roary-pan_genome_reorder_spreadsheet +cp bin/roary-query_pan_genome blib/script/roary-query_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-create_pan_genome_plots.R "/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 +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-query_pan_genome cp bin/transfer_annotation_to_groups blib/script/transfer_annotation_to_groups +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-unique_genes_per_sample "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/transfer_annotation_to_groups Manifying 16 pod documents Manifying 26 pod documents @@ -1970,203 +2006,203 @@ dh_testroot dh_prep dh_auto_install -D .build/debian-build --destdir=debian/roary/ - cd .build/debian-build && make -j11 install DESTDIR=/build/reproducible-path/roary-3.13.0\+dfsg/debian/roary AM_UPDATE_INFO_DIR=no PREFIX=/usr + cd .build/debian-build && make -j21 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/MergeMultifastaAlignments.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/GroupLabels.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/SampleOrder.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/SplitGroups.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/ReformatInputGFFs.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/ExtractCoreGenesFromSpreadsheet.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/LookupGeneFiles.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/ContigsToGeneIDsFromGFF.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/SplitGroups.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/AnalyseGroups.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/UniqueGenesPerSample.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/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/SequenceLengths.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/SampleOrder.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/SortFasta.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/PostAnalysis.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/ExtractProteomeFromGFF.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/InflateClusters.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/PresenceAbsenceMatrix.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/FilterFullClusters.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/ExtractProteomeFromGFF.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/ClustersRole.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/PrepareInputFiles.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/Exceptions.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/GroupStatistics.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/FilterUnknownsFromFasta.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/EmblGroups.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/ChunkFastaFile.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/SortFasta.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/ReorderSpreadsheet.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/BedFromGFFRole.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/LookupGeneFiles.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/DifferenceBetweenSets.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/GroupsMultifastasNucleotide.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/DifferenceBetweenSets.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/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/CommandLine/IterativeCdhit.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/TransferAnnotationToGroups.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/NumberOfGroups.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/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/RoaryCoreAlignment.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/AssemblyStatistics.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/QueryRoary.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/CreatePanGenome.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/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/RoaryPostAnalysis.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/Role.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/QC/Report.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/perl5/Bio/Roary/CommandLine/TransferAnnotationToGroups.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/AssemblyStatistics.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/External/PostAnalysis.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/IterativeCdhit.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/Mafft.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/CheckTools.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/PostAnalysis.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/GeneAlignmentFromNucleotides.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/Cdhit.pm -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/parallel_all_against_all_blastp.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/roary-unique_genes_per_sample.1p +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/IterativeCdhit.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/Blastp.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/JobRunner/Role.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/Local.pm 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/man1/roary.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/create_pan_genome.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/pan_genome_post_analysis.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/pan_genome_reorder_spreadsheet.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/parallel_all_against_all_blastp.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/iterative_cdhit.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/transfer_annotation_to_groups.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/man3/Bio::Roary::External::GeneAlignmentFromNucleotides.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::RoaryCoreAlignment.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/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-unique_genes_per_sample.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/create_pan_genome_plots.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/create_pan_genome.1p +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::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::Exceptions.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::FilterFullClusters.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::Makeblastdb.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::MergeMultifastaAlignments.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::NumberOfGroups.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::EmblGroups.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::CommandLine::QueryRoary.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::External::Cdhit.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::CommandLine::AssemblyStatistics.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::PrepareInputFiles.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::Exceptions.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::PostAnalysis.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::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::External::Prank.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::External::PostAnalysis.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::FilterUnknownsFromFasta.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::QueryGroups.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::ExtractProteomeFromGFFs.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::ReformatInputGFFs.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::BedFromGFFRole.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::External::IterativeCdhit.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::AnalyseGroups.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::JobRunner::Parallel.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::AssemblyStatistics.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::ExtractProteomeFromGFF.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::SampleOrder.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::ParallelAllAgainstAllBlast.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::SpreadsheetRole.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::CommandLine::ParallelAllAgainstAllBlastp.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::AccessoryBinaryFasta.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::JobRunner::Parallel.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::ReorderSpreadsheet.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::AccessoryBinaryFasta.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::QC::Report.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::GeneNamesFromGFF.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::SpreadsheetRole.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::CombinedProteome.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::SplitGroups.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::AssemblyStatistics.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::BedFromGFFRole.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::MergeMultifastaAlignments.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::LookupGeneFiles.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::PrepareInputFiles.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::InflateClusters.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::AccessoryClustering.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::GroupLabels.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::GroupsMultifastaNucleotide.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::PresenceAbsenceMatrix.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::CheckTools.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::CommandLine::AssemblyStatistics.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::GroupsMultifastaProtein.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::External::GeneAlignmentFromNucleotides.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::Common.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::ClustersRole.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::ReformatInputGFFs.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::GeneNamesFromGFF.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::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::ContigsToGeneIDsFromGFF.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::FilterFullClusters.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::UniqueGenesPerSample.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::Output::DifferenceBetweenSets.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::External::Cdhit.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::ExtractCoreGenesFromSpreadsheet.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::CommandLine::RoaryPostAnalysis.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::CommandLine::GeneAlignmentFromNucleotides.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::Output::NumberOfGroups.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::JobRunner::Role.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::SequenceLengths.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::UniqueGenesPerSample.3pm 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/query_pan_genome -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-create_pan_genome_plots.R 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/pan_genome_reorder_spreadsheet -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/pan_genome_post_analysis -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 -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/create_pan_genome_plots 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-query_pan_genome +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/roary +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/extract_proteome_from_gff +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/pan_genome_core_alignment -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/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-create_pan_genome_plots.R +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/transfer_annotation_to_groups +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/query_pan_genome make[1]: Leaving directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' dh_installdocs dh_installchangelogs @@ -2190,12 +2226,14 @@ 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/29825/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/29825/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/12241 and its subdirectories -I: Current time: Thu Nov 21 21:02:15 -12 2024 -I: pbuilder-time-stamp: 1732266135 +I: removing directory /srv/workspace/pbuilder/29825 and its subdirectories +I: Current time: Fri Dec 26 05:26:22 +14 2025 +I: pbuilder-time-stamp: 1766676382 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/roary_3.13.0+dfsg-1.diff: 89.0% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/roary_3.13.0+dfsg-1.diff.gz b2/build.log: 83.2% -- replaced with stdout Compressing the 1st log... b1/build.log: 83.5% -- replaced with stdout Fri Nov 22 09:03:25 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_i386_1732266205 + touch /var/log/reproducible-builds/diffoscope_stamp_roary_trixie_i386_1732266205 + RESULT=0 + systemd-run '--description=diffoscope on roary/3.13.0+dfsg-1 in trixie/i386' --slice=rb-build-diffoscope.slice -u rb-diffoscope-i386_9-32171 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.h5cOr7Lo --run-session -c jenkins-reproducible-trixie-diffoscope-d66c6a77-1f2e-4d0b-a739-86efdae56c7e -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.h5cOr7Lo/dbd-tmp-5amnNQV ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.h5cOr7Lo/roary_3.13.0+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.h5cOr7Lo/roary_3.13.0+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.h5cOr7Lo/roary_3.13.0+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.h5cOr7Lo/b1/roary_3.13.0+dfsg-1_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.h5cOr7Lo/b2/roary_3.13.0+dfsg-1_i386.changes' + false + set +x Running as unit: rb-diffoscope-i386_9-32171.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.h5cOr7Lo/roary_3.13.0+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.h5cOr7Lo/roary_3.13.0+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.h5cOr7Lo/roary_3.13.0+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.h5cOr7Lo/b1/roary_3.13.0+dfsg-1_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.h5cOr7Lo/b2/roary_3.13.0+dfsg-1_i386.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: 0.327s) 0.327s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.015s) 0.015s 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: 648ms CPU time consumed: 627ms _ __ ___ __ _ _ __ _ _ | '__/ _ \ / _` | '__| | | | | | | (_) | (_| | | | |_| | |_| \___/ \__,_|_| \__, | |___/ Fri Nov 22 09:03:26 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Fri Nov 22 09:03:26 UTC 2024 I: roary from trixie built successfully and reproducibly on i386. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-22 09:03:26] INFO: Starting at 2024-11-22 09:03:26.727146 [2024-11-22 09:03:26] INFO: Generating the pages of 1 package(s) [2024-11-22 09:03:27] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/i386/roary didn't produce a buildlog, even though it has been built. [2024-11-22 09:03:27] INFO: Finished at 2024-11-22 09:03:27.437149, took: 0:00:00.710012 Fri Nov 22 09:03:27 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/i386/roary.html Fri Nov 22 09:03:27 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Nov 22 09:03:27 UTC 2024 I: Submitting 16K b1/roary_3.13.0+dfsg-1_i386.buildinfo.asc https://buildinfo.debian.net/48ecc2f35142a2833948d6c00429297f754bba6e/roary_3.13.0+dfsg-1_all Fri Nov 22 09:03:28 UTC 2024 I: Submitting 16K b2/roary_3.13.0+dfsg-1_i386.buildinfo.asc https://buildinfo.debian.net/cca990da60792394d477ab967457238c99d8e175/roary_3.13.0+dfsg-1_all Fri Nov 22 09:03:29 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Nov 22 09:03:29 UTC 2024 I: Done submitting .buildinfo files. Fri Nov 22 09:03:29 UTC 2024 I: Removing signed roary_3.13.0+dfsg-1_i386.buildinfo.asc files: removed './b1/roary_3.13.0+dfsg-1_i386.buildinfo.asc' removed './b2/roary_3.13.0+dfsg-1_i386.buildinfo.asc' 1732266209 i386 trixie roary Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/i386/roary_3.13.0+dfsg-1.rbuild.log: 82.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/i386/roary_3.13.0+dfsg-1.rbuild.log.gz [2024-11-22 09:03:29] INFO: Starting at 2024-11-22 09:03:29.596922 [2024-11-22 09:03:29] INFO: Generating the pages of 1 package(s) [2024-11-22 09:03:30] INFO: Finished at 2024-11-22 09:03:30.435512, took: 0:00:00.838598 All cleanup done. Fri Nov 22 09:03:30 UTC 2024 - total duration: 0h 3m 11s. Fri Nov 22 09:03:30 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-p3eeq3hC, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 3min 15.450s CPU time consumed: 8.171s