Wed May 15 03:40:47 UTC 2024 I: starting to build roary/trixie/amd64 on jenkins on '2024-05-15 03:40' Wed May 15 03:40:47 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_32/6845/console.log Wed May 15 03:40:48 UTC 2024 I: Downloading source for trixie/roary=3.13.0+dfsg-1 --2024-05-15 03:40:48-- 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% 247M=0s 2024-05-15 03:40:48 (247 MB/s) - ‘roary_3.13.0+dfsg-1.dsc’ saved [2501/2501] Wed May 15 03:40:48 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----- Wed May 15 03:40:48 UTC 2024 I: Checking whether the package is not for us Wed May 15 03:40:48 UTC 2024 I: Starting 1st build on remote node ionos5-amd64.debian.net. Wed May 15 03:40:48 UTC 2024 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Wed May 15 03:42:52 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jun 16 22:03:51 -12 2025 I: pbuilder-time-stamp: 1750154631 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [roary_3.13.0+dfsg-1.dsc] I: copying [./roary_3.13.0+dfsg.orig.tar.xz] I: copying [./roary_3.13.0+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Nov 8 13:51:49 2019 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./roary_3.13.0+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting roary in roary-3.13.0+dfsg dpkg-source: info: unpacking roary_3.13.0+dfsg.orig.tar.xz dpkg-source: info: unpacking roary_3.13.0+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying rename_R_script.patch dpkg-source: info: applying use-dz-starter.patch dpkg-source: info: applying use-debian-perl-path.patch dpkg-source: info: applying new-bioperl-require.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3669327/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='bcd7755fb9f14902bafe8b59de9e0ced' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3669327' 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.OJEQepqD/pbuilderrc_mXqJ --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.OJEQepqD/b1 --logfile b1/build.log roary_3.13.0+dfsg-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 16 17:46 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3669327/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 12~), dh-dist-zilla, libdist-zilla-plugin-podweaver-perl, bioperl (>= 1.7.4), libarray-utils-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, mafft, fasttree, perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19699 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} libbsd0{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} 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} libpython3.11-minimal{a} libpython3.11-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-override-perl{a} libsub-quote-perl{a} libsub-uplevel-perl{a} libsyntax-keyword-junction-perl{a} libsyntax-perl{a} libtask-weaken-perl{a} libtcl8.6{a} libterm-encoding-perl{a} libterm-readkey-perl{a} libterm-table-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} 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} python3.11{a} python3.11-minimal{a} r-base-core{a} readline-common{a} sensible-utils{a} sysstat{a} tzdata{a} ucf{a} unzip{a} x11-common{a} xdg-utils{a} zip{a} The following packages are RECOMMENDED but will NOT be installed: bash-completion bcron bioperl-run cpanminus cron cronie curl devscripts krb5-locales libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libarchive-tar-wrapper-perl libarray-compare-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libcache-cache-perl libclass-c3-xs-perl libconvert-binary-c-perl libdata-dump-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libdevel-lexalias-perl libdevel-partialdump-perl libfile-mimeinfo-perl libgd-perl libglib2.0-data libgraphviz-perl libhtml-form-perl libhtml-format-perl libhtml-tableextract-perl libhttp-daemon-perl libio-compress-brotli-perl libipc-shareable-perl libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libmailtools-perl libmime-lite-perl libmldbm-perl libnet-dbus-perl libpod-coverage-trustpod-perl libpostscript-perl libref-util-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl libterm-readline-gnu-perl libterm-ui-perl libtest-cpan-meta-perl libtest-pod-coverage-perl libtest-pod-perl libtext-csv-xs-perl libtype-tiny-xs-perl libunicode-linebreak-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 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, 317 newly installed, 0 to remove and 0 not upgraded. Need to get 113 MB of archives. After unpacking 375 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get: 39 http://deb.debian.org/debian trixie/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 bioperl all 1.7.8-1 [246 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 cd-hit amd64 4.8.1-4 [522 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 59 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libparams-util-perl amd64 1.102-3 [24.0 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b1 [10.6 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.009-1 [15.9 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b3 [22.4 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libclass-load-perl all 0.25-2 [15.3 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libio-stringy-perl all 2.111-3 [56.5 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libparams-validate-perl amd64 1.31-2+b2 [63.7 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libgetopt-long-descriptive-perl all 0.111-1 [27.8 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libio-tiecombine-perl all 1.005-3 [10.8 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libmodule-pluggable-perl all 5.2-5 [23.0 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libstring-rewriteprefix-perl all 0.009-1 [7140 B] Get: 86 http://deb.debian.org/debian trixie/main amd64 libapp-cmd-perl all 0.336-1 [65.8 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libscope-guard-perl all 0.21-2 [8212 B] Get: 88 http://deb.debian.org/debian trixie/main amd64 libautobox-perl amd64 3.0.1-2+b3 [33.4 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libperlio-utf8-strict-perl amd64 0.010-1+b2 [11.4 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libmixin-linewise-perl all 0.111-1 [14.4 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libconfig-ini-perl all 1:0.029-1 [23.7 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libclass-load-xs-perl amd64 0.10-2+b3 [14.1 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get: 94 http://deb.debian.org/debian trixie/main amd64 libdevel-globaldestruction-perl all 0.14-4 [7144 B] Get: 95 http://deb.debian.org/debian trixie/main amd64 libalgorithm-c3-perl all 0.11-2 [10.8 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libclass-c3-perl all 0.35-2 [21.0 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libmro-compat-perl all 0.15-2 [11.8 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libdevel-overloadinfo-perl all 0.007-1 [7896 B] Get: 99 http://deb.debian.org/debian trixie/main amd64 libeval-closure-perl all 0.14-3 [11.2 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libdist-checkconflicts-perl all 0.11-2 [10.5 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-conflicts-perl all 0.003-2 [7356 B] Get: 102 http://deb.debian.org/debian trixie/main amd64 libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libpackage-stash-xs-perl amd64 0.30-1+b3 [20.2 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libmoose-perl amd64 2.2207-1+b1 [766 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libvariable-magic-perl amd64 0.64-1 [44.7 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libsub-identify-perl amd64 0.14-3+b2 [11.2 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libsub-name-perl amd64 0.27-1+b2 [12.5 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libnamespace-autoclean-perl all 0.29-2 [13.5 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libmoosex-role-parameterized-perl all 1.11-2 [41.9 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libmoosex-oneargnew-perl all 0.007-1 [8180 B] Get: 113 http://deb.debian.org/debian trixie/main amd64 libcpanel-json-xs-perl amd64 4.37-1+b2 [128 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libjson-maybexs-perl all 1.004005-1 [12.9 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libstring-formatter-perl all 1.235-1 [22.1 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libstring-errf-perl all 0.009-1 [12.9 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 librole-hasmessage-perl all 0.007-1 [9112 B] Get: 119 http://deb.debian.org/debian trixie/main amd64 librole-identifiable-perl all 0.009-1 [10.4 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b3 [36.2 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libthrowable-perl all 1.001-2 [15.7 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libtie-ixhash-perl all 1.23-4 [11.7 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libconfig-mvp-perl all 2.200013-1 [47.1 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libconfig-mvp-reader-ini-perl all 2.101465-1 [6900 B] Get: 130 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 131 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-1+b1 [339 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.28-1 [98.6 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.82-1 [98.9 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.46-1+b2 [13.7 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libterm-readkey-perl amd64 2.38-2+b3 [24.7 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libcpan-uploader-perl all 0.103018-1 [16.3 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libdata-section-perl all 0.200008-1 [13.1 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libclass-inspector-perl all 1.36-3 [17.5 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libfile-sharedir-perl all 1.118-3 [16.0 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libparams-validationcompiler-perl all 0.31-1 [30.9 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 libxstring-perl amd64 0.005-2+b3 [8088 B] Get: 157 http://deb.debian.org/debian trixie/main amd64 libspecio-perl all 0.48-1 [142 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libdatetime-locale-perl all 1:1.41-1 [3131 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libclass-singleton-perl all 1.6-2 [12.5 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libdatetime-timezone-perl all 1:2.62-1+2024a [262 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libdatetime-perl amd64 2:1.65-1+b1 [116 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libfile-copy-recursive-perl all 0.45-4 [20.0 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libnumber-compare-perl all 0.03-3 [6332 B] Get: 164 http://deb.debian.org/debian trixie/main amd64 libtext-glob-perl all 0.11-3 [7676 B] Get: 165 http://deb.debian.org/debian trixie/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libfile-pushd-perl all 1.016-2 [13.5 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libfile-sharedir-install-perl all 0.14-2 [11.6 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libhash-merge-simple-perl all 0.051-3 [7404 B] Get: 169 http://deb.debian.org/debian trixie/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 liblog-dispatch-perl all 2.71-1 [75.8 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 liblog-dispatch-array-perl all 1.005-1 [6700 B] Get: 172 http://deb.debian.org/debian trixie/main amd64 libstring-flogger-perl all 1.101246-1 [7380 B] Get: 173 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-globexporter-perl all 0.006-1 [8024 B] Get: 174 http://deb.debian.org/debian trixie/main amd64 liblog-dispatchouli-perl all 3.007-1 [35.0 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libexporter-tiny-perl all 1.006002-1 [38.7 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 liblist-moreutils-xs-perl amd64 0.430-4+b1 [42.3 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 libsyntax-perl all 0.004-1.1 [6548 B] Get: 179 http://deb.debian.org/debian trixie/main amd64 libsyntax-keyword-junction-perl all 0.003008-4 [11.7 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 libmoose-autobox-perl all 0.16-2 [52.8 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 libaliased-perl all 0.34-3 [13.5 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 libmoosex-lazyrequire-perl all 0.11-2 [9212 B] Get: 183 http://deb.debian.org/debian trixie/main amd64 libmoosex-setonce-perl all 0.200002-2 [6632 B] Get: 184 http://deb.debian.org/debian trixie/main amd64 libcarp-clan-perl all 6.08-2 [14.1 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-formethods-perl all 0.100055-1 [8024 B] Get: 186 http://deb.debian.org/debian trixie/main amd64 libmoosex-types-perl all 0.50-2 [54.6 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libmoosex-types-perl-perl all 0.101344-1 [8160 B] Get: 188 http://deb.debian.org/debian trixie/main amd64 libpath-tiny-perl all 0.144-1 [56.4 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libmodule-path-perl all 0.19-3 [12.3 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 libtask-weaken-perl all 1.06-2 [9364 B] Get: 191 http://deb.debian.org/debian trixie/main amd64 libppi-perl all 1.278-1 [294 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 libtype-tiny-perl all 2.004000-1 [357 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 libperl-prereqscanner-perl all 1.100-1 [31.0 kB] Get: 194 http://deb.debian.org/debian trixie/main amd64 libperl-version-perl all 1.017-1 [29.0 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 libtext-template-perl all 1.61-1 [54.4 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 libsoftware-license-perl all 0.104006-1 [116 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 libterm-encoding-perl all 0.03-2 [4980 B] Get: 198 http://deb.debian.org/debian trixie/main amd64 libyaml-tiny-perl all 1.74-1 [30.7 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 libdist-zilla-perl all 6.030-1 [376 kB] Get: 200 http://deb.debian.org/debian trixie/main amd64 dh-dist-zilla all 1.4.1 [17.9 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 209 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 libarray-utils-perl all 0.5-3 [6184 B] Get: 211 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 220 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 223 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get: 224 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 225 http://deb.debian.org/debian trixie/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get: 226 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 227 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 229 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 230 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 231 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 232 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 233 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 234 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 235 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 236 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 237 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 238 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.7.1-5 [441 kB] Get: 239 http://deb.debian.org/debian trixie/main amd64 libdata-compare-perl all 1.29-1 [19.6 kB] Get: 240 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get: 241 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 242 http://deb.debian.org/debian trixie/main amd64 libpod-eventual-perl all 0.094003-1 [14.2 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 libstring-truncate-perl all 1.100603-1 [10.2 kB] Get: 244 http://deb.debian.org/debian trixie/main amd64 libpod-elemental-perl all 0.103006-1 [67.2 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 libpod-elemental-perlmunger-perl all 0.200007-1 [10.5 kB] Get: 246 http://deb.debian.org/debian trixie/main amd64 libpod-weaver-perl all 4.020-1 [70.1 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 libdist-zilla-plugin-podweaver-perl all 4.010-1 [9580 B] Get: 248 http://deb.debian.org/debian trixie/main amd64 libenv-path-perl all 0.19-4 [19.1 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 libfile-chdir-perl all 0.1008-1.2 [11.9 kB] Get: 250 http://deb.debian.org/debian trixie/main amd64 libfile-grep-perl all 0.02-3 [8352 B] Get: 251 http://deb.debian.org/debian trixie/main amd64 libfile-slurper-perl all 0.014-1 [8560 B] Get: 252 http://deb.debian.org/debian trixie/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 253 http://deb.debian.org/debian trixie/main amd64 libfindbin-libs-perl all 3.0.2-1 [29.7 kB] Get: 254 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get: 255 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get: 256 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.80.2-1 [1485 kB] Get: 257 http://deb.debian.org/debian trixie/main amd64 libheap-perl all 0.80-5 [34.3 kB] Get: 258 http://deb.debian.org/debian trixie/main amd64 libset-object-perl amd64 1.42-1+b4 [37.5 kB] Get: 259 http://deb.debian.org/debian trixie/main amd64 libgraph-perl all 1:0.9727-1 [111 kB] Get: 260 http://deb.debian.org/debian trixie/main amd64 libspiffy-perl all 0.46-1 [25.7 kB] Get: 261 http://deb.debian.org/debian trixie/main amd64 libio-all-perl all 0.87-2 [67.3 kB] Get: 262 http://deb.debian.org/debian trixie/main amd64 libparse-yapp-perl all 1.21-3 [42.5 kB] Get: 263 http://deb.debian.org/debian trixie/main amd64 libxml-parser-perl amd64 2.47-1+b2 [199 kB] Get: 264 http://deb.debian.org/debian trixie/main amd64 libxml-writer-perl all 0.900-2 [26.8 kB] Get: 265 http://deb.debian.org/debian trixie/main amd64 libgraph-readwrite-perl all 2.10-1 [45.2 kB] Get: 266 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 267 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 268 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 269 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get: 270 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 271 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 272 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 273 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 274 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get: 275 http://deb.debian.org/debian trixie/main amd64 liblog-log4perl-perl all 1.57-1 [367 kB] Get: 276 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get: 277 http://deb.debian.org/debian trixie/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get: 278 http://deb.debian.org/debian trixie/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get: 279 http://deb.debian.org/debian trixie/main amd64 libpadwalker-perl amd64 2.5-1+b5 [18.6 kB] Get: 280 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 281 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get: 282 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.52.2+ds-1 [218 kB] Get: 283 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.52.2+ds-1 [48.1 kB] Get: 284 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.52.2+ds-1 [35.0 kB] Get: 285 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB] Get: 286 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B] Get: 287 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get: 288 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-9 [34.6 kB] Get: 289 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get: 290 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get: 291 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get: 292 http://deb.debian.org/debian trixie/main amd64 libterm-table-perl all 0.018-1 [29.0 kB] Get: 293 http://deb.debian.org/debian trixie/main amd64 libtest-file-perl all 1.993-1 [24.5 kB] Get: 294 http://deb.debian.org/debian trixie/main amd64 libtest2-suite-perl all 0.000159-1 [402 kB] Get: 295 http://deb.debian.org/debian trixie/main amd64 libtest-files-perl all 0.26-1 [21.6 kB] Get: 296 http://deb.debian.org/debian trixie/main amd64 libtest-output-perl all 1.034-1 [16.0 kB] Get: 297 http://deb.debian.org/debian trixie/main amd64 libtext-csv-perl all 2.04-1 [112 kB] Get: 298 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get: 299 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 300 http://deb.debian.org/debian trixie/main amd64 libtingea0 amd64 21-361-2+b1 [51.3 kB] Get: 301 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 302 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get: 303 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get: 304 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB] Get: 305 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get: 306 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get: 307 http://deb.debian.org/debian trixie/main amd64 mafft amd64 7.505-1 [1078 kB] Get: 308 http://deb.debian.org/debian trixie/main amd64 mcl amd64 1:22-282+ds-2 [474 kB] Get: 309 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg2-2 [3544 kB] Get: 310 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.12.0+ds-4+b1 [12.5 MB] Get: 311 http://deb.debian.org/debian trixie/main amd64 sysstat amd64 12.7.5-2 [623 kB] Get: 312 http://deb.debian.org/debian trixie/main amd64 parallel all 20240222+ds-2 [2163 kB] Get: 313 http://deb.debian.org/debian trixie/main amd64 prank amd64 0.0.170427+dfsg-3 [395 kB] Get: 314 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-13 [230 kB] Get: 315 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 316 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 317 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.0-2 [28.2 MB] Fetched 113 MB in 15s (7524 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... 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 ... 20015 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... 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 ... 21007 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libproc2-0:amd64. 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../290-libxft2_2.3.6-1+b1_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b1) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../291-libxss1_1%3a1.2.3-1+b1_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1+b1) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../292-libtk8.6_8.6.14-1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.14-1) ... Selecting previously unselected package libxt6t64:amd64. Preparing to unpack .../293-libxt6t64_1%3a1.2.1-1.2_amd64.deb ... Unpacking libxt6t64:amd64 (1:1.2.1-1.2) ... Selecting previously unselected package mafft. 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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 .../300-prank_0.0.170427+dfsg-3_amd64.deb ... Unpacking prank (0.0.170427+dfsg-3) ... Selecting previously unselected package zip. Preparing to unpack .../301-zip_3.0-13_amd64.deb ... Unpacking zip (3.0-13) ... Selecting previously unselected package unzip. Preparing to unpack .../302-unzip_6.0-28_amd64.deb ... Unpacking unzip (6.0-28) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../303-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 .../304-r-base-core_4.4.0-2_amd64.deb ... Unpacking r-base-core (4.4.0-2) ... 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:amd64 (1.5.7-2) ... Setting up liblmdb0:amd64 (0.9.31-1+b1) ... Setting up libgraphite2-3:amd64 (1.3.14-2) ... Setting up libfile-sharedir-install-perl (0.14-2) ... Setting up ncbi-data (6.1.20170106+dfsg2-2) ... Setting up libpixman-1-0:amd64 (0.42.2-1+b1) ... Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... Setting up libfile-slurper-perl (0.014-1) ... Setting up libfile-which-perl (1.27-2) ... Setting up libxau6:amd64 (1:1.0.9-1+b1) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libtie-ixhash-perl (1.23-4) ... Setting up libtask-weaken-perl (1.06-2) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up libterm-table-perl (0.018-1) ... Setting up liblerc4:amd64 (4.0.0+ds-4+b1) ... Setting up libhash-merge-simple-perl (0.051-3) ... Setting up bsdextrautils (2.40-8) ... Setting up libparse-yapp-perl (1.21-3) ... Setting up libmbedcrypto7t64:amd64 (2.28.8-1) ... Setting up libclass-inspector-perl (1.36-3) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libdatrie1:amd64 (0.2.13-3) ... 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) ... Setting up mafft (7.505-1) ... Setting up libclone-perl:amd64 (0.46-1+b2) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libsub-identify-perl (0.14-3+b2) ... Setting up libcpanel-json-xs-perl:amd64 (4.37-1+b2) ... Setting up libio-stringy-perl (2.111-3) ... 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 (13.15.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libheap-perl (0.80-5) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libtry-tiny-perl (0.31-2) ... Setting up libsensors-config (1:3.6.0-9) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.61.0-1+b1) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libclass-singleton-perl (1.6-2) ... Setting up libpadwalker-perl (2.5-1+b5) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libfindbin-libs-perl (3.0.2-1) ... Setting up libcom-err2:amd64 (1.47.1~rc2-1) ... Setting up file (1:5.45-3) ... Setting up libxstring-perl:amd64 (0.005-2+b3) ... Setting up libyaml-tiny-perl (1.74-1) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up libsub-install-perl (0.929-1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libtest2-suite-perl (0.000159-1) ... Setting up libkrb5support0:amd64 (1.20.1-6+b1) ... Setting up libterm-encoding-perl (0.03-2) ... Setting up libnumber-compare-perl (0.03-3) ... Setting up libscope-guard-perl (0.21-2) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up libfile-copy-recursive-perl (0.45-4) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Jun 17 10:05:11 UTC 2025. Universal Time is now: Tue Jun 17 10:05:11 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libjson-maybexs-perl (1.004005-1) ... Setting up libio-string-perl (1.08-4) ... Setting up zip (3.0-13) ... Setting up libpackage-stash-xs-perl:amd64 (0.30-1+b3) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:amd64 (2.80.2-1) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libalgorithm-c3-perl (0.11-2) ... Setting up libset-object-perl (1.42-1+b4) ... Setting up liblog-log4perl-perl (1.57-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libtext-diff-perl (1.45-2) ... Setting up libfile-find-rule-perl (0.34-3) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libio-tiecombine-perl (1.005-3) ... Setting up libperlio-utf8-strict-perl (0.010-1+b2) ... Setting up libxml-writer-perl (0.900-2) ... Setting up libenv-path-perl (0.19-4) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... Setting up libproc2-0:amd64 (2:4.0.4-4) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up libvariable-magic-perl (0.64-1) ... Setting up libio-html-perl (1.004-3) ... Setting up libtext-template-perl (1.61-1) ... Setting up libtcl8.6:amd64 (8.6.14+dfsg-1) ... Setting up autopoint (0.21-14) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b1) ... 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+b1) ... Setting up libsensors5:amd64 (1:3.6.0-9) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libparams-util-perl (1.102-3) ... Setting up libspiffy-perl (0.46-1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up libgfortran5:amd64 (14-20240330-1) ... Setting up autoconf (2.71-3) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libwebp7:amd64 (1.4.0-0.1) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libsub-name-perl:amd64 (0.27-1+b2) ... 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 (0.0.22) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up libpath-tiny-perl (0.144-1) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-4) ... Setting up libjson-perl (4.10000-1) ... Setting up libtingea0:amd64 (21-361-2+b1) ... 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 libsub-override-perl (0.10-1) ... 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) ... 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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 (1.33-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/roary-3.13.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../roary_3.13.0+dfsg-1_source.changes dpkg-buildpackage: info: source package roary dpkg-buildpackage: info: source version 3.13.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with dist-zilla dh_dzil_clean dh_clean debian/rules build dh build --with dist-zilla dh_update_autotools_config dh_autoreconf debian/rules override_dh_dzil_build make[1]: Entering directory '/build/reproducible-path/roary-3.13.0+dfsg' mv bin/create_pan_genome_plots.R bin/create_pan_genome_plots dh_dzil_build -- [DZ] beginning to build Bio-Roary [DZ] writing Bio-Roary in .build/debian-build [DZ] built in .build/debian-build make[1]: Leaving directory '/build/reproducible-path/roary-3.13.0+dfsg' dh_auto_configure -D .build/debian-build cd .build/debian-build && /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/roary-3.13.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/roary-3.13.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro" Warning: prerequisite Digest::MD5::File 0 not found. Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::Roary Writing MYMETA.yml and MYMETA.json dh_auto_build -D .build/debian-build cd .build/debian-build && make -j42 make[1]: Entering directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' cp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm cp lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm cp lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm cp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.pm cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.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/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.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/Exceptions.pm blib/lib/Bio/Roary/Exceptions.pm cp lib/Bio/Roary/AssemblyStatistics.pm blib/lib/Bio/Roary/AssemblyStatistics.pm cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm cp lib/Bio/Roary/AccessoryBinaryFasta.pm blib/lib/Bio/Roary/AccessoryBinaryFasta.pm cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm cp lib/Bio/Roary/AccessoryClustering.pm blib/lib/Bio/Roary/AccessoryClustering.pm cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm cp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm cp lib/Bio/Roary/CommandLine/IterativeCdhit.pm blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pm cp lib/Bio/Roary/CommandLine/AssemblyStatistics.pm blib/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.pm cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm cp lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm cp lib/Bio/Roary/JobRunner/Parallel.pm blib/lib/Bio/Roary/JobRunner/Parallel.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/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.pm cp lib/Bio/Roary/External/Mafft.pm blib/lib/Bio/Roary/External/Mafft.pm cp lib/Bio/Roary/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.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/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm cp lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm cp lib/Bio/Roary/MergeMultifastaAlignments.pm blib/lib/Bio/Roary/MergeMultifastaAlignments.pm cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm cp lib/Bio/Roary/GeneNamesFromGFF.pm blib/lib/Bio/Roary/GeneNamesFromGFF.pm cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm cp lib/Bio/Roary/External/Mcl.pm blib/lib/Bio/Roary/External/Mcl.pm cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm cp lib/Bio/Roary/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pm cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.pm cp lib/Bio/Roary/External/IterativeCdhit.pm blib/lib/Bio/Roary/External/IterativeCdhit.pm cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm cp lib/Bio/Roary/Output/EMBLHeaderCommon.pm blib/lib/Bio/Roary/Output/EMBLHeaderCommon.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/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/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm cp lib/Bio/Roary/Output/QueryGroups.pm blib/lib/Bio/Roary/Output/QueryGroups.pm cp lib/Bio/Roary/SequenceLengths.pm blib/lib/Bio/Roary/SequenceLengths.pm cp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm cp lib/Bio/Roary/ReorderSpreadsheet.pm blib/lib/Bio/Roary/ReorderSpreadsheet.pm cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm cp lib/Bio/Roary/PresenceAbsenceMatrix.pm blib/lib/Bio/Roary/PresenceAbsenceMatrix.pm cp lib/Bio/Roary/SampleOrder.pm blib/lib/Bio/Roary/SampleOrder.pm cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm cp lib/Bio/Roary/SpreadsheetRole.pm blib/lib/Bio/Roary/SpreadsheetRole.pm cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm cp bin/create_pan_genome blib/script/create_pan_genome cp bin/create_pan_genome_plots blib/script/create_pan_genome_plots cp bin/extract_proteome_from_gff blib/script/extract_proteome_from_gff cp bin/iterative_cdhit blib/script/iterative_cdhit "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome_plots "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/extract_proteome_from_gff "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/iterative_cdhit cp bin/pan_genome_assembly_statistics blib/script/pan_genome_assembly_statistics cp bin/pan_genome_core_alignment blib/script/pan_genome_core_alignment "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_assembly_statistics "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_core_alignment cp bin/pan_genome_post_analysis blib/script/pan_genome_post_analysis cp bin/pan_genome_reorder_spreadsheet blib/script/pan_genome_reorder_spreadsheet cp bin/parallel_all_against_all_blastp blib/script/parallel_all_against_all_blastp cp bin/protein_alignment_from_nucleotides blib/script/protein_alignment_from_nucleotides "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_post_analysis "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_reorder_spreadsheet cp bin/query_pan_genome blib/script/query_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/protein_alignment_from_nucleotides "/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/query_pan_genome cp bin/roary blib/script/roary "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary cp bin/roary-create_pan_genome_plots.R blib/script/roary-create_pan_genome_plots.R cp bin/roary-pan_genome_reorder_spreadsheet blib/script/roary-pan_genome_reorder_spreadsheet cp bin/roary-query_pan_genome blib/script/roary-query_pan_genome 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-create_pan_genome_plots.R "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-pan_genome_reorder_spreadsheet "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-query_pan_genome 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 -j42 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/ParseGFFAnnotationRole.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/BedFromGFFRole.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/ReorderSpreadsheet.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/ExtractProteomeFromGFF.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/PresenceAbsenceMatrix.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/InflateClusters.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/Exceptions.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GeneNamesFromGFF.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CombinedProteome.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AssemblyStatistics.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/SplitGroups.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/AnalyseGroups.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/ReformatInputGFFs.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/PostAnalysis.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/ExtractCoreGenesFromSpreadsheet.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/UniqueGenesPerSample.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/IterativeCdhit.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/PrepareInputFiles.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/GroupStatistics.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/SampleOrder.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/CommandLine/RoaryCoreAlignment.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/ParallelAllAgainstAllBlastp.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/AssemblyStatistics.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/RoaryReorderSpreadsheet.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/UniqueGenesPerSample.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/IterativeCdhit.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/TransferAnnotationToGroups.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/Output/GroupsMultifastaNucleotide.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/BlastIdentityFrequency.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/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/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/Output/GroupsMultifastas.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/EMBLHeaderCommon.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/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/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/Makeblastdb.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Blastp.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Cdhit.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/Mcl.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-query_pan_genome.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/create_pan_genome_plots.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/pan_genome_core_alignment.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_post_analysis.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/transfer_annotation_to_groups.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-unique_genes_per_sample.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/parallel_all_against_all_blastp.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/extract_proteome_from_gff.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/protein_alignment_from_nucleotides.1p 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::AccessoryBinaryFasta.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::TransferAnnotationToGroups.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Blastp.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::External::CheckTools.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::ExtractProteomeFromGFF.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::CommandLine::ParallelAllAgainstAllBlastp.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::NumberOfGroups.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::PrepareInputFiles.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupMultifasta.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::GeneAlignmentFromNucleotides.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::CreatePanGenome.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::ParseGFFAnnotationRole.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::GroupsMultifastaNucleotide.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::Output::EmblGroups.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Mcl.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::ChunkFastaFile.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Cdhit.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CombinedProteome.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::DifferenceBetweenSets.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::ParallelAllAgainstAllBlast.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::IterativeCdhit.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::QueryGroups.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::PresenceAbsenceMatrix.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::UniqueGenesPerSample.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ExtractProteomeFromGff.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryPostAnalysis.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::JobRunner::Local.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::ReorderSpreadsheet.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::OrderGenes.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::SpreadsheetRole.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GeneNamesFromGFF.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastas.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::AssemblyStatistics.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::IterativeCdhit.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::ExtractCoreGenesFromSpreadsheet.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::SequenceLengths.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::AnalyseGroups.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::GeneAlignmentFromNucleotides.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::Output::CoreGeneAlignmentCoordinatesEMBL.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::SampleOrder.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::External::Mafft.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::CommandLine::RoaryCoreAlignment.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::MergeMultifastaAlignments.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::AccessoryClustering.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::FilterUnknownsFromFasta.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/roary-pan_genome_reorder_spreadsheet 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/parallel_all_against_all_blastp 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/create_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/pan_genome_core_alignment 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-query_pan_genome Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-create_pan_genome_plots.R Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_assembly_statistics 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/create_pan_genome_plots Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/transfer_annotation_to_groups Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_post_analysis Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/iterative_cdhit make[1]: Leaving directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'roary' in '../roary_3.13.0+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../roary_3.13.0+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../roary_3.13.0+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3669327 and its subdirectories I: Current time: Mon Jun 16 22:05:51 -12 2025 I: pbuilder-time-stamp: 1750154751 Wed May 15 03:42:53 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Wed May 15 03:42:53 UTC 2024 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Wed May 15 03:46:49 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Wed May 15 03:46:50 UTC 2024 I: roary_3.13.0+dfsg-1_amd64.changes: Format: 1.8 Date: Fri, 08 Nov 2019 14:37:07 +0100 Source: roary Binary: roary Architecture: all Version: 3.13.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.13.0+dfsg-1) unstable; urgency=medium . * New upstream release. * Use debhelper 12. * Bump Standards-Version. * Update source lintian override location and tags. Checksums-Sha1: 0021e1eb04b5d559154d7719815ca05bc7ff56fc 173452 roary_3.13.0+dfsg-1_all.deb 74005e6b7ce8281bbd1d6c7de8585013237ca99c 14699 roary_3.13.0+dfsg-1_amd64.buildinfo Checksums-Sha256: 653f659a68f65d6b5b5d6afeb057f5d9ea233d786d106109cf1bf4e14bd29e91 173452 roary_3.13.0+dfsg-1_all.deb a1a77a4bfaa27adbcada1d2ea696f6dc2e1efc4a41ecf3c686c0c49ee4be74df 14699 roary_3.13.0+dfsg-1_amd64.buildinfo Files: 80050bd178d42d3c94ba0e0febaaa66b 173452 science optional roary_3.13.0+dfsg-1_all.deb d152671e756d411497eca04a72e096e8 14699 science optional roary_3.13.0+dfsg-1_amd64.buildinfo Wed May 15 03:46:51 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_32-6845.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.OJEQepqD/roary_3.13.0+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.OJEQepqD/roary_3.13.0+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.OJEQepqD/roary_3.13.0+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.OJEQepqD/b1/roary_3.13.0+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.OJEQepqD/b2/roary_3.13.0+dfsg-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.365s) 0.365s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.016s) 0.016s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 714ms CPU time consumed: 712ms Wed May 15 03:46:52 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Wed May 15 03:46:52 UTC 2024 I: roary from trixie built successfully and reproducibly on amd64. Wed May 15 03:46:53 UTC 2024 I: Submitting .buildinfo files to external archives: Wed May 15 03:46:53 UTC 2024 I: Submitting 16K b1/roary_3.13.0+dfsg-1_amd64.buildinfo.asc Wed May 15 03:46:54 UTC 2024 I: Submitting 16K b2/roary_3.13.0+dfsg-1_amd64.buildinfo.asc Wed May 15 03:46:55 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed May 15 03:46:55 UTC 2024 I: Done submitting .buildinfo files. Wed May 15 03:46:55 UTC 2024 I: Removing signed roary_3.13.0+dfsg-1_amd64.buildinfo.asc files: removed './b1/roary_3.13.0+dfsg-1_amd64.buildinfo.asc' removed './b2/roary_3.13.0+dfsg-1_amd64.buildinfo.asc'