sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | roary 3.13.0+dfsg-1 (amd64) Mon, 16 Sep 2024 17:02:31 +0000 | +==============================================================================+ Package: roary Version: 3.13.0+dfsg-1 Source Version: 3.13.0+dfsg-1 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-2e1bfcee-271a-4e11-a5d7-7c0266d96c00' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup roary_3.13.0+dfsg-1 perl-5.40-throwaway amd64 -------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup roary_3.13.0+dfsg-1 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/roary-u1RNHQ/resolver-MaSb14' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Hit:3 http://localhost:3142/debian sid InRelease Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/roary_3.13.0+dfsg-1.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/roary-u1RNHQ/roary-3.13.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/roary-u1RNHQ' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged 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-essential, fakeroot, perl Filtered 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-essential, fakeroot, perl dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [615 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [1166 B] Get:5 copy:/<>/apt_archive ./ Packages [1179 B] Fetched 2960 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bedtools bioperl bsdextrautils ca-certificates cd-hit debhelper dh-autoreconf dh-dist-zilla dh-strip-nondeterminism dwz fakeroot fasttree file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base groff-base intltool-debian libalgorithm-c3-perl libalgorithm-diff-perl libaliased-perl libapp-cmd-perl libarchive-zip-perl libarray-utils-perl libautobox-perl libb-hooks-endofscope-perl libb-hooks-op-check-perl libbio-perl-perl libblas3 libbrotli1 libcairo2 libcapture-tiny-perl libcarp-clan-perl libclass-c3-perl libclass-data-inheritable-perl libclass-inspector-perl libclass-load-perl libclass-load-xs-perl libclass-method-modifiers-perl libclass-singleton-perl libclass-xsaccessor-perl libclone-perl libcom-err2 libconfig-ini-perl libconfig-mvp-perl libconfig-mvp-reader-ini-perl libconst-fast-perl libcpan-uploader-perl libcpanel-json-xs-perl libcurl4t64 libdata-compare-perl libdata-optlist-perl libdata-section-perl libdata-stag-perl libdatetime-locale-perl libdatetime-perl libdatetime-timezone-perl libdatrie1 libdebhelper-perl libdeflate0 libdevel-callchecker-perl libdevel-globaldestruction-perl libdevel-overloadinfo-perl libdevel-stacktrace-perl libdist-checkconflicts-perl libdist-zilla-perl libdist-zilla-plugin-podweaver-perl libdynaloader-functions-perl libelf1t64 libencode-locale-perl libenv-path-perl libeval-closure-perl libexception-class-perl libexpat1 libexporter-tiny-perl libfakeroot libfile-chdir-perl libfile-copy-recursive-perl libfile-find-rule-perl libfile-grep-perl libfile-listing-perl libfile-pushd-perl libfile-sharedir-install-perl libfile-sharedir-perl libfile-slurper-perl libfile-stripnondeterminism-perl libfile-which-perl libfindbin-libs-perl libfontconfig1 libfreetype6 libfribidi0 libgetopt-long-descriptive-perl libgfortran5 libglib2.0-0t64 libgraph-perl libgraph-readwrite-perl libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhash-merge-simple-perl libheap-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu72 libimport-into-perl libio-all-perl libio-html-perl libio-socket-ssl-perl libio-string-perl libio-stringy-perl libio-tiecombine-perl libjbig0 libjpeg62-turbo libjson-maybexs-perl libjson-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblerc4 liblist-moreutils-perl liblist-moreutils-xs-perl liblmdb0 liblog-dispatch-array-perl liblog-dispatch-perl liblog-dispatchouli-perl liblog-log4perl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libmixin-linewise-perl libmodule-implementation-perl libmodule-path-perl libmodule-pluggable-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoo-perl libmoose-autobox-perl libmoose-perl libmoosex-lazyrequire-perl libmoosex-oneargnew-perl libmoosex-role-parameterized-perl libmoosex-setonce-perl libmoosex-types-perl libmoosex-types-perl-perl libmro-compat-perl libnamespace-autoclean-perl libnamespace-clean-perl libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnsl2 libnumber-compare-perl libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpadwalker-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparams-util-perl libparams-validate-perl libparams-validationcompiler-perl libparse-yapp-perl libpath-tiny-perl libperl-prereqscanner-perl libperl-version-perl libperlio-utf8-strict-perl libpipeline1 libpixman-1-0 libpng16-16t64 libpod-elemental-perl libpod-elemental-perlmunger-perl libpod-eventual-perl libpod-weaver-perl libppi-perl libproc2-0 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib librole-hasmessage-perl librole-identifiable-perl librole-tiny-perl librtmp1 libscope-guard-perl libsensors-config libsensors5 libset-object-perl libsharpyuv0 libsm6 libsoftware-license-perl libspecio-perl libspiffy-perl libssh2-1t64 libstring-errf-perl libstring-flogger-perl libstring-formatter-perl libstring-rewriteprefix-perl libstring-truncate-perl libsub-exporter-formethods-perl libsub-exporter-globexporter-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsub-uplevel-perl libsyntax-keyword-junction-perl libtask-weaken-perl libtcl8.6 libterm-encoding-perl libterm-readkey-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl libtest-warn-perl libtest2-suite-perl libtext-csv-perl libtext-diff-perl libtext-glob-perl libtext-template-perl libthai-data libthai0 libthrowable-perl libtie-ixhash-perl libtiff6 libtimedate-perl libtingea0 libtirpc-common libtirpc3t64 libtk8.6 libtool libtry-tiny-perl libtype-tiny-perl libuchardet0 liburi-perl libuv1t64 libvariable-magic-perl libwebp7 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml-writer-perl libxml2 libxrender1 libxss1 libxstring-perl libxt6t64 libyaml-tiny-perl m4 mafft man-db mcl media-types ncbi-blast+ ncbi-data netbase openssl parallel perl-openssl-defaults po-debconf prank procps python3 python3-minimal python3.12 python3.12-minimal r-base-core sensible-utils sysstat tzdata ucf unzip x11-common xdg-utils zip Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make libdist-zilla-app-command-authordebs-perl pristine-tar gettext-doc libasprintf-dev libgettextpo-dev groff libxml-sax-expatxs-perl libscalar-properties-perl low-memory-monitor krb5-doc krb5-user libdata-dump-perl libdb-file-lock-perl libfile-mimeinfo-perl libfile-readbackwards-perl libfreezethaw-perl libmldbm-perl libdbd-csv-perl liblog-dispatch-filerotate-perl librrds-perl libxml-dom-perl libcrypt-ssleay-perl libscalar-number-perl lm-sensors libtest-fatal-perl tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk libdevel-lexalias-perl libbusiness-isbn-perl libmime-base32-perl libregexp-ipv6-perl libauthen-ntlm-perl m4-doc apparmor less www-browser mcl-doc csh fish ksh tcsh zsh libmail-box-perl python3-doc python3-tk python3-venv python3.12-venv python3.12-doc binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html isag Recommended packages: bioperl-run perl-doc libcache-cache-perl libbio-perl-run-perl libdbi-perl libgd-gd2-perl libapache-dbi-perl libxml-simple-perl libyaml-perl libace-perl libxml-twig-perl libset-scalar-perl devscripts curl | wget | lynx libalgorithm-diff-xs-perl bioperl-run | libbio-perl-run-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgd-perl libgraphviz-perl libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl libxml-dom-xpath-perl libxml-sax-perl libxml-sax-writer-perl libxml-libxml-perl libclass-c3-xs-perl perl-tk libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libxml-perl bash-completion cpanminus libarchive-tar-wrapper-perl libpod-coverage-trustpod-perl libterm-readline-gnu-perl libterm-ui-perl libtest-cpan-meta-perl libtest-pod-coverage-perl libtest-pod-perl libdevel-lexalias-perl libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libhtml-format-perl libio-compress-brotli-perl libjson-xs-perl krb5-locales libmail-sendmail-perl libmailtools-perl libmime-lite-perl libipc-shareable-perl libdevel-partialdump-perl libunicode-utf8-perl publicsuffix libref-util-perl libtext-csv-xs-perl libltdl-dev libtype-tiny-xs-perl libdata-dump-perl libhtml-form-perl libhttp-daemon-perl blast2 lynx ruby psmisc linux-sysctl-defaults r-recommended r-base-dev r-doc-html systemd | cron | cron-daemon libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bedtools bioperl bsdextrautils ca-certificates cd-hit debhelper dh-autoreconf dh-dist-zilla dh-strip-nondeterminism dwz fakeroot fasttree file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base groff-base intltool-debian libalgorithm-c3-perl libalgorithm-diff-perl libaliased-perl libapp-cmd-perl libarchive-zip-perl libarray-utils-perl libautobox-perl libb-hooks-endofscope-perl libb-hooks-op-check-perl libbio-perl-perl libblas3 libbrotli1 libcairo2 libcapture-tiny-perl libcarp-clan-perl libclass-c3-perl libclass-data-inheritable-perl libclass-inspector-perl libclass-load-perl libclass-load-xs-perl libclass-method-modifiers-perl libclass-singleton-perl libclass-xsaccessor-perl libclone-perl libcom-err2 libconfig-ini-perl libconfig-mvp-perl libconfig-mvp-reader-ini-perl libconst-fast-perl libcpan-uploader-perl libcpanel-json-xs-perl libcurl4t64 libdata-compare-perl libdata-optlist-perl libdata-section-perl libdata-stag-perl libdatetime-locale-perl libdatetime-perl libdatetime-timezone-perl libdatrie1 libdebhelper-perl libdeflate0 libdevel-callchecker-perl libdevel-globaldestruction-perl libdevel-overloadinfo-perl libdevel-stacktrace-perl libdist-checkconflicts-perl libdist-zilla-perl libdist-zilla-plugin-podweaver-perl libdynaloader-functions-perl libelf1t64 libencode-locale-perl libenv-path-perl libeval-closure-perl libexception-class-perl libexpat1 libexporter-tiny-perl libfakeroot libfile-chdir-perl libfile-copy-recursive-perl libfile-find-rule-perl libfile-grep-perl libfile-listing-perl libfile-pushd-perl libfile-sharedir-install-perl libfile-sharedir-perl libfile-slurper-perl libfile-stripnondeterminism-perl libfile-which-perl libfindbin-libs-perl libfontconfig1 libfreetype6 libfribidi0 libgetopt-long-descriptive-perl libgfortran5 libglib2.0-0t64 libgraph-perl libgraph-readwrite-perl libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhash-merge-simple-perl libheap-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu72 libimport-into-perl libio-all-perl libio-html-perl libio-socket-ssl-perl libio-string-perl libio-stringy-perl libio-tiecombine-perl libjbig0 libjpeg62-turbo libjson-maybexs-perl libjson-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblerc4 liblist-moreutils-perl liblist-moreutils-xs-perl liblmdb0 liblog-dispatch-array-perl liblog-dispatch-perl liblog-dispatchouli-perl liblog-log4perl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libmixin-linewise-perl libmodule-implementation-perl libmodule-path-perl libmodule-pluggable-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoo-perl libmoose-autobox-perl libmoose-perl libmoosex-lazyrequire-perl libmoosex-oneargnew-perl libmoosex-role-parameterized-perl libmoosex-setonce-perl libmoosex-types-perl libmoosex-types-perl-perl libmro-compat-perl libnamespace-autoclean-perl libnamespace-clean-perl libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnsl2 libnumber-compare-perl libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpadwalker-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparams-util-perl libparams-validate-perl libparams-validationcompiler-perl libparse-yapp-perl libpath-tiny-perl libperl-prereqscanner-perl libperl-version-perl libperlio-utf8-strict-perl libpipeline1 libpixman-1-0 libpng16-16t64 libpod-elemental-perl libpod-elemental-perlmunger-perl libpod-eventual-perl libpod-weaver-perl libppi-perl libproc2-0 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib librole-hasmessage-perl librole-identifiable-perl librole-tiny-perl librtmp1 libscope-guard-perl libsensors-config libsensors5 libset-object-perl libsharpyuv0 libsm6 libsoftware-license-perl libspecio-perl libspiffy-perl libssh2-1t64 libstring-errf-perl libstring-flogger-perl libstring-formatter-perl libstring-rewriteprefix-perl libstring-truncate-perl libsub-exporter-formethods-perl libsub-exporter-globexporter-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsub-uplevel-perl libsyntax-keyword-junction-perl libtask-weaken-perl libtcl8.6 libterm-encoding-perl libterm-readkey-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl libtest-warn-perl libtest2-suite-perl libtext-csv-perl libtext-diff-perl libtext-glob-perl libtext-template-perl libthai-data libthai0 libthrowable-perl libtie-ixhash-perl libtiff6 libtimedate-perl libtingea0 libtirpc-common libtirpc3t64 libtk8.6 libtool libtry-tiny-perl libtype-tiny-perl libuchardet0 liburi-perl libuv1t64 libvariable-magic-perl libwebp7 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml-writer-perl libxml2 libxrender1 libxss1 libxstring-perl libxt6t64 libyaml-tiny-perl m4 mafft man-db mcl media-types ncbi-blast+ ncbi-data netbase openssl parallel perl-openssl-defaults po-debconf prank procps python3 python3-minimal python3.12 python3.12-minimal r-base-core sbuild-build-depends-main-dummy sensible-utils sysstat tzdata ucf unzip x11-common xdg-utils zip 0 upgraded, 313 newly installed, 0 to remove and 0 not upgraded. Need to get 113 MB/115 MB of archives. After this operation, 391 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.40/main amd64 libparams-util-perl amd64 1.102-3+b1 [24.3 kB] Get:2 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1112 B] Get:3 file:/srv/reprepro perl-5.40/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB] Get:4 file:/srv/reprepro perl-5.40/main amd64 libdevel-callchecker-perl amd64 0.009-1+b1 [16.1 kB] Get:5 file:/srv/reprepro perl-5.40/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.4 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.6-1 [814 kB] Get:7 file:/srv/reprepro perl-5.40/main amd64 libparams-validate-perl amd64 1.31-2+b3 [63.4 kB] Get:8 file:/srv/reprepro perl-5.40/main amd64 libautobox-perl amd64 3.0.2-1+b1 [32.9 kB] Get:9 file:/srv/reprepro perl-5.40/main amd64 libperlio-utf8-strict-perl amd64 0.010-1+b3 [11.4 kB] Get:10 file:/srv/reprepro perl-5.40/main amd64 libclass-load-xs-perl amd64 0.10-2+b4 [14.1 kB] Get:11 file:/srv/reprepro perl-5.40/main amd64 libpackage-stash-xs-perl amd64 0.30-1+b4 [20.7 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.3-1 [105 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB] Get:14 file:/srv/reprepro perl-5.40/main amd64 libmoose-perl amd64 2.2207-1+b2 [766 kB] Get:15 file:/srv/reprepro perl-5.40/main amd64 libvariable-magic-perl amd64 0.64-1+b1 [44.9 kB] Get:16 file:/srv/reprepro perl-5.40/main amd64 libsub-identify-perl amd64 0.14-3+b3 [11.3 kB] Get:17 file:/srv/reprepro perl-5.40/main amd64 libsub-name-perl amd64 0.27-1+b3 [12.5 kB] Get:18 file:/srv/reprepro perl-5.40/main amd64 libcpanel-json-xs-perl amd64 4.38-1+b1 [129 kB] Get:19 file:/srv/reprepro perl-5.40/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b4 [36.1 kB] Get:20 file:/srv/reprepro perl-5.40/main amd64 libnet-ssleay-perl amd64 1.94-1+b2 [339 kB] Get:21 file:/srv/reprepro perl-5.40/main amd64 libhtml-parser-perl amd64 3.83-1+b1 [99.7 kB] Get:22 file:/srv/reprepro perl-5.40/main amd64 libclone-perl amd64 0.47-1+b1 [13.8 kB] Get:23 file:/srv/reprepro perl-5.40/main amd64 libterm-readkey-perl amd64 2.38-2+b4 [24.6 kB] Get:24 file:/srv/reprepro perl-5.40/main amd64 libxstring-perl amd64 0.005-2+b4 [8056 B] Get:25 file:/srv/reprepro perl-5.40/main amd64 libdatetime-perl amd64 2:1.65-1+b2 [116 kB] Get:26 file:/srv/reprepro perl-5.40/main amd64 liblist-moreutils-xs-perl amd64 0.430-4+b2 [42.1 kB] Get:27 file:/srv/reprepro perl-5.40/main amd64 libset-object-perl amd64 1.42-1+b5 [37.6 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.5-1+b1 [27.0 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:36 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:37 file:/srv/reprepro perl-5.40/main amd64 libxml-parser-perl amd64 2.47-1+b3 [198 kB] Get:38 file:/srv/reprepro perl-5.40/main amd64 libpadwalker-perl amd64 2.5-1+b6 [18.6 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.5-1+b1 [9884 B] Get:46 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.5-1+b1 [27.9 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-5 [64.7 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-5 [878 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.3.2-1 [1381 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-8 [97.3 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:72 http://deb.debian.org/debian unstable/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 bioperl all 1.7.8-1 [246 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 cd-hit amd64 4.8.1-4 [522 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:91 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3+b1 [671 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libclass-load-perl all 0.25-2 [15.3 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 libio-stringy-perl all 2.113-2 [48.3 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libgetopt-long-descriptive-perl all 0.111-1 [27.8 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 libio-tiecombine-perl all 1.005-3 [10.8 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libmodule-pluggable-perl all 5.2-5 [23.0 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libstring-rewriteprefix-perl all 0.009-1 [7140 B] Get:113 http://deb.debian.org/debian unstable/main amd64 libapp-cmd-perl all 0.336-1 [65.8 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 libscope-guard-perl all 0.21-2 [8212 B] Get:115 http://deb.debian.org/debian unstable/main amd64 libmixin-linewise-perl all 0.111-1 [14.4 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 libconfig-ini-perl all 1:0.029-1 [23.7 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:118 http://deb.debian.org/debian unstable/main amd64 libdevel-globaldestruction-perl all 0.14-4 [7144 B] Get:119 http://deb.debian.org/debian unstable/main amd64 libalgorithm-c3-perl all 0.11-2 [10.8 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 libclass-c3-perl all 0.35-2 [21.0 kB] Get:121 http://deb.debian.org/debian unstable/main amd64 libmro-compat-perl all 0.15-2 [11.8 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 libdevel-overloadinfo-perl all 0.007-1 [7896 B] Get:123 http://deb.debian.org/debian unstable/main amd64 libeval-closure-perl all 0.14-3 [11.2 kB] Get:124 http://deb.debian.org/debian unstable/main amd64 libdist-checkconflicts-perl all 0.11-2 [10.5 kB] Get:125 http://deb.debian.org/debian unstable/main amd64 libmodule-runtime-conflicts-perl all 0.003-2 [7356 B] Get:126 http://deb.debian.org/debian unstable/main amd64 libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB] Get:127 http://deb.debian.org/debian unstable/main amd64 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:129 http://deb.debian.org/debian unstable/main amd64 libnamespace-autoclean-perl all 0.29-2 [13.5 kB] Get:130 http://deb.debian.org/debian unstable/main amd64 libmoosex-role-parameterized-perl all 1.11-2 [41.9 kB] Get:131 http://deb.debian.org/debian unstable/main amd64 libmoosex-oneargnew-perl all 0.007-1 [8180 B] Get:132 http://deb.debian.org/debian unstable/main amd64 libjson-maybexs-perl all 1.004008-1 [12.9 kB] Get:133 http://deb.debian.org/debian unstable/main amd64 libstring-formatter-perl all 1.235-1 [22.1 kB] Get:134 http://deb.debian.org/debian unstable/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:135 http://deb.debian.org/debian unstable/main amd64 libstring-errf-perl all 0.009-1 [12.9 kB] Get:136 http://deb.debian.org/debian unstable/main amd64 librole-hasmessage-perl all 0.007-1 [9112 B] Get:137 http://deb.debian.org/debian unstable/main amd64 librole-identifiable-perl all 0.009-1 [10.4 kB] Get:138 http://deb.debian.org/debian unstable/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get:139 http://deb.debian.org/debian unstable/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:140 http://deb.debian.org/debian unstable/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:141 http://deb.debian.org/debian unstable/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get:142 http://deb.debian.org/debian unstable/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get:143 http://deb.debian.org/debian unstable/main amd64 libthrowable-perl all 1.001-2 [15.7 kB] Get:144 http://deb.debian.org/debian unstable/main amd64 libtie-ixhash-perl all 1.23-4 [11.7 kB] Get:145 http://deb.debian.org/debian unstable/main amd64 libconfig-mvp-perl all 2.200013-1 [47.1 kB] Get:146 http://deb.debian.org/debian unstable/main amd64 libconfig-mvp-reader-ini-perl all 2.101465-1 [6900 B] Get:147 http://deb.debian.org/debian unstable/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get:148 http://deb.debian.org/debian unstable/main amd64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get:149 http://deb.debian.org/debian unstable/main amd64 liburi-perl all 5.29-1 [103 kB] Get:150 http://deb.debian.org/debian unstable/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get:151 http://deb.debian.org/debian unstable/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:152 http://deb.debian.org/debian unstable/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:153 http://deb.debian.org/debian unstable/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:154 http://deb.debian.org/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get:155 http://deb.debian.org/debian unstable/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:156 http://deb.debian.org/debian unstable/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:157 http://deb.debian.org/debian unstable/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:158 http://deb.debian.org/debian unstable/main amd64 libhttp-message-perl all 6.46-1 [79.7 kB] Get:159 http://deb.debian.org/debian unstable/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:160 http://deb.debian.org/debian unstable/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:161 http://deb.debian.org/debian unstable/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:162 http://deb.debian.org/debian unstable/main amd64 libwww-perl all 6.77-1 [183 kB] Get:163 http://deb.debian.org/debian unstable/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get:164 http://deb.debian.org/debian unstable/main amd64 libcpan-uploader-perl all 0.103018-1 [16.3 kB] Get:165 http://deb.debian.org/debian unstable/main amd64 libdata-section-perl all 0.200008-1 [13.1 kB] Get:166 http://deb.debian.org/debian unstable/main amd64 libclass-inspector-perl all 1.36-3 [17.5 kB] Get:167 http://deb.debian.org/debian unstable/main amd64 libfile-sharedir-perl all 1.118-3 [16.0 kB] Get:168 http://deb.debian.org/debian unstable/main amd64 libparams-validationcompiler-perl all 0.31-1 [30.9 kB] Get:169 http://deb.debian.org/debian unstable/main amd64 libspecio-perl all 0.48-1 [142 kB] Get:170 http://deb.debian.org/debian unstable/main amd64 libdatetime-locale-perl all 1:1.41-1 [3131 kB] Get:171 http://deb.debian.org/debian unstable/main amd64 libclass-singleton-perl all 1.6-2 [12.5 kB] Get:172 http://deb.debian.org/debian unstable/main amd64 libdatetime-timezone-perl all 1:2.62-1+2024a [262 kB] Get:173 http://deb.debian.org/debian unstable/main amd64 libfile-copy-recursive-perl all 0.45-4 [20.0 kB] Get:174 http://deb.debian.org/debian unstable/main amd64 libnumber-compare-perl all 0.03-3 [6332 B] Get:175 http://deb.debian.org/debian unstable/main amd64 libtext-glob-perl all 0.11-3 [7676 B] Get:176 http://deb.debian.org/debian unstable/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get:177 http://deb.debian.org/debian unstable/main amd64 libfile-pushd-perl all 1.016-2 [13.5 kB] Get:178 http://deb.debian.org/debian unstable/main amd64 libfile-sharedir-install-perl all 0.14-2 [11.6 kB] Get:179 http://deb.debian.org/debian unstable/main amd64 libhash-merge-simple-perl all 0.051-3 [7404 B] Get:180 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get:181 http://deb.debian.org/debian unstable/main amd64 liblog-dispatch-perl all 2.71-1 [75.8 kB] Get:182 http://deb.debian.org/debian unstable/main amd64 liblog-dispatch-array-perl all 1.005-1 [6700 B] Get:183 http://deb.debian.org/debian unstable/main amd64 libstring-flogger-perl all 1.101246-1 [7380 B] Get:184 http://deb.debian.org/debian unstable/main amd64 libsub-exporter-globexporter-perl all 0.006-1 [8024 B] Get:185 http://deb.debian.org/debian unstable/main amd64 liblog-dispatchouli-perl all 3.007-1 [35.0 kB] Get:186 http://deb.debian.org/debian unstable/main amd64 libexporter-tiny-perl all 1.006002-1 [38.7 kB] Get:187 http://deb.debian.org/debian unstable/main amd64 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get:188 http://deb.debian.org/debian unstable/main amd64 libsyntax-keyword-junction-perl all 0.003009-1 [12.7 kB] Get:189 http://deb.debian.org/debian unstable/main amd64 libmoose-autobox-perl all 0.16-2 [52.8 kB] Get:190 http://deb.debian.org/debian unstable/main amd64 libaliased-perl all 0.34-3 [13.5 kB] Get:191 http://deb.debian.org/debian unstable/main amd64 libmoosex-lazyrequire-perl all 0.11-2 [9212 B] Get:192 http://deb.debian.org/debian unstable/main amd64 libmoosex-setonce-perl all 0.200002-2 [6632 B] Get:193 http://deb.debian.org/debian unstable/main amd64 libcarp-clan-perl all 6.08-2 [14.1 kB] Get:194 http://deb.debian.org/debian unstable/main amd64 libsub-exporter-formethods-perl all 0.100055-1 [8024 B] Get:195 http://deb.debian.org/debian unstable/main amd64 libmoosex-types-perl all 0.50-2 [54.6 kB] Get:196 http://deb.debian.org/debian unstable/main amd64 libmoosex-types-perl-perl all 0.101344-1 [8160 B] Get:197 http://deb.debian.org/debian unstable/main amd64 libpath-tiny-perl all 0.146-1 [56.2 kB] Get:198 http://deb.debian.org/debian unstable/main amd64 libmodule-path-perl all 0.19-3 [12.3 kB] Get:199 http://deb.debian.org/debian unstable/main amd64 libtask-weaken-perl all 1.06-2 [9364 B] Get:200 http://deb.debian.org/debian unstable/main amd64 libppi-perl all 1.279-1 [294 kB] Get:201 http://deb.debian.org/debian unstable/main amd64 libtype-tiny-perl all 2.004000-1 [357 kB] Get:202 http://deb.debian.org/debian unstable/main amd64 libperl-prereqscanner-perl all 1.100-1 [31.0 kB] Get:203 http://deb.debian.org/debian unstable/main amd64 libperl-version-perl all 1.017-1 [29.0 kB] Get:204 http://deb.debian.org/debian unstable/main amd64 libtext-template-perl all 1.61-1 [54.4 kB] Get:205 http://deb.debian.org/debian unstable/main amd64 libsoftware-license-perl all 0.104006-1 [116 kB] Get:206 http://deb.debian.org/debian unstable/main amd64 libterm-encoding-perl all 0.03-2 [4980 B] Get:207 http://deb.debian.org/debian unstable/main amd64 libyaml-tiny-perl all 1.74-1 [30.7 kB] Get:208 http://deb.debian.org/debian unstable/main amd64 libdist-zilla-perl all 6.032-1 [343 kB] Get:209 http://deb.debian.org/debian unstable/main amd64 dh-dist-zilla all 1.4.1 [17.9 kB] Get:210 http://deb.debian.org/debian unstable/main amd64 libfakeroot amd64 1.36-1 [29.1 kB] Get:211 http://deb.debian.org/debian unstable/main amd64 fakeroot amd64 1.36-1 [75.1 kB] Get:212 http://deb.debian.org/debian unstable/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get:213 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get:214 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get:215 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:216 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:217 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:218 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get:219 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get:220 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get:221 http://deb.debian.org/debian unstable/main amd64 libarray-utils-perl all 0.5-3 [6184 B] Get:222 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:223 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:224 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get:225 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get:226 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get:227 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:228 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get:229 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2 [115 kB] Get:230 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB] Get:231 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:232 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get:233 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-1 [534 kB] Get:234 http://deb.debian.org/debian unstable/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get:235 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get:236 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:237 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:238 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB] Get:239 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.10.0-2 [352 kB] Get:240 http://deb.debian.org/debian unstable/main amd64 libdata-compare-perl all 1.29-1 [19.6 kB] Get:241 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get:242 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.21-1 [47.3 kB] Get:243 http://deb.debian.org/debian unstable/main amd64 libpod-eventual-perl all 0.094003-1 [14.2 kB] Get:244 http://deb.debian.org/debian unstable/main amd64 libstring-truncate-perl all 1.100603-1 [10.2 kB] Get:245 http://deb.debian.org/debian unstable/main amd64 libpod-elemental-perl all 0.103006-1 [67.2 kB] Get:246 http://deb.debian.org/debian unstable/main amd64 libpod-elemental-perlmunger-perl all 0.200007-1 [10.5 kB] Get:247 http://deb.debian.org/debian unstable/main amd64 libpod-weaver-perl all 4.020-1 [70.1 kB] Get:248 http://deb.debian.org/debian unstable/main amd64 libdist-zilla-plugin-podweaver-perl all 4.010-1 [9580 B] Get:249 http://deb.debian.org/debian unstable/main amd64 libenv-path-perl all 0.19-4 [19.1 kB] Get:250 http://deb.debian.org/debian unstable/main amd64 libfile-chdir-perl all 0.1008-1.2 [11.9 kB] Get:251 http://deb.debian.org/debian unstable/main amd64 libfile-grep-perl all 0.02-3 [8352 B] Get:252 http://deb.debian.org/debian unstable/main amd64 libfile-slurper-perl all 0.014-1 [8560 B] Get:253 http://deb.debian.org/debian unstable/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get:254 http://deb.debian.org/debian unstable/main amd64 libfindbin-libs-perl all 3.0.2-1 [29.7 kB] Get:255 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get:256 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-5 [837 kB] Get:257 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.82.0-1 [1498 kB] Get:258 http://deb.debian.org/debian unstable/main amd64 libheap-perl all 0.80-5 [34.3 kB] Get:259 http://deb.debian.org/debian unstable/main amd64 libgraph-perl all 1:0.9729-1 [108 kB] Get:260 http://deb.debian.org/debian unstable/main amd64 libspiffy-perl all 0.46-1 [25.7 kB] Get:261 http://deb.debian.org/debian unstable/main amd64 libio-all-perl all 0.87-2 [67.3 kB] Get:262 http://deb.debian.org/debian unstable/main amd64 libparse-yapp-perl all 1.21-4 [41.5 kB] Get:263 http://deb.debian.org/debian unstable/main amd64 libxml-writer-perl all 0.900-2 [26.8 kB] Get:264 http://deb.debian.org/debian unstable/main amd64 libgraph-readwrite-perl all 2.10-1 [45.2 kB] Get:265 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:266 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 9.0.0-1 [474 kB] Get:267 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:268 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get:269 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get:270 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get:271 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:272 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:273 http://deb.debian.org/debian unstable/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get:274 http://deb.debian.org/debian unstable/main amd64 liblog-log4perl-perl all 1.57-1 [367 kB] Get:275 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get:276 http://deb.debian.org/debian unstable/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get:277 http://deb.debian.org/debian unstable/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get:278 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:279 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get:280 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.54.0+ds-2 [223 kB] Get:281 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-2 [54.4 kB] Get:282 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-2 [35.2 kB] Get:283 http://deb.debian.org/debian unstable/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB] Get:284 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B] Get:285 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get:286 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-10 [34.7 kB] Get:287 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get:288 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get:289 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get:290 http://deb.debian.org/debian unstable/main amd64 libtest-file-perl all 1.993-1 [24.5 kB] Get:291 http://deb.debian.org/debian unstable/main amd64 libtest2-suite-perl all 0.000163-1 [383 kB] Get:292 http://deb.debian.org/debian unstable/main amd64 libtest-files-perl all 0.26-1 [21.6 kB] Get:293 http://deb.debian.org/debian unstable/main amd64 libtest-output-perl all 1.034-1 [16.0 kB] Get:294 http://deb.debian.org/debian unstable/main amd64 libtext-csv-perl all 2.04-1 [112 kB] Get:295 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get:296 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:297 http://deb.debian.org/debian unstable/main amd64 libtingea0 amd64 21-361-2+b1 [51.3 kB] Get:298 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get:299 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB] Get:300 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get:301 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-6 [148 kB] Get:302 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get:303 http://deb.debian.org/debian unstable/main amd64 mafft amd64 7.505-1 [1078 kB] Get:304 http://deb.debian.org/debian unstable/main amd64 mcl amd64 1:22-282+ds-2 [474 kB] Get:305 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-4 [3540 kB] Get:306 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+ amd64 2.16.0+ds-6 [15.2 MB] Get:307 http://deb.debian.org/debian unstable/main amd64 sysstat amd64 12.7.5-2 [623 kB] Get:308 http://deb.debian.org/debian unstable/main amd64 parallel all 20240222+ds-2 [2163 kB] Get:309 http://deb.debian.org/debian unstable/main amd64 prank amd64 0.0.170427+dfsg-3 [395 kB] Get:310 http://deb.debian.org/debian unstable/main amd64 zip amd64 3.0-14 [233 kB] Get:311 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB] Get:312 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:313 http://deb.debian.org/debian unstable/main amd64 r-base-core amd64 4.4.1-3 [28.3 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 113 MB in 1s (103 MB/s) Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... 22986 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.6-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_amd64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:amd64 (3.12.6-1) ... Setting up libexpat1:amd64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 23306 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.5-1+b1_amd64.deb ... Unpacking python3-minimal (3.12.5-1+b1) ... Selecting previously unselected package media-types. 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Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b2) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../13-libpython3.12-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../14-python3.12_3.12.6-1_amd64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../15-libpython3-stdlib_3.12.5-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.5-1+b1) ... Setting up python3-minimal (3.12.5-1+b1) ... Selecting previously unselected package python3. (Reading database ... 24348 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.5-1+b1_amd64.deb ... Unpacking python3 (3.12.5-1+b1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-5_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-5) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-5_amd64.deb ... Unpacking procps (2:4.0.4-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.3.2-1_amd64.deb ... Unpacking openssl (3.3.2-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../007-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../010-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../012-bsdextrautils_2.40.2-8_amd64.deb ... Unpacking bsdextrautils (2.40.2-8) ... Selecting previously unselected package libpipeline1:amd64. 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Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../026-libdevel-stacktrace-perl_2.0500-1_all.deb ... Unpacking libdevel-stacktrace-perl (2.0500-1) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../027-libexception-class-perl_1.45-1_all.deb ... Unpacking libexception-class-perl (1.45-1) ... Selecting previously unselected package libtest-deep-perl. Preparing to unpack .../028-libtest-deep-perl_1.204-1_all.deb ... Unpacking libtest-deep-perl (1.204-1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../029-libcapture-tiny-perl_0.48-2_all.deb ... Unpacking libcapture-tiny-perl (0.48-2) ... Selecting previously unselected package libalgorithm-diff-perl. Preparing to unpack .../030-libalgorithm-diff-perl_1.201-1_all.deb ... Unpacking libalgorithm-diff-perl (1.201-1) ... Selecting previously unselected package libtext-diff-perl. 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Selecting previously unselected package libfile-sharedir-perl. Preparing to unpack .../140-libfile-sharedir-perl_1.118-3_all.deb ... Unpacking libfile-sharedir-perl (1.118-3) ... Selecting previously unselected package libparams-validationcompiler-perl. Preparing to unpack .../141-libparams-validationcompiler-perl_0.31-1_all.deb ... Unpacking libparams-validationcompiler-perl (0.31-1) ... Selecting previously unselected package libxstring-perl:amd64. Preparing to unpack .../142-libxstring-perl_0.005-2+b4_amd64.deb ... Unpacking libxstring-perl:amd64 (0.005-2+b4) ... Selecting previously unselected package libspecio-perl. Preparing to unpack .../143-libspecio-perl_0.48-1_all.deb ... Unpacking libspecio-perl (0.48-1) ... Selecting previously unselected package libdatetime-locale-perl. Preparing to unpack .../144-libdatetime-locale-perl_1%3a1.41-1_all.deb ... Unpacking libdatetime-locale-perl (1:1.41-1) ... Selecting previously unselected package libclass-singleton-perl. 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Unpacking ncbi-blast+ (2.16.0+ds-6) ... Selecting previously unselected package sysstat. Preparing to unpack .../286-sysstat_12.7.5-2_amd64.deb ... Unpacking sysstat (12.7.5-2) ... Selecting previously unselected package parallel. Preparing to unpack .../287-parallel_20240222+ds-2_all.deb ... Adding 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel' Adding 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel' Unpacking parallel (20240222+ds-2) ... Selecting previously unselected package prank. Preparing to unpack .../288-prank_0.0.170427+dfsg-3_amd64.deb ... Unpacking prank (0.0.170427+dfsg-3) ... Selecting previously unselected package zip. Preparing to unpack .../289-zip_3.0-14_amd64.deb ... Unpacking zip (3.0-14) ... Selecting previously unselected package unzip. Preparing to unpack .../290-unzip_6.0-28_amd64.deb ... Unpacking unzip (6.0-28) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../291-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 .../292-r-base-core_4.4.1-3_amd64.deb ... Unpacking r-base-core (4.4.1-3) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../293-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... 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 (1.5.8-1) ... 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+dfsg2-4) ... 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 libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libxcb1:amd64 (1.17.0-2) ... Setting up libtie-ixhash-perl (1.23-4) ... Setting up libtask-weaken-perl (1.06-2) ... Setting up libicu72:amd64 (72.1-5) ... Setting up liblerc4:amd64 (4.0.0+ds-4+b1) ... Setting up libhash-merge-simple-perl (0.051-3) ... Setting up bsdextrautils (2.40.2-8) ... Setting up libparse-yapp-perl (1.21-4) ... Setting up libmbedcrypto7t64:amd64 (2.28.8-1) ... Setting up libclass-inspector-perl (1.36-3) ... Setting up libdynaloader-functions-perl (0.004-1) ... 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 libxcb-render0:amd64 (1.17.0-2) ... Setting up mafft (7.505-1) ... Setting up libclone-perl:amd64 (0.47-1+b1) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libsub-identify-perl (0.14-3+b3) ... Setting up libcpanel-json-xs-perl:amd64 (4.38-1+b1) ... Setting up libio-stringy-perl (2.113-2) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libtest-file-perl (1.993-1) ... Setting up unzip (6.0-28) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:amd64 (1.1.0-2+b4) ... Setting up libheap-perl (0.80-5) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libuv1t64:amd64 (1.48.0-6) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: WARNING: No init system and policy-rc.d missing! Defaulting to block. Setting up libtry-tiny-perl (0.32-1) ... Setting up libsensors-config (1:3.6.0-10) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.63.0-1) ... Setting up libdeflate0:amd64 (1.21-1) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libclass-singleton-perl (1.6-2) ... Setting up libpadwalker-perl (2.5-1+b6) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libxcb-shm0:amd64 (1.17.0-2) ... Setting up libfindbin-libs-perl (3.0.2-1) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libxstring-perl:amd64 (0.005-2+b4) ... Setting up libyaml-tiny-perl (1.74-1) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up libfakeroot:amd64 (1.36-1) ... Setting up libsub-install-perl (0.929-1) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up libtest2-suite-perl (0.000163-1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libterm-encoding-perl (0.03-2) ... Setting up libnumber-compare-perl (0.03-3) ... Setting up libscope-guard-perl (0.21-2) ... Setting up libfile-copy-recursive-perl (0.45-4) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Sep 16 17:03:04 UTC 2024. Universal Time is now: Mon Sep 16 17:03:04 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.36-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up libjson-maybexs-perl (1.004008-1) ... Setting up libio-string-perl (1.08-4) ... Setting up zip (3.0-14) ... Setting up libpackage-stash-xs-perl:amd64 (0.30-1+b4) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:amd64 (2.82.0-1) ... 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+b5) ... 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+b3) ... Setting up libxml-writer-perl (0.900-2) ... Setting up libenv-path-perl (0.19-4) ... Setting up libfribidi0:amd64 (1.0.15-1) ... Setting up libproc2-0:amd64 (2:4.0.4-5) ... 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+b1) ... 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 (0.22.5-2) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b2) ... Setting up libfile-grep-perl (0.02-3) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up liblist-moreutils-xs-perl (0.430-4+b2) ... Setting up libsensors5:amd64 (1:3.6.0-10) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libparams-util-perl (1.102-3+b1) ... Setting up libspiffy-perl (0.46-1) ... Setting up libgfortran5:amd64 (14.2.0-5) ... Setting up autoconf (2.72-3) ... 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+b3) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up libfile-chdir-perl (0.1008-1.2) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up libpath-tiny-perl (0.146-1) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-5) ... 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 libx11-6:amd64 (2:1.8.7-1+b1) ... 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) ... Configuration file '/etc/protocols' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Configuration file '/etc/services' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Setting up libsub-quote-perl (2.006008-1) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b4) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libmodule-path-perl (0.19-3) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libssh2-1t64:amd64 (1.11.0-7) ... Setting up libexporter-tiny-perl (1.006002-1) ... Setting up libterm-readkey-perl (2.38-2+b4) ... Setting up libperl-version-perl (1.017-1) ... Setting up openssl (3.3.2-1) ... Setting up libautobox-perl (3.0.2-1+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up bedtools (2.31.1+dfsg-2) ... Setting up liburi-perl (5.29-1) ... Setting up prank (0.0.170427+dfsg-3) ... Setting up libtext-csv-perl (2.04-1) ... Setting up libnet-ssleay-perl:amd64 (1.94-1+b2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libice6:amd64 (2:1.0.10-1+b1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libmbedx509-1t64:amd64 (2.28.8-1) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up libtool (2.4.7-7) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up liblist-moreutils-perl (0.430-2) ... Setting up libtest-warn-perl (0.37-2) ... Setting up libtype-tiny-perl (2.004000-1) ... Setting up libtest-differences-perl (0.71-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libnet-http-perl (6.23-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libio-all-perl (0.87-2) ... Setting up libclass-c3-perl (0.35-2) ... Setting up libgraph-perl (1:0.9729-1) ... Setting up libdevel-callchecker-perl:amd64 (0.009-1+b1) ... Setting up libdata-compare-perl (1.29-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libtest-exception-perl (0.43-3) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up mcl (1:22-282+ds-2) ... Setting up libppi-perl (1.279-1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up libtest-output-perl (1.034-1) ... Setting up ucf (3.0043+nmu1) ... Setting up libsyntax-keyword-junction-perl (0.003009-1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libmbedtls14t64:amd64 (2.28.8-1) ... Setting up groff-base (1.23.0-5) ... Setting up libhtml-parser-perl:amd64 (3.83-1+b1) ... Setting up libharfbuzz0b:amd64 (9.0.0-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up libmro-compat-perl (0.15-2) ... Setting up libsm6:amd64 (2:1.2.3-1+b1) ... Setting up sysstat (12.7.5-2) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Setting up libio-socket-ssl-perl (2.089-1) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libhttp-message-perl (6.46-1) ... Setting up libeval-closure-perl (0.14-3) ... Setting up libstring-truncate-perl (1.100603-1) ... Setting up libpaper1:amd64 (1.1.29+b1) ... Creating config file /etc/papersize with new version Setting up libstring-flogger-perl (1.101246-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libparams-validationcompiler-perl (0.31-1) ... Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libcurl4t64:amd64 (8.10.0-2) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libtest-most-perl (0.38-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libtk8.6:amd64 (8.6.14-1) ... Setting up libparams-classify-perl:amd64 (0.015-2+b4) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-2) ... Setting up libsub-exporter-formethods-perl (0.100055-1) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libmixin-linewise-perl (0.111-1) ... Setting up libcairo2:amd64 (1.18.2-1) ... Setting up libconfig-ini-perl (1:0.029-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up libdist-checkconflicts-perl (0.11-2) ... Setting up libstring-formatter-perl (1.235-1) ... Setting up parallel (20240222+ds-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-section-perl (0.200008-1) ... Setting up libnsl2:amd64 (1.3.0-3+b2) ... Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-2) ... Setting up libsub-exporter-globexporter-perl (0.006-1) ... Setting up libstring-rewriteprefix-perl (0.009-1) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-2) ... Setting up bioperl (1.7.8-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.6-1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up python3.12 (3.12.6-1) ... Setting up debhelper (13.20) ... Setting up libpod-eventual-perl (0.094003-1) ... Setting up libmodule-runtime-conflicts-perl (0.003-2) ... Setting up libtest-files-perl (0.26-1) ... Setting up libsoftware-license-perl (0.104006-1) ... Setting up libclass-load-perl (0.25-2) ... Setting up libstring-errf-perl (0.009-1) ... Setting up libspecio-perl (0.48-1) ... Setting up r-base-core (4.4.1-3) ... Creating config file /etc/R/Renviron with new version Setting up libpackage-deprecationmanager-perl (0.18-1) ... Setting up libdevel-overloadinfo-perl (0.007-1) ... Setting up libclass-load-xs-perl (0.10-2+b4) ... Setting up libparams-validate-perl:amd64 (1.31-2+b3) ... Setting up libb-hooks-endofscope-perl (0.28-1) ... Setting up libpython3-stdlib:amd64 (3.12.5-1+b1) ... Setting up libthrowable-perl (1.001-2) ... Setting up libmoose-perl:amd64 (2.2207-1+b2) ... Setting up python3 (3.12.5-1+b1) ... Setting up ncbi-blast+ (2.16.0+ds-6) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libmoosex-setonce-perl (0.200002-2) ... Setting up libgetopt-long-descriptive-perl (0.111-1) ... Setting up librole-identifiable-perl (0.009-1) ... Setting up libnamespace-autoclean-perl (0.29-2) ... Setting up libdatetime-locale-perl (1:1.41-1) ... Setting up libmoosex-role-parameterized-perl (1.11-2) ... Setting up libmoose-autobox-perl (0.16-2) ... Setting up libapp-cmd-perl (0.336-1) ... Setting up librole-hasmessage-perl (0.007-1) ... Setting up libperl-prereqscanner-perl (1.100-1) ... Setting up libdatetime-timezone-perl (1:2.62-1+2024a) ... Setting up libmoosex-types-perl (0.50-2) ... Setting up libmoosex-oneargnew-perl (0.007-1) ... Setting up libmoosex-lazyrequire-perl (0.11-2) ... Setting up liblog-dispatch-perl (2.71-1) ... Setting up libconfig-mvp-perl (2.200013-1) ... Setting up libdatetime-perl (2:1.65-1+b2) ... Setting up libpod-elemental-perl (0.103006-1) ... Setting up libmoosex-types-perl-perl (0.101344-1) ... Setting up libconfig-mvp-reader-ini-perl (2.101465-1) ... Setting up liblog-dispatch-array-perl (1.005-1) ... Setting up libpod-elemental-perlmunger-perl (0.200007-1) ... Setting up liblog-dispatchouli-perl (3.007-1) ... Setting up libpod-weaver-perl (4.020-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libwww-perl (6.77-1) ... Setting up libcpan-uploader-perl (0.103018-1) ... Setting up libdist-zilla-perl (6.032-1) ... Setting up libdist-zilla-plugin-podweaver-perl (4.010-1) ... Setting up libxml-parser-perl (2.47-1+b3) ... Setting up dh-dist-zilla (1.4.1) ... Setting up libgraph-readwrite-perl (2.10-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.40-2) ... 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. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.9.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1 (2024-06-27) amd64 (x86_64) Toolchain package versions: binutils_2.43.1-4 dpkg-dev_1.22.11 g++-13_13.3.0-6 g++-14_14.2.0-5 gcc-13_13.3.0-6 gcc-14_14.2.0-5 libc6-dev_2.40-2 libstdc++-13-dev_13.3.0-6 libstdc++-14-dev_14.2.0-5 libstdc++6_14.2.0-5 linux-libc-dev_6.10.9-1 Package versions: adduser_3.137 apt_2.9.8 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.4 bash_5.2.32-1+b1 bedtools_2.31.1+dfsg-2 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+------------------------------------------------------------------------------+ Unpack source ------------- -----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----- gpgv: Signature made Fri Nov 8 13:51:49 2019 UTC 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 /<> 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 Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network roary_3.13.0+dfsg-1 perl-5.40-throwaway amd64 -------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network roary_3.13.0+dfsg-1 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-2e1bfcee-271a-4e11-a5d7-7c0266d96c00 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -Zxz 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 -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with dist-zilla dh_dzil_clean dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building roary using existing ./roary_3.13.0+dfsg.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building roary in roary_3.13.0+dfsg-1.debian.tar.xz dpkg-source: info: building roary in roary_3.13.0+dfsg-1.dsc debian/rules build dh build --with dist-zilla dh_update_autotools_config dh_autoreconf debian/rules override_dh_dzil_build make[1]: Entering directory '/<>' 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 '/<>' 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=/<>=. -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=/<>=. -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 -j2 make[1]: Entering directory '/<>/.build/debian-build' cp lib/Bio/Roary/AccessoryBinaryFasta.pm blib/lib/Bio/Roary/AccessoryBinaryFasta.pm cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm cp lib/Bio/Roary/CommandLine/AssemblyStatistics.pm blib/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm cp lib/Bio/Roary/AccessoryClustering.pm blib/lib/Bio/Roary/AccessoryClustering.pm cp lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm blib/lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm cp lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.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/AssemblyStatistics.pm blib/lib/Bio/Roary/AssemblyStatistics.pm cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.pm cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm cp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.pm cp lib/Bio/Roary/AnnotateGroups.pm blib/lib/Bio/Roary/AnnotateGroups.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/CommandLine/ExtractProteomeFromGff.pm blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm cp lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm cp lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm blib/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.pm cp lib/Bio/Roary/CommandLine/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/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.pm cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pm cp lib/Bio/Roary/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.pm cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm cp lib/Bio/Roary/Output/EMBLHeaderCommon.pm blib/lib/Bio/Roary/Output/EMBLHeaderCommon.pm cp lib/Bio/Roary/External/IterativeCdhit.pm blib/lib/Bio/Roary/External/IterativeCdhit.pm cp lib/Bio/Roary/External/Fasttree.pm blib/lib/Bio/Roary/External/Fasttree.pm cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm cp lib/Bio/Roary/External/Mcl.pm blib/lib/Bio/Roary/External/Mcl.pm cp lib/Bio/Roary/External/Mafft.pm blib/lib/Bio/Roary/External/Mafft.pm cp lib/Bio/Roary/Output/GroupMultifasta.pm blib/lib/Bio/Roary/Output/GroupMultifasta.pm cp lib/Bio/Roary/JobRunner/Parallel.pm blib/lib/Bio/Roary/JobRunner/Parallel.pm cp lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm cp lib/Bio/Roary/GeneNamesFromGFF.pm blib/lib/Bio/Roary/GeneNamesFromGFF.pm cp lib/Bio/Roary/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pm cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm cp lib/Bio/Roary/MergeMultifastaAlignments.pm blib/lib/Bio/Roary/MergeMultifastaAlignments.pm cp lib/Bio/Roary/SpreadsheetRole.pm blib/lib/Bio/Roary/SpreadsheetRole.pm cp lib/Bio/Roary/SequenceLengths.pm blib/lib/Bio/Roary/SequenceLengths.pm cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm cp lib/Bio/Roary/UniqueGenesPerSample.pm blib/lib/Bio/Roary/UniqueGenesPerSample.pm cp lib/Bio/Roary/SampleOrder.pm blib/lib/Bio/Roary/SampleOrder.pm cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.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/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm cp lib/Bio/Roary/ReorderSpreadsheet.pm blib/lib/Bio/Roary/ReorderSpreadsheet.pm cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm cp lib/Bio/Roary/PresenceAbsenceMatrix.pm blib/lib/Bio/Roary/PresenceAbsenceMatrix.pm cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm cp lib/Bio/Roary/Output/QueryGroups.pm blib/lib/Bio/Roary/Output/QueryGroups.pm cp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm cp bin/create_pan_genome blib/script/create_pan_genome cp bin/create_pan_genome_plots blib/script/create_pan_genome_plots "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome_plots "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome cp bin/extract_proteome_from_gff blib/script/extract_proteome_from_gff "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- 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/iterative_cdhit cp bin/pan_genome_assembly_statistics blib/script/pan_genome_assembly_statistics "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_assembly_statistics cp bin/pan_genome_core_alignment blib/script/pan_genome_core_alignment "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_core_alignment cp bin/pan_genome_post_analysis blib/script/pan_genome_post_analysis cp bin/pan_genome_reorder_spreadsheet blib/script/pan_genome_reorder_spreadsheet "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_post_analysis "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_reorder_spreadsheet cp bin/parallel_all_against_all_blastp blib/script/parallel_all_against_all_blastp "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/parallel_all_against_all_blastp cp bin/protein_alignment_from_nucleotides blib/script/protein_alignment_from_nucleotides "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/protein_alignment_from_nucleotides cp bin/query_pan_genome blib/script/query_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/query_pan_genome cp bin/roary blib/script/roary "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary cp bin/roary-create_pan_genome_plots.R blib/script/roary-create_pan_genome_plots.R "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-create_pan_genome_plots.R cp bin/roary-pan_genome_reorder_spreadsheet blib/script/roary-pan_genome_reorder_spreadsheet "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-pan_genome_reorder_spreadsheet cp bin/roary-query_pan_genome blib/script/roary-query_pan_genome cp bin/roary-unique_genes_per_sample blib/script/roary-unique_genes_per_sample "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-query_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-unique_genes_per_sample cp bin/transfer_annotation_to_groups blib/script/transfer_annotation_to_groups "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/transfer_annotation_to_groups Manifying 16 pod documents Manifying 26 pod documents Manifying 28 pod documents Manifying 25 pod documents make[1]: Leaving directory '/<>/.build/debian-build' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' # Hmmm, seems the test is not automatically run anyway by the build system dh_auto_test || true make[1]: Leaving directory '/<>' 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 -j2 install DESTDIR=/<>/roary-3.13.0\+dfsg/debian/roary AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/<>/.build/debian-build' Manifying 16 pod documents Manifying 26 pod documents Manifying 28 pod documents Manifying 25 pod documents Installing /<>/debian/roary/usr/share/perl5/Bio/Roary.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/LookupGeneFiles.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/AnnotateGroups.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/AccessoryClustering.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFFs.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/GroupStatistics.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/IterativeCdhit.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/CombinedProteome.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/ParallelAllAgainstAllBlast.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/ReorderSpreadsheet.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/ReformatInputGFFs.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/ParseGFFAnnotationRole.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/UniqueGenesPerSample.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/GroupLabels.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/SortFasta.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/FilterFullClusters.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/PresenceAbsenceMatrix.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/SplitGroups.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/ClustersRole.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/PrepareInputFiles.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/Exceptions.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/SpreadsheetRole.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/PostAnalysis.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/InflateClusters.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/ChunkFastaFile.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/AnalyseGroups.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/BedFromGFFRole.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/ContigsToGeneIDsFromGFF.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/OrderGenes.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/GeneNamesFromGFF.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFF.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/SampleOrder.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/AssemblyStatistics.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/AccessoryBinaryFasta.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/SequenceLengths.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/MergeMultifastaAlignments.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/FilterUnknownsFromFasta.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/External/Cdhit.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/External/Mafft.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/External/IterativeCdhit.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/External/Mcl.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/External/Fasttree.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/External/Blastp.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/External/CheckTools.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/External/PostAnalysis.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/External/GeneAlignmentFromNucleotides.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/External/Makeblastdb.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/External/Prank.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Local.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Parallel.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Role.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaProtein.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastas.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/Output/EmblGroups.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupMultifasta.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaNucleotide.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/Output/NumberOfGroups.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/Output/EMBLHeaderCommon.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastasNucleotide.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/Output/QueryGroups.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/Output/BlastIdentityFrequency.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/Output/DifferenceBetweenSets.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/QC/Report.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/QueryRoary.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/IterativeCdhit.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/UniqueGenesPerSample.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Common.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryCoreAlignment.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Roary.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryPostAnalysis.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/AssemblyStatistics.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/CreatePanGenome.pm Installing /<>/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm Installing /<>/debian/roary/usr/share/man/man1/roary-pan_genome_reorder_spreadsheet.1p Installing /<>/debian/roary/usr/share/man/man1/extract_proteome_from_gff.1p Installing /<>/debian/roary/usr/share/man/man1/roary-unique_genes_per_sample.1p Installing /<>/debian/roary/usr/share/man/man1/create_pan_genome.1p Installing /<>/debian/roary/usr/share/man/man1/protein_alignment_from_nucleotides.1p Installing /<>/debian/roary/usr/share/man/man1/query_pan_genome.1p Installing /<>/debian/roary/usr/share/man/man1/pan_genome_post_analysis.1p Installing /<>/debian/roary/usr/share/man/man1/pan_genome_reorder_spreadsheet.1p Installing /<>/debian/roary/usr/share/man/man1/parallel_all_against_all_blastp.1p Installing /<>/debian/roary/usr/share/man/man1/transfer_annotation_to_groups.1p Installing /<>/debian/roary/usr/share/man/man1/pan_genome_assembly_statistics.1p Installing /<>/debian/roary/usr/share/man/man1/iterative_cdhit.1p Installing /<>/debian/roary/usr/share/man/man1/roary.1p Installing /<>/debian/roary/usr/share/man/man1/create_pan_genome_plots.1p Installing /<>/debian/roary/usr/share/man/man1/pan_genome_core_alignment.1p Installing /<>/debian/roary/usr/share/man/man1/roary-query_pan_genome.1p Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupMultifasta.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::ParseGFFAnnotationRole.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::SampleOrder.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::ChunkFastaFile.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::Output::QueryGroups.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::OrderGenes.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::PostAnalysis.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::PrepareInputFiles.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Parallel.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::ReorderSpreadsheet.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::External::CheckTools.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::TransferAnnotationToGroups.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::CombinedProteome.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::UniqueGenesPerSample.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::AnnotateGroups.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Local.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::External::Cdhit.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::QueryRoary.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::AssemblyStatistics.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Roary.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::IterativeCdhit.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::AccessoryBinaryFasta.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::QC::Report.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::LookupGeneFiles.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::FilterFullClusters.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::AnalyseGroups.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::GeneNamesFromGFF.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFF.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::External::Makeblastdb.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::GroupStatistics.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::Output::BlastIdentityFrequency.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::Exceptions.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::AssemblyStatistics.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::External::PostAnalysis.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::ClustersRole.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::FilterUnknownsFromFasta.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::External::Blastp.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::UniqueGenesPerSample.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastasNucleotide.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::External::Fasttree.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::ExtractCoreGenesFromSpreadsheet.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::GeneAlignmentFromNucleotides.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::SplitGroups.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaNucleotide.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryReorderSpreadsheet.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Role.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryPostAnalysis.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::ParallelAllAgainstAllBlast.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::Output::EmblGroups.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::MergeMultifastaAlignments.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::ContigsToGeneIDsFromGFF.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::External::GeneAlignmentFromNucleotides.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastas.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::Output::DifferenceBetweenSets.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryCoreAlignment.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::Output::NumberOfGroups.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::External::Prank.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaProtein.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::SpreadsheetRole.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::PresenceAbsenceMatrix.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::External::Mafft.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::ReformatInputGFFs.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::SequenceLengths.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Common.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFFs.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::External::Mcl.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ExtractProteomeFromGff.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::CreatePanGenome.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::IterativeCdhit.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::InflateClusters.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::SortFasta.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::External::IterativeCdhit.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::BedFromGFFRole.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::Output::EMBLHeaderCommon.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::AccessoryClustering.3pm Installing /<>/debian/roary/usr/share/man/man3/Bio::Roary::GroupLabels.3pm Installing /<>/debian/roary/usr/bin/pan_genome_post_analysis Installing /<>/debian/roary/usr/bin/iterative_cdhit Installing /<>/debian/roary/usr/bin/pan_genome_assembly_statistics Installing /<>/debian/roary/usr/bin/protein_alignment_from_nucleotides Installing /<>/debian/roary/usr/bin/roary Installing /<>/debian/roary/usr/bin/roary-pan_genome_reorder_spreadsheet Installing /<>/debian/roary/usr/bin/pan_genome_core_alignment Installing /<>/debian/roary/usr/bin/pan_genome_reorder_spreadsheet Installing /<>/debian/roary/usr/bin/extract_proteome_from_gff Installing /<>/debian/roary/usr/bin/create_pan_genome Installing /<>/debian/roary/usr/bin/transfer_annotation_to_groups Installing /<>/debian/roary/usr/bin/parallel_all_against_all_blastp Installing /<>/debian/roary/usr/bin/roary-create_pan_genome_plots.R Installing /<>/debian/roary/usr/bin/roary-query_pan_genome Installing /<>/debian/roary/usr/bin/roary-unique_genes_per_sample Installing /<>/debian/roary/usr/bin/query_pan_genome Installing /<>/debian/roary/usr/bin/create_pan_genome_plots make[1]: Leaving directory '/<>/.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 -O../roary_3.13.0+dfsg-1_amd64.buildinfo dpkg-genchanges -O../roary_3.13.0+dfsg-1_amd64.changes dpkg-genchanges: info: including full source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: full upload (original source is included) -------------------------------------------------------------------------------- Build finished at 2024-09-16T17:03:46Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ 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: source all Version: 3.13.0+dfsg-1 Distribution: perl-5.40-throwaway 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: c33723a08eb94adfc095298047c9475104e124e4 1618 roary_3.13.0+dfsg-1.dsc ec41e9813412b1e168328131cabc91ae1ea06162 207348 roary_3.13.0+dfsg.orig.tar.xz 87a70a4f5c4608d5bfaee00eb633ca1d214e7c76 6620 roary_3.13.0+dfsg-1.debian.tar.xz d98d02d7ee7612a8d5c9f9bf8c6f0786aba8c4b3 172956 roary_3.13.0+dfsg-1_all.deb 1f06eb388035ba1de6a1027bf47995ba906f7f06 14783 roary_3.13.0+dfsg-1_amd64.buildinfo Checksums-Sha256: c7576e2832ab5dab3c43caff9fec27c83de135c65a23b3b35e345725531758fd 1618 roary_3.13.0+dfsg-1.dsc 5450fe6f4bab8b27829d2ec6836c0a8c9a38d42b3891fab29b10a9587dee2fd1 207348 roary_3.13.0+dfsg.orig.tar.xz 17ad80f231e28e09ef7e779b1a4d50cdf9a3b7266e8c6ac5beefe1231374f0bf 6620 roary_3.13.0+dfsg-1.debian.tar.xz 407c586f74905ca1cd02fa839d4f37a5975f5f0fb0e1a730dd4949f3f62a08c3 172956 roary_3.13.0+dfsg-1_all.deb 84171aa422d3d7e269aa0dbdeb950a65fea95fa445e6d93b4e25cb38b4a4e8a7 14783 roary_3.13.0+dfsg-1_amd64.buildinfo Files: fbd7962ca55c9b38a13e1cbbffc0e7e5 1618 science optional roary_3.13.0+dfsg-1.dsc fe3935332843c9d4dfb4d4c5cb9080a6 207348 science optional roary_3.13.0+dfsg.orig.tar.xz 42e8827558347115a86700a1c086295e 6620 science optional roary_3.13.0+dfsg-1.debian.tar.xz af01483d1d735e74de6bd65123abd903 172956 science optional roary_3.13.0+dfsg-1_all.deb df5f6e7af28cf86d821c39411bdcb57f 14783 science optional roary_3.13.0+dfsg-1_amd64.buildinfo +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: roary Binary: roary Architecture: all source Version: 3.13.0+dfsg-1 Checksums-Md5: fbd7962ca55c9b38a13e1cbbffc0e7e5 1618 roary_3.13.0+dfsg-1.dsc af01483d1d735e74de6bd65123abd903 172956 roary_3.13.0+dfsg-1_all.deb Checksums-Sha1: c33723a08eb94adfc095298047c9475104e124e4 1618 roary_3.13.0+dfsg-1.dsc d98d02d7ee7612a8d5c9f9bf8c6f0786aba8c4b3 172956 roary_3.13.0+dfsg-1_all.deb Checksums-Sha256: c7576e2832ab5dab3c43caff9fec27c83de135c65a23b3b35e345725531758fd 1618 roary_3.13.0+dfsg-1.dsc 407c586f74905ca1cd02fa839d4f37a5975f5f0fb0e1a730dd4949f3f62a08c3 172956 roary_3.13.0+dfsg-1_all.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 16 Sep 2024 17:03:45 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3), automake (= 1:1.16.5-1.3), autopoint (= 0.22.5-2), autotools-dev (= 20220109.1), base-files (= 13.5), base-passwd (= 3.6.4), bash (= 5.2.32-1+b1), bedtools (= 2.31.1+dfsg-2), binutils (= 2.43.1-4), binutils-common (= 2.43.1-4), binutils-x86-64-linux-gnu (= 2.43.1-4), bioperl (= 1.7.8-1), bsdextrautils (= 2.40.2-8), bsdutils (= 1:2.40.2-8), build-essential (= 12.10), bzip2 (= 1.0.8-6), ca-certificates (= 20240203), cd-hit (= 4.8.1-4), coreutils (= 9.4-3.1), cpp (= 4:14.1.0-2), cpp-13 (= 13.3.0-6), cpp-13-x86-64-linux-gnu (= 13.3.0-6), cpp-14 (= 14.2.0-5), cpp-14-x86-64-linux-gnu (= 14.2.0-5), cpp-x86-64-linux-gnu (= 4:14.1.0-2), dash (= 0.5.12-9), debconf (= 1.5.87), debhelper (= 13.20), debianutils (= 5.20), dh-autoreconf (= 20), dh-dist-zilla (= 1.4.1), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.11), dpkg-dev (= 1.22.11), dwz (= 0.15-1+b1), fasttree (= 2.1.11-2), file (= 1:5.45-3), findutils (= 4.10.0-3), fontconfig (= 2.15.0-1.1), fontconfig-config (= 2.15.0-1.1), fonts-dejavu-core (= 2.37-8), fonts-dejavu-mono (= 2.37-8), g++ (= 4:14.1.0-2), g++-14 (= 14.2.0-5), g++-14-x86-64-linux-gnu (= 14.2.0-5), g++-x86-64-linux-gnu (= 4:14.1.0-2), gcc (= 4:14.1.0-2), gcc-13 (= 13.3.0-6), gcc-13-base (= 13.3.0-6), gcc-13-x86-64-linux-gnu (= 13.3.0-6), gcc-14 (= 14.2.0-5), gcc-14-base (= 14.2.0-5), gcc-14-x86-64-linux-gnu (= 14.2.0-5), gcc-x86-64-linux-gnu (= 4:14.1.0-2), gettext (= 0.22.5-2), gettext-base (= 0.22.5-2), grep (= 3.11-4), groff-base (= 1.23.0-5), gzip (= 1.12-1.1), hostname (= 3.23+nmu2), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2), libalgorithm-c3-perl (= 0.11-2), libalgorithm-diff-perl (= 1.201-1), libaliased-perl (= 0.34-3), libapp-cmd-perl (= 0.336-1), libarchive-zip-perl (= 1.68-1), libarray-utils-perl (= 0.5-3), libasan8 (= 14.2.0-5), libatomic1 (= 14.2.0-5), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:4.0.1-1), libaudit1 (= 1:4.0.1-1), libautobox-perl (= 3.0.2-1+b1), libb-hooks-endofscope-perl (= 0.28-1), libb-hooks-op-check-perl (= 0.22-3+b2), libbinutils (= 2.43.1-4), libbio-perl-perl (= 1.7.8-1), libblas3 (= 3.12.0-3), libblkid1 (= 2.40.2-8), libbrotli1 (= 1.1.0-2+b4), libbsd0 (= 0.12.2-1), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.40-2), libc-dev-bin (= 2.40-2), libc6 (= 2.40-2), libc6-dev (= 2.40-2), libcairo2 (= 1.18.2-1), libcap-ng0 (= 0.8.5-2), libcap2 (= 1:2.66-5), libcapture-tiny-perl (= 0.48-2), libcarp-clan-perl (= 6.08-2), libcc1-0 (= 14.2.0-5), libclass-c3-perl (= 0.35-2), libclass-data-inheritable-perl (= 0.08-3), libclass-inspector-perl (= 1.36-3), libclass-load-perl (= 0.25-2), libclass-load-xs-perl (= 0.10-2+b4), libclass-method-modifiers-perl (= 2.15-1), libclass-singleton-perl (= 1.6-2), libclass-xsaccessor-perl (= 1.19-4+b4), libclone-perl (= 0.47-1+b1), libcom-err2 (= 1.47.1-1), libconfig-ini-perl (= 1:0.029-1), libconfig-mvp-perl (= 2.200013-1), libconfig-mvp-reader-ini-perl (= 2.101465-1), libconst-fast-perl (= 0.014-2), libcpan-uploader-perl (= 0.103018-1), libcpanel-json-xs-perl (= 4.38-1+b1), libcrypt-dev (= 1:4.4.36-5), libcrypt1 (= 1:4.4.36-5), libctf-nobfd0 (= 2.43.1-4), libctf0 (= 2.43.1-4), libcurl4t64 (= 8.10.0-2), libdata-compare-perl (= 1.29-1), libdata-optlist-perl (= 0.114-1), libdata-section-perl (= 0.200008-1), libdata-stag-perl (= 0.14-3), libdatetime-locale-perl (= 1:1.41-1), libdatetime-perl (= 2:1.65-1+b2), libdatetime-timezone-perl (= 1:2.62-1+2024a), libdatrie1 (= 0.2.13-3), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.20), libdeflate0 (= 1.21-1), libdevel-callchecker-perl (= 0.009-1+b1), libdevel-globaldestruction-perl (= 0.14-4), libdevel-overloadinfo-perl (= 0.007-1), libdevel-stacktrace-perl (= 2.0500-1), libdist-checkconflicts-perl (= 0.11-2), libdist-zilla-perl (= 6.032-1), libdist-zilla-plugin-podweaver-perl (= 4.010-1), libdpkg-perl (= 1.22.11), libdynaloader-functions-perl (= 0.004-1), libelf1t64 (= 0.191-2), libencode-locale-perl (= 1.05-3), libenv-path-perl (= 0.19-4), libeval-closure-perl (= 0.14-3), libexception-class-perl (= 1.45-1), libexpat1 (= 2.6.3-1), libexporter-tiny-perl (= 1.006002-1), libffi8 (= 3.4.6-1), libfile-chdir-perl (= 0.1008-1.2), libfile-copy-recursive-perl (= 0.45-4), libfile-find-rule-perl (= 0.34-3), libfile-grep-perl (= 0.02-3), libfile-listing-perl (= 6.16-1), libfile-pushd-perl (= 1.016-2), libfile-sharedir-install-perl (= 0.14-2), libfile-sharedir-perl (= 1.118-3), libfile-slurper-perl (= 0.014-1), libfile-stripnondeterminism-perl (= 1.14.0-1), libfile-which-perl (= 1.27-2), libfindbin-libs-perl (= 3.0.2-1), libfontconfig1 (= 2.15.0-1.1), libfreetype6 (= 2.13.3+dfsg-1), libfribidi0 (= 1.0.15-1), libgcc-13-dev (= 13.3.0-6), libgcc-14-dev (= 14.2.0-5), libgcc-s1 (= 14.2.0-5), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgetopt-long-descriptive-perl (= 0.111-1), libgfortran5 (= 14.2.0-5), libglib2.0-0t64 (= 2.82.0-1), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgnutls30t64 (= 3.8.6-2), libgomp1 (= 14.2.0-5), libgprofng0 (= 2.43.1-4), libgraph-perl (= 1:0.9729-1), libgraph-readwrite-perl (= 2.10-1), libgraphite2-3 (= 1.3.14-2), libgssapi-krb5-2 (= 1.21.3-3), libharfbuzz0b (= 9.0.0-1), libhash-merge-simple-perl (= 0.051-3), libheap-perl (= 0.80-5), libhogweed6t64 (= 3.10-1), libhtml-parser-perl (= 3.83-1+b1), libhtml-tagset-perl (= 3.24-1), libhtml-tree-perl (= 5.07-3), libhttp-cookies-perl (= 6.11-1), libhttp-date-perl (= 6.06-1), libhttp-message-perl (= 6.46-1), libhttp-negotiate-perl (= 6.01-2), libhwasan0 (= 14.2.0-5), libice6 (= 2:1.0.10-1+b1), libicu72 (= 72.1-5), libidn2-0 (= 2.3.7-2), libimport-into-perl (= 1.002005-2), libio-all-perl (= 0.87-2), libio-html-perl (= 1.004-3), libio-socket-ssl-perl (= 2.089-1), libio-string-perl (= 1.08-4), libio-stringy-perl (= 2.113-2), libio-tiecombine-perl (= 1.005-3), libisl23 (= 0.27-1), libitm1 (= 14.2.0-5), libjansson4 (= 2.14-2+b2), libjbig0 (= 2.1-6.1+b1), libjpeg62-turbo (= 1:2.1.5-3), libjson-maybexs-perl (= 1.004008-1), libjson-perl (= 4.10000-1), libk5crypto3 (= 1.21.3-3), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.21.3-3), libkrb5support0 (= 1.21.3-3), liblapack3 (= 3.12.0-3), libldap-2.5-0 (= 2.5.18+dfsg-3+b1), liblerc4 (= 4.0.0+ds-4+b1), liblist-moreutils-perl (= 0.430-2), liblist-moreutils-xs-perl (= 0.430-4+b2), liblmdb0 (= 0.9.31-1+b1), liblog-dispatch-array-perl (= 1.005-1), liblog-dispatch-perl (= 2.71-1), liblog-dispatchouli-perl (= 3.007-1), liblog-log4perl-perl (= 1.57-1), liblsan0 (= 14.2.0-5), liblwp-mediatypes-perl (= 6.04-2), liblwp-protocol-https-perl (= 6.14-1), liblzma5 (= 5.6.2-2), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmbedcrypto7t64 (= 2.28.8-1), libmbedtls14t64 (= 2.28.8-1), libmbedx509-1t64 (= 2.28.8-1), libmd0 (= 1.1.0-2), libmixin-linewise-perl (= 0.111-1), libmodule-implementation-perl (= 0.09-2), libmodule-path-perl (= 0.19-3), libmodule-pluggable-perl (= 5.2-5), libmodule-runtime-conflicts-perl (= 0.003-2), libmodule-runtime-perl (= 0.016-2), libmoo-perl (= 2.005005-1), libmoose-autobox-perl (= 0.16-2), libmoose-perl (= 2.2207-1+b2), libmoosex-lazyrequire-perl (= 0.11-2), libmoosex-oneargnew-perl (= 0.007-1), libmoosex-role-parameterized-perl (= 1.11-2), libmoosex-setonce-perl (= 0.200002-2), libmoosex-types-perl (= 0.50-2), libmoosex-types-perl-perl (= 0.101344-1), libmount1 (= 2.40.2-8), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libmro-compat-perl (= 0.15-2), libnamespace-autoclean-perl (= 0.29-2), libnamespace-clean-perl (= 0.27-2), libncursesw6 (= 6.5-2), libnet-http-perl (= 6.23-1), libnet-ssleay-perl (= 1.94-1+b2), libnettle8t64 (= 3.10-1), libnghttp2-14 (= 1.63.0-1), libnsl2 (= 1.3.0-3+b2), libnumber-compare-perl (= 0.03-3), libp11-kit0 (= 0.25.5-2), libpackage-deprecationmanager-perl (= 0.18-1), libpackage-stash-perl (= 0.40-1), libpackage-stash-xs-perl (= 0.30-1+b4), libpadwalker-perl (= 2.5-1+b6), libpam-modules (= 1.5.3-7), libpam-modules-bin (= 1.5.3-7), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7), libpango-1.0-0 (= 1.54.0+ds-2), libpangocairo-1.0-0 (= 1.54.0+ds-2), libpangoft2-1.0-0 (= 1.54.0+ds-2), libpaper-utils (= 1.1.29+b1), libpaper1 (= 1.1.29+b1), libparams-classify-perl (= 0.015-2+b4), libparams-util-perl (= 1.102-3+b1), libparams-validate-perl (= 1.31-2+b3), libparams-validationcompiler-perl (= 0.31-1), libparse-yapp-perl (= 1.21-4), libpath-tiny-perl (= 0.146-1), libpcre2-8-0 (= 10.42-4+b1), libperl-prereqscanner-perl (= 1.100-1), libperl-version-perl (= 1.017-1), libperl5.40 (= 5.40.0-5), libperlio-utf8-strict-perl (= 0.010-1+b3), libpipeline1 (= 1.5.8-1), libpixman-1-0 (= 0.42.2-1+b1), libpng16-16t64 (= 1.6.43-5), libpod-elemental-perl (= 0.103006-1), libpod-elemental-perlmunger-perl (= 0.200007-1), libpod-eventual-perl (= 0.094003-1), libpod-weaver-perl (= 4.020-1), libppi-perl (= 1.279-1), libproc2-0 (= 2:4.0.4-5), libpsl5t64 (= 0.21.2-1.1), libpython3-stdlib (= 3.12.5-1+b1), libpython3.12-minimal (= 3.12.6-1), libpython3.12-stdlib (= 3.12.6-1), libquadmath0 (= 14.2.0-5), libreadline8t64 (= 8.2-5), librole-hasmessage-perl (= 0.007-1), librole-identifiable-perl (= 0.009-1), librole-tiny-perl (= 2.002004-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b4), libsasl2-2 (= 2.1.28+dfsg1-8), libsasl2-modules-db (= 2.1.28+dfsg1-8), libscope-guard-perl (= 0.21-2), libseccomp2 (= 2.5.5-1+b1), libselinux1 (= 3.7-3), libsensors-config (= 1:3.6.0-10), libsensors5 (= 1:3.6.0-10), libset-object-perl (= 1.42-1+b5), libsframe1 (= 2.43.1-4), libsharpyuv0 (= 1.4.0-0.1), libsm6 (= 2:1.2.3-1+b1), libsmartcols1 (= 2.40.2-8), libsoftware-license-perl (= 0.104006-1), libspecio-perl (= 0.48-1), libspiffy-perl (= 0.46-1), libsqlite3-0 (= 3.46.1-1), libssh2-1t64 (= 1.11.0-7), libssl3t64 (= 3.3.2-1), libstdc++-14-dev (= 14.2.0-5), libstdc++6 (= 14.2.0-5), libstring-errf-perl (= 0.009-1), libstring-flogger-perl (= 1.101246-1), libstring-formatter-perl (= 1.235-1), libstring-rewriteprefix-perl (= 0.009-1), libstring-truncate-perl (= 1.100603-1), libsub-exporter-formethods-perl (= 0.100055-1), libsub-exporter-globexporter-perl (= 0.006-1), libsub-exporter-perl (= 0.990-1), libsub-exporter-progressive-perl (= 0.001013-3), libsub-identify-perl (= 0.14-3+b3), libsub-install-perl (= 0.929-1), libsub-name-perl (= 0.27-1+b3), libsub-quote-perl (= 2.006008-1), libsub-uplevel-perl (= 0.2800-3), libsyntax-keyword-junction-perl (= 0.003009-1), libsystemd0 (= 256.6-1), libtask-weaken-perl (= 1.06-2), libtasn1-6 (= 4.19.0-3+b2), libtcl8.6 (= 8.6.14+dfsg-1), libterm-encoding-perl (= 0.03-2), libterm-readkey-perl (= 2.38-2+b4), libtest-deep-perl (= 1.204-1), libtest-differences-perl (= 0.71-1), libtest-exception-perl (= 0.43-3), libtest-file-perl (= 1.993-1), libtest-files-perl (= 0.26-1), libtest-most-perl (= 0.38-1), libtest-output-perl (= 1.034-1), libtest-warn-perl (= 0.37-2), libtest2-suite-perl (= 0.000163-1), libtext-csv-perl (= 2.04-1), libtext-diff-perl (= 1.45-2), libtext-glob-perl (= 0.11-3), libtext-template-perl (= 1.61-1), libthai-data (= 0.1.29-2), libthai0 (= 0.1.29-2), libthrowable-perl (= 1.001-2), libtie-ixhash-perl (= 1.23-4), libtiff6 (= 4.5.1+git230720-5), libtimedate-perl (= 2.3300-2), libtinfo6 (= 6.5-2), libtingea0 (= 21-361-2+b1), libtirpc-common (= 1.3.4+ds-1.3), libtirpc3t64 (= 1.3.4+ds-1.3), libtk8.6 (= 8.6.14-1), libtool (= 2.4.7-7), libtry-tiny-perl (= 0.32-1), libtsan2 (= 14.2.0-5), libtype-tiny-perl (= 2.004000-1), libubsan1 (= 14.2.0-5), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256.6-1), libunistring5 (= 1.2-1), liburi-perl (= 5.29-1), libuuid1 (= 2.40.2-8), libuv1t64 (= 1.48.0-6), libvariable-magic-perl (= 0.64-1+b1), libwebp7 (= 1.4.0-0.1), libwww-perl (= 6.77-1), libwww-robotrules-perl (= 6.02-1), libx11-6 (= 2:1.8.7-1+b1), libx11-data (= 2:1.8.7-1), libxau6 (= 1:1.0.9-1+b1), libxcb-render0 (= 1.17.0-2), libxcb-shm0 (= 1.17.0-2), libxcb1 (= 1.17.0-2), libxdmcp6 (= 1:1.1.2-3+b1), libxext6 (= 2:1.3.4-1+b1), libxft2 (= 2.3.6-1+b1), libxml-parser-perl (= 2.47-1+b3), libxml-writer-perl (= 0.900-2), libxml2 (= 2.12.7+dfsg-3+b1), libxrender1 (= 1:0.9.10-1.1+b1), libxss1 (= 1:1.2.3-1+b1), libxstring-perl (= 0.005-2+b4), libxt6t64 (= 1:1.2.1-1.2), libyaml-tiny-perl (= 1.74-1), libzstd1 (= 1.5.6+dfsg-1), linux-libc-dev (= 6.10.9-1), m4 (= 1.4.19-4), mafft (= 7.505-1), make (= 4.3-4.1), man-db (= 2.13.0-1), mawk (= 1.3.4.20240905-1), mcl (= 1:22-282+ds-2), media-types (= 10.1.0), ncbi-blast+ (= 2.16.0+ds-6), ncbi-data (= 6.1.20170106+dfsg2-4), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), netbase (= 6.4), openssl (= 3.3.2-1), openssl-provider-legacy (= 3.3.2-1), parallel (= 20240222+ds-2), patch (= 2.7.6-7), perl (= 5.40.0-5), perl-base (= 5.40.0-5), perl-modules-5.40 (= 5.40.0-5), perl-openssl-defaults (= 7+b2), po-debconf (= 1.0.21+nmu1), prank (= 0.0.170427+dfsg-3), procps (= 2:4.0.4-5), python3 (= 3.12.5-1+b1), python3-minimal (= 3.12.5-1+b1), python3.12 (= 3.12.6-1), python3.12-minimal (= 3.12.6-1), r-base-core (= 4.4.1-3), readline-common (= 8.2-5), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.24), sysstat (= 12.7.5-2), sysvinit-utils (= 3.10-2), tar (= 1.35+dfsg-3), tzdata (= 2024a-4), ucf (= 3.0043+nmu1), unzip (= 6.0-28), usr-is-merged (= 39), util-linux (= 2.40.2-8), x11-common (= 1:7.7+23.1), xdg-utils (= 1.1.3-4.1), xz-utils (= 5.6.2-2), zip (= 3.0-14), zlib1g (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1573220227" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ roary_3.13.0+dfsg-1_all.deb --------------------------- new Debian package, version 2.0. size 172956 bytes: control archive=6132 bytes. 1489 bytes, 19 lines control 16882 bytes, 195 lines md5sums Package: roary Version: 3.13.0+dfsg-1 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 669 Depends: perl:any, bioperl (>= 1.7.4), libarray-utils-perl, libdigest-md5-file-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, r-cran-ggplot2, mafft, fasttree Section: science Priority: optional Homepage: http://sanger-pathogens.github.io/Roary/ Description: high speed stand alone pan genome pipeline Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (as produced, for instance, by Prokka) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM. Roary is not intended for meta-genomics or for comparing extremely diverse sets of genomes. drwxr-xr-x root/root 0 2019-11-08 13:37 ./ drwxr-xr-x root/root 0 2019-11-08 13:37 ./usr/ drwxr-xr-x root/root 0 2019-11-08 13:37 ./usr/bin/ -rwxr-xr-x root/root 969 2019-11-08 13:37 ./usr/bin/create_pan_genome -rwxr-xr-x root/root 3198 2019-11-08 13:37 ./usr/bin/create_pan_genome_plots -rwxr-xr-x root/root 950 2019-11-08 13:37 ./usr/bin/extract_proteome_from_gff -rwxr-xr-x root/root 839 2019-11-08 13:37 ./usr/bin/iterative_cdhit -rwxr-xr-x root/root 1043 2019-11-08 13:37 ./usr/bin/pan_genome_assembly_statistics -rwxr-xr-x root/root 1157 2019-11-08 13:37 ./usr/bin/pan_genome_core_alignment -rwxr-xr-x root/root 934 2019-11-08 13:37 ./usr/bin/pan_genome_post_analysis -rwxr-xr-x root/root 1042 2019-11-08 13:37 ./usr/bin/pan_genome_reorder_spreadsheet -rwxr-xr-x root/root 1030 2019-11-08 13:37 ./usr/bin/parallel_all_against_all_blastp -rwxr-xr-x root/root 1109 2019-11-08 13:37 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4407 2019-11-08 13:37 ./usr/share/perl5/Bio/Roary/ReorderSpreadsheet.pm -rw-r--r-- root/root 1766 2019-11-08 13:37 ./usr/share/perl5/Bio/Roary/SampleOrder.pm -rw-r--r-- root/root 1599 2019-11-08 13:37 ./usr/share/perl5/Bio/Roary/SequenceLengths.pm -rw-r--r-- root/root 4493 2019-11-08 13:37 ./usr/share/perl5/Bio/Roary/SortFasta.pm -rw-r--r-- root/root 8854 2019-11-08 13:37 ./usr/share/perl5/Bio/Roary/SplitGroups.pm -rw-r--r-- root/root 2329 2019-11-08 13:37 ./usr/share/perl5/Bio/Roary/SpreadsheetRole.pm -rw-r--r-- root/root 2909 2019-11-08 13:37 ./usr/share/perl5/Bio/Roary/UniqueGenesPerSample.pm +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 10512 Build-Time: 30 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 39 Job: /srv/debomatic/incoming/roary_3.13.0+dfsg-1.dsc Machine Architecture: amd64 Package: roary Package-Time: 75 Source-Version: 3.13.0+dfsg-1 Space: 10512 Status: successful Version: 3.13.0+dfsg-1 -------------------------------------------------------------------------------- Finished at 2024-09-16T17:03:46Z Build needed 00:01:15, 10512k disk space