Fri Aug 4 18:38:38 UTC 2023 I: starting to build roary/bullseye/amd64 on jenkins on '2023-08-04 18:38' Fri Aug 4 18:38:38 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_13/3951/console.log Fri Aug 4 18:38:38 UTC 2023 I: Downloading source for bullseye/roary=3.13.0+dfsg-1 --2023-08-04 18:38:38-- http://cdn-fastly.deb.debian.org/debian/pool/main/r/roary/roary_3.13.0%2bdfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2501 (2.4K) [text/prs.lines.tag] Saving to: ‘roary_3.13.0+dfsg-1.dsc’ 0K .. 100% 164M=0s 2023-08-04 18:38:38 (164 MB/s) - ‘roary_3.13.0+dfsg-1.dsc’ saved [2501/2501] Fri Aug 4 18:38:38 UTC 2023 I: roary_3.13.0+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: roary Binary: roary Architecture: all Version: 3.13.0+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Sascha Steinbiss Homepage: http://sanger-pathogens.github.io/Roary/ Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/roary Vcs-Git: https://salsa.debian.org/med-team/roary.git Testsuite: autopkgtest Build-Depends: debhelper (>= 12~), dh-dist-zilla, libdist-zilla-plugin-podweaver-perl, bioperl (>= 1.7.4), libarray-utils-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, mafft, fasttree Build-Depends-Indep: perl Package-List: roary deb science optional arch=all Checksums-Sha1: ec41e9813412b1e168328131cabc91ae1ea06162 207348 roary_3.13.0+dfsg.orig.tar.xz 00f683879e2465a2f91d2214d806d3209ace2dcd 6612 roary_3.13.0+dfsg-1.debian.tar.xz Checksums-Sha256: 5450fe6f4bab8b27829d2ec6836c0a8c9a38d42b3891fab29b10a9587dee2fd1 207348 roary_3.13.0+dfsg.orig.tar.xz f316c055c6c368084b80133c39749d78c70f229ecb1e5a8134ee35c4e7d1e830 6612 roary_3.13.0+dfsg-1.debian.tar.xz Files: fe3935332843c9d4dfb4d4c5cb9080a6 207348 roary_3.13.0+dfsg.orig.tar.xz 5e189111d062819d48d66eff830c7c36 6612 roary_3.13.0+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAl3FcvUACgkQ6NN64vCf SHIkCw//bXPQle1oBgKz8vCLiooiAPBtRcz6YLBaHWO3ZdkMiGa2H/05t98nAaxE luasIS44vFXJggCWEce7DvGAhu6VPlLjhZirZfHlGl/PISyJsYvH2/chaYbaslVF Ql/KG0lx5NUDp1aaPtoRrv2KDcqeJsTNXRmyel3yuSwsHJvtPee4f1aBIV0QjVDB 3NJu5hUCTKtC9P42Qaz/YrXJKoWIEI2jl8oaj8PygRSvL+238bnowDPTJNyQmS/j FiubtiuwsDNiKglVNHO8nyLJG7+0MinpKYl5jGtT3sqrASZsLgE01YXY0kS/05el KSEGIIa7yAl0d/k/x9YPx7svWwX0UfomWlrmSI++09r8OAqFbswi0wzXS75hnO7w 7hkKL9VfddKkSDol+ILRKJM6qQuy+fTlQz8HOWNXpXYsEqnOMQ0nHNW9d7nNa38f pjkoPbbqtrMZL6YOuygb3aIuTXfGjZMa3j8pemnx7K8fm2epiefFVYFia46u+bsJ KEtx8vwfYp+voak/r6Edjob/J7EeFI46oYfy5o2u3TGnQ3XOQM00m8pv3os/+g7P dn6NprfUztjCEpzpYfQAFSxqpC/yuPfnbLpy5+y1iqqy3BGXdMBee+Ej9M0p0hRq UD+PbkpQTLTqGjHEymTL8bwTsYARC7V/LQhbyalFKCPBm6fc+Vc= =4hyZ -----END PGP SIGNATURE----- Fri Aug 4 18:38:38 UTC 2023 I: Checking whether the package is not for us Fri Aug 4 18:38:38 UTC 2023 I: Starting 1st build on remote node ionos11-amd64.debian.net. Fri Aug 4 18:38:38 UTC 2023 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Fri Aug 4 18:44:53 UTC 2023 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Aug 4 06:38:41 -12 2023 I: pbuilder-time-stamp: 1691174321 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [roary_3.13.0+dfsg-1.dsc] I: copying [./roary_3.13.0+dfsg.orig.tar.xz] I: copying [./roary_3.13.0+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.uM3bLCUX/trustedkeys.kbx': General error gpgv: Signature made Fri Nov 8 01:51:49 2019 -12 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./roary_3.13.0+dfsg-1.dsc dpkg-source: info: extracting roary in roary-3.13.0+dfsg dpkg-source: info: unpacking roary_3.13.0+dfsg.orig.tar.xz dpkg-source: info: unpacking roary_3.13.0+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying rename_R_script.patch dpkg-source: info: applying use-dz-starter.patch dpkg-source: info: applying use-debian-perl-path.patch dpkg-source: info: applying new-bioperl-require.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1239721/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15 ' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='770d2c547c9a40158924a6965283a8d7' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1239721' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.wCwejBai/pbuilderrc_XCcR --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wCwejBai/b1 --logfile b1/build.log roary_3.13.0+dfsg-1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 6.1.0-10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.38-2 (2023-07-27) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 20 2022 more -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 6 21:25 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jan 20 2022 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/1239721/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 12~), dh-dist-zilla, libdist-zilla-plugin-podweaver-perl, bioperl (>= 1.7.4), libarray-utils-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, mafft, fasttree, perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19707 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 12~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-dist-zilla; however: Package dh-dist-zilla is not installed. pbuilder-satisfydepends-dummy depends on libdist-zilla-plugin-podweaver-perl; however: Package libdist-zilla-plugin-podweaver-perl is not installed. pbuilder-satisfydepends-dummy depends on bioperl (>= 1.7.4); however: Package bioperl is not installed. pbuilder-satisfydepends-dummy depends on libarray-utils-perl; however: Package libarray-utils-perl is not installed. pbuilder-satisfydepends-dummy depends on libenv-path-perl; however: Package libenv-path-perl is not installed. pbuilder-satisfydepends-dummy depends on libexception-class-perl; however: Package libexception-class-perl is not installed. pbuilder-satisfydepends-dummy depends on libfile-find-rule-perl; however: Package libfile-find-rule-perl is not installed. pbuilder-satisfydepends-dummy depends on libfile-grep-perl; however: Package libfile-grep-perl is not installed. pbuilder-satisfydepends-dummy depends on libfile-slurper-perl; however: Package libfile-slurper-perl is not installed. pbuilder-satisfydepends-dummy depends on libfile-which-perl; however: Package libfile-which-perl is not installed. pbuilder-satisfydepends-dummy depends on libfindbin-libs-perl; however: Package libfindbin-libs-perl is not installed. pbuilder-satisfydepends-dummy depends on libgraph-perl; however: Package libgraph-perl is not installed. pbuilder-satisfydepends-dummy depends on libgraph-readwrite-perl; however: Package libgraph-readwrite-perl is not installed. pbuilder-satisfydepends-dummy depends on liblog-log4perl-perl; however: Package liblog-log4perl-perl is not installed. pbuilder-satisfydepends-dummy depends on libmoose-perl; however: Package libmoose-perl is not installed. pbuilder-satisfydepends-dummy depends on libperlio-utf8-strict-perl; however: Package libperlio-utf8-strict-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-most-perl; however: Package libtest-most-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-file-perl; however: Package libtest-file-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-files-perl; however: Package libtest-files-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-output-perl; however: Package libtest-output-perl is not installed. pbuilder-satisfydepends-dummy depends on libtext-csv-perl; however: Package libtext-csv-perl is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on cd-hit; however: Package cd-hit is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on mcl; however: Package mcl is not installed. pbuilder-satisfydepends-dummy depends on parallel; however: Package parallel is not installed. pbuilder-satisfydepends-dummy depends on prank; however: Package prank is not installed. pbuilder-satisfydepends-dummy depends on r-base-core; however: Package r-base-core is not installed. pbuilder-satisfydepends-dummy depends on mafft; however: Package mafft is not installed. pbuilder-satisfydepends-dummy depends on fasttree; however: Package fasttree is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bioperl{a} bsdextrautils{a} ca-certificates{a} cd-hit{a} debhelper{a} dh-autoreconf{a} dh-dist-zilla{a} dh-strip-nondeterminism{a} dwz{a} fasttree{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libalgorithm-c3-perl{a} libalgorithm-diff-perl{a} libaliased-perl{a} libapp-cmd-perl{a} libarchive-zip-perl{a} libarray-utils-perl{a} libautobox-perl{a} libb-hooks-endofscope-perl{a} libb-hooks-op-check-perl{a} libbio-perl-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcapture-tiny-perl{a} libcarp-clan-perl{a} libclass-c3-perl{a} libclass-data-inheritable-perl{a} libclass-inspector-perl{a} libclass-load-perl{a} libclass-load-xs-perl{a} libclass-method-modifiers-perl{a} libclass-singleton-perl{a} libclone-perl{a} libconfig-ini-perl{a} libconfig-mvp-perl{a} libconfig-mvp-reader-ini-perl{a} libcpan-uploader-perl{a} libcpanel-json-xs-perl{a} libcurl4{a} libdata-optlist-perl{a} libdata-section-perl{a} libdata-stag-perl{a} libdatetime-locale-perl{a} libdatetime-perl{a} libdatetime-timezone-perl{a} libdatrie1{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-globaldestruction-perl{a} libdevel-overloadinfo-perl{a} libdevel-stacktrace-perl{a} libdist-checkconflicts-perl{a} libdist-zilla-perl{a} libdist-zilla-plugin-podweaver-perl{a} libdynaloader-functions-perl{a} libelf1{a} libencode-locale-perl{a} libenv-path-perl{a} libeval-closure-perl{a} libexception-class-perl{a} libexpat1{a} libexporter-tiny-perl{a} libfile-copy-recursive-perl{a} libfile-find-rule-perl{a} libfile-grep-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-pushd-perl{a} libfile-sharedir-install-perl{a} libfile-sharedir-perl{a} libfile-slurp-tiny-perl{a} libfile-slurper-perl{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libfindbin-libs-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgetopt-long-descriptive-perl{a} libgfortran5{a} libglib2.0-0{a} libgraph-perl{a} libgraph-readwrite-perl{a} libgraphite2-3{a} libharfbuzz0b{a} libhash-merge-simple-perl{a} libheap-perl{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libice6{a} libicu67{a} libimport-into-perl{a} libio-all-perl{a} libio-html-perl{a} libio-socket-ssl-perl{a} libio-string-perl{a} libio-stringy-perl{a} libio-tiecombine-perl{a} libjbig0{a} libjpeg62-turbo{a} libjson-maybexs-perl{a} libjson-perl{a} liblapack3{a} libldap-2.4-2{a} liblist-moreutils-perl{a} liblist-moreutils-xs-perl{a} liblmdb0{a} liblog-dispatch-array-perl{a} liblog-dispatch-perl{a} liblog-dispatchouli-perl{a} liblog-log4perl-perl{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto3{a} libmbedtls12{a} libmbedx509-0{a} libmd0{a} libmixin-linewise-perl{a} libmodule-implementation-perl{a} libmodule-path-perl{a} libmodule-pluggable-perl{a} libmodule-runtime-conflicts-perl{a} libmodule-runtime-perl{a} libmoo-perl{a} libmoose-autobox-perl{a} libmoose-perl{a} libmoosex-lazyrequire-perl{a} libmoosex-oneargnew-perl{a} libmoosex-role-parameterized-perl{a} libmoosex-setonce-perl{a} libmoosex-types-perl{a} libmoosex-types-perl-perl{a} libmpdec3{a} libmro-compat-perl{a} libnamespace-autoclean-perl{a} libnamespace-clean-perl{a} libncurses6{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libnumber-compare-perl{a} libpackage-deprecationmanager-perl{a} libpackage-stash-perl{a} libpackage-stash-xs-perl{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libparams-classify-perl{a} libparams-util-perl{a} libparams-validate-perl{a} libparams-validationcompiler-perl{a} libparse-yapp-perl{a} libpath-tiny-perl{a} libperl-prereqscanner-perl{a} libperl-version-perl{a} libperlio-utf8-strict-perl{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpod-elemental-perl{a} libpod-elemental-perlmunger-perl{a} libpod-eventual-perl{a} libpod-weaver-perl{a} libppi-perl{a} libprocps8{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librole-hasmessage-perl{a} librole-identifiable-perl{a} librole-tiny-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libscope-guard-perl{a} libsensors-config{a} libsensors5{a} libset-object-perl{a} libsigsegv2{a} libsm6{a} libsoftware-license-perl{a} libspecio-perl{a} libspiffy-perl{a} libssh2-1{a} libstrictures-perl{a} libstring-errf-perl{a} libstring-flogger-perl{a} libstring-formatter-perl{a} libstring-rewriteprefix-perl{a} libstring-truncate-perl{a} libsub-exporter-formethods-perl{a} libsub-exporter-globexporter-perl{a} libsub-exporter-perl{a} libsub-exporter-progressive-perl{a} libsub-identify-perl{a} libsub-install-perl{a} libsub-name-perl{a} libsub-override-perl{a} libsub-quote-perl{a} libsub-uplevel-perl{a} libsyntax-keyword-junction-perl{a} libsyntax-perl{a} libtask-weaken-perl{a} libtcl8.6{a} libterm-encoding-perl{a} libterm-readkey-perl{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-file-perl{a} libtest-files-perl{a} libtest-most-perl{a} libtest-output-perl{a} libtest-warn-perl{a} libtext-csv-perl{a} libtext-diff-perl{a} libtext-glob-perl{a} libtext-template-perl{a} libthai-data{a} libthai0{a} libthrowable-perl{a} libtie-ixhash-perl{a} libtiff5{a} libtimedate-perl{a} libtk8.6{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} liburi-perl{a} libvariable-magic-perl{a} libwebp6{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml-parser-perl{a} libxml-writer-perl{a} libxml2{a} libxrender1{a} libxss1{a} libxstring-perl{a} libxt6{a} libyaml-tiny-perl{a} m4{a} mafft{a} man-db{a} mcl{a} media-types{a} ncbi-blast+{a} ncbi-data{a} netbase{a} openssl{a} parallel{a} perl-openssl-defaults{a} po-debconf{a} prank{a} procps{a} python3{a} python3-minimal{a} python3.9{a} python3.9-minimal{a} r-base-core{a} readline-common{a} sensible-utils{a} sysstat{a} ucf{a} unzip{a} x11-common{a} xdg-utils{a} zip{a} The following packages are RECOMMENDED but will NOT be installed: bash-completion bcron bioperl-run cpanminus cron curl devscripts libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libarchive-tar-wrapper-perl libarray-compare-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libcache-cache-perl libclass-c3-xs-perl libclass-xsaccessor-perl libconvert-binary-c-perl libdata-dump-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libdevel-lexalias-perl libdevel-partialdump-perl libfile-mimeinfo-perl libgd-perl libglib2.0-data libgpm2 libgraphviz-perl libhtml-form-perl libhtml-format-perl libhtml-tableextract-perl libhttp-daemon-perl libipc-shareable-perl libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libmailtools-perl libmime-lite-perl libmldbm-perl libnet-dbus-perl libpod-coverage-trustpod-perl libpostscript-perl libref-util-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl libterm-readline-gnu-perl libterm-ui-perl libtest-cpan-meta-perl libtest-pod-coverage-perl libtest-pod-perl libtext-csv-xs-perl libunicode-utf8-perl libx11-protocol-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libyaml-perl lynx perl-doc perl-tk psmisc publicsuffix r-base-dev r-doc-html r-recommended ruby shared-mime-info systemd systemd-cron wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 303 newly installed, 0 to remove and 0 not upgraded. Need to get 101 MB of archives. After unpacking 337 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 netbase all 6.3 [19.9 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2+deb11u1 [102 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1n-0+deb11u4 [853 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 bedtools amd64 2.30.0+dfsg-1 [663 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libio-string-perl all 1.08-3.1 [11.8 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libdata-stag-perl all 0.14-2 [448 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libbio-perl-perl all 1.7.7-2 [2607 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libexception-class-perl all 1.44-1 [32.3 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libtest-deep-perl all 1.130-1 [49.3 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libtext-diff-perl all 1.45-1 [27.7 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 libtest-differences-perl all 0.67-1 [18.7 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 libsub-uplevel-perl all 0.2800-1.1 [16.5 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libtest-exception-perl all 0.43-1 [18.7 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libtest-warn-perl all 0.36-1 [16.2 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 libtest-most-perl all 0.37-1 [24.9 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 bioperl all 1.7.7-2 [246 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 cd-hit amd64 4.8.1-3 [522 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libparams-util-perl amd64 1.102-1+b1 [25.6 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libsub-install-perl all 0.928-1.1 [10.8 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libdata-optlist-perl all 0.110-1.1 [10.8 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b3 [11.3 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libdynaloader-functions-perl all 0.003-1.1 [12.7 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libdevel-callchecker-perl amd64 0.008-1+b2 [15.9 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libparams-classify-perl amd64 0.015-1+b3 [25.7 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libmodule-implementation-perl all 0.09-1.1 [12.4 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libpackage-stash-perl all 0.39-1 [21.9 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 libclass-load-perl all 0.25-1 [16.1 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 libio-stringy-perl all 2.111-3 [56.5 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 libparams-validate-perl amd64 1.30-1+b1 [68.2 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libsub-exporter-perl all 0.987-1 [47.2 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 libgetopt-long-descriptive-perl all 0.105-1 [28.4 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 libio-tiecombine-perl all 1.005-1.1 [11.1 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libmodule-pluggable-perl all 5.2-1 [25.7 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 libstring-rewriteprefix-perl all 0.008-1 [6980 B] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libapp-cmd-perl all 0.331-1 [63.9 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 libscope-guard-perl all 0.21-1.1 [7876 B] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libautobox-perl amd64 3.0.1-1+b3 [34.4 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 libperlio-utf8-strict-perl amd64 0.008-1+b1 [12.0 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 libmixin-linewise-perl all 0.108-1.1 [13.3 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 libconfig-ini-perl all 1:0.025-1.1 [22.9 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 libclass-load-xs-perl amd64 0.10-1+b5 [14.6 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get: 96 http://deb.debian.org/debian bullseye/main amd64 libdevel-globaldestruction-perl all 0.14-1.1 [8312 B] Get: 97 http://deb.debian.org/debian bullseye/main amd64 libalgorithm-c3-perl all 0.11-1 [11.7 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 libclass-c3-perl all 0.35-1 [22.9 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 libmro-compat-perl all 0.13-1 [12.2 kB] Get: 100 http://deb.debian.org/debian bullseye/main amd64 libsub-identify-perl amd64 0.14-1+b3 [12.0 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 libdevel-overloadinfo-perl all 0.005-1 [7212 B] Get: 102 http://deb.debian.org/debian bullseye/main amd64 libeval-closure-perl all 0.14-1 [11.5 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 libdist-checkconflicts-perl all 0.11-1.1 [10.2 kB] Get: 104 http://deb.debian.org/debian bullseye/main amd64 libmodule-runtime-conflicts-perl all 0.003-1.1 [7156 B] Get: 105 http://deb.debian.org/debian bullseye/main amd64 libsub-name-perl amd64 0.26-1+b1 [13.8 kB] Get: 106 http://deb.debian.org/debian bullseye/main amd64 libpackage-deprecationmanager-perl all 0.17-1.1 [16.6 kB] Get: 107 http://deb.debian.org/debian bullseye/main amd64 libpackage-stash-xs-perl amd64 0.29-1+b2 [20.2 kB] Get: 108 http://deb.debian.org/debian bullseye/main amd64 libmoose-perl amd64 2.2014-2 [802 kB] Get: 109 http://deb.debian.org/debian bullseye/main amd64 libvariable-magic-perl amd64 0.62-1+b3 [45.7 kB] Get: 110 http://deb.debian.org/debian bullseye/main amd64 libb-hooks-endofscope-perl all 0.24-1.1 [18.9 kB] Get: 111 http://deb.debian.org/debian bullseye/main amd64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get: 112 http://deb.debian.org/debian bullseye/main amd64 libnamespace-autoclean-perl all 0.29-1 [15.0 kB] Get: 113 http://deb.debian.org/debian bullseye/main amd64 libmoosex-role-parameterized-perl all 1.11-1 [43.2 kB] Get: 114 http://deb.debian.org/debian bullseye/main amd64 libmoosex-oneargnew-perl all 0.005-1 [7284 B] Get: 115 http://deb.debian.org/debian bullseye/main amd64 libcpanel-json-xs-perl amd64 4.25-1+b1 [129 kB] Get: 116 http://deb.debian.org/debian bullseye/main amd64 libjson-maybexs-perl all 1.004003-1 [13.1 kB] Get: 117 http://deb.debian.org/debian bullseye/main amd64 libstring-formatter-perl all 0.102084-1.1 [20.2 kB] Get: 118 http://deb.debian.org/debian bullseye/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 119 http://deb.debian.org/debian bullseye/main amd64 libstring-errf-perl all 0.008-1.1 [12.8 kB] Get: 120 http://deb.debian.org/debian bullseye/main amd64 librole-hasmessage-perl all 0.006-1.1 [7728 B] Get: 121 http://deb.debian.org/debian bullseye/main amd64 librole-identifiable-perl all 0.007-1 [7332 B] Get: 122 http://deb.debian.org/debian bullseye/main amd64 libclass-method-modifiers-perl all 2.13-1 [19.2 kB] Get: 123 http://deb.debian.org/debian bullseye/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB] Get: 124 http://deb.debian.org/debian bullseye/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 125 http://deb.debian.org/debian bullseye/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get: 126 http://deb.debian.org/debian bullseye/main amd64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get: 127 http://deb.debian.org/debian bullseye/main amd64 libmoo-perl all 2.004004-1 [59.9 kB] Get: 128 http://deb.debian.org/debian bullseye/main amd64 libthrowable-perl all 0.200013-1.1 [14.2 kB] Get: 129 http://deb.debian.org/debian bullseye/main amd64 libtie-ixhash-perl all 1.23-2.1 [11.8 kB] Get: 130 http://deb.debian.org/debian bullseye/main amd64 libconfig-mvp-perl all 2.200012-1 [44.9 kB] Get: 131 http://deb.debian.org/debian bullseye/main amd64 libconfig-mvp-reader-ini-perl all 2.101463-1.1 [6016 B] Get: 132 http://deb.debian.org/debian bullseye/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get: 133 http://deb.debian.org/debian bullseye/main amd64 libfile-homedir-perl all 1.006-1 [43.8 kB] Get: 134 http://deb.debian.org/debian bullseye/main amd64 perl-openssl-defaults amd64 5 [7360 B] Get: 135 http://deb.debian.org/debian bullseye/main amd64 libnet-ssleay-perl amd64 1.88-3+b1 [321 kB] Get: 136 http://deb.debian.org/debian bullseye/main amd64 libio-socket-ssl-perl all 2.069-1 [215 kB] Get: 137 http://deb.debian.org/debian bullseye/main amd64 liburi-perl all 5.08-1 [90.6 kB] Get: 138 http://deb.debian.org/debian bullseye/main amd64 libnet-http-perl all 6.20-1 [25.1 kB] Get: 139 http://deb.debian.org/debian bullseye/main amd64 libencode-locale-perl all 1.05-1.1 [13.2 kB] Get: 140 http://deb.debian.org/debian bullseye/main amd64 libhttp-date-perl all 6.05-1 [10.4 kB] Get: 141 http://deb.debian.org/debian bullseye/main amd64 libfile-listing-perl all 6.14-1 [12.4 kB] Get: 142 http://deb.debian.org/debian bullseye/main amd64 libhtml-tagset-perl all 3.20-4 [13.0 kB] Get: 143 http://deb.debian.org/debian bullseye/main amd64 libhtml-parser-perl amd64 3.75-1+b1 [105 kB] Get: 144 http://deb.debian.org/debian bullseye/main amd64 libhtml-tree-perl all 5.07-2 [213 kB] Get: 145 http://deb.debian.org/debian bullseye/main amd64 libio-html-perl all 1.004-2 [16.1 kB] Get: 146 http://deb.debian.org/debian bullseye/main amd64 liblwp-mediatypes-perl all 6.04-1 [19.9 kB] Get: 147 http://deb.debian.org/debian bullseye/main amd64 libhttp-message-perl all 6.28-1 [79.6 kB] Get: 148 http://deb.debian.org/debian bullseye/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get: 149 http://deb.debian.org/debian bullseye/main amd64 libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get: 150 http://deb.debian.org/debian bullseye/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 151 http://deb.debian.org/debian bullseye/main amd64 libwww-perl all 6.52-1 [192 kB] Get: 152 http://deb.debian.org/debian bullseye/main amd64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get: 153 http://deb.debian.org/debian bullseye/main amd64 libterm-readkey-perl amd64 2.38-1+b2 [27.8 kB] Get: 154 http://deb.debian.org/debian bullseye/main amd64 libcpan-uploader-perl all 0.103015-1 [16.3 kB] Get: 155 http://deb.debian.org/debian bullseye/main amd64 libdata-section-perl all 0.200007-1 [13.4 kB] Get: 156 http://deb.debian.org/debian bullseye/main amd64 libclass-inspector-perl all 1.36-1 [19.6 kB] Get: 157 http://deb.debian.org/debian bullseye/main amd64 libfile-sharedir-perl all 1.118-1 [17.3 kB] Get: 158 http://deb.debian.org/debian bullseye/main amd64 libparams-validationcompiler-perl all 0.30-1 [31.6 kB] Get: 159 http://deb.debian.org/debian bullseye/main amd64 libxstring-perl amd64 0.005-1+b1 [8260 B] Get: 160 http://deb.debian.org/debian bullseye/main amd64 libspecio-perl all 0.47-1 [145 kB] Get: 161 http://deb.debian.org/debian bullseye/main amd64 libdatetime-locale-perl all 1:1.31-1 [2604 kB] Get: 162 http://deb.debian.org/debian bullseye/main amd64 libclass-singleton-perl all 1.6-1 [13.5 kB] Get: 163 http://deb.debian.org/debian bullseye/main amd64 libdatetime-timezone-perl all 1:2.47-1+2023c [276 kB] Get: 164 http://deb.debian.org/debian bullseye/main amd64 libdatetime-perl amd64 2:1.54-1 [120 kB] Get: 165 http://deb.debian.org/debian bullseye/main amd64 libfile-copy-recursive-perl all 0.45-1 [21.2 kB] Get: 166 http://deb.debian.org/debian bullseye/main amd64 libnumber-compare-perl all 0.03-1.1 [6956 B] Get: 167 http://deb.debian.org/debian bullseye/main amd64 libtext-glob-perl all 0.11-1 [8888 B] Get: 168 http://deb.debian.org/debian bullseye/main amd64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get: 169 http://deb.debian.org/debian bullseye/main amd64 libfile-pushd-perl all 1.016-1 [13.9 kB] Get: 170 http://deb.debian.org/debian bullseye/main amd64 libfile-sharedir-install-perl all 0.13-1.1 [12.3 kB] Get: 171 http://deb.debian.org/debian bullseye/main amd64 libhash-merge-simple-perl all 0.051-2.1 [8004 B] Get: 172 http://deb.debian.org/debian bullseye/main amd64 libjson-perl all 4.03000-1 [88.6 kB] Get: 173 http://deb.debian.org/debian bullseye/main amd64 liblog-dispatch-perl all 2.70-1 [78.4 kB] Get: 174 http://deb.debian.org/debian bullseye/main amd64 liblog-dispatch-array-perl all 1.003-1 [5696 B] Get: 175 http://deb.debian.org/debian bullseye/main amd64 libstring-flogger-perl all 1.101245-2 [6788 B] Get: 176 http://deb.debian.org/debian bullseye/main amd64 libsub-exporter-globexporter-perl all 0.005-1 [7784 B] Get: 177 http://deb.debian.org/debian bullseye/main amd64 liblog-dispatchouli-perl all 2.022-1 [27.4 kB] Get: 178 http://deb.debian.org/debian bullseye/main amd64 libexporter-tiny-perl all 1.002002-1 [37.8 kB] Get: 179 http://deb.debian.org/debian bullseye/main amd64 liblist-moreutils-xs-perl amd64 0.430-2 [40.9 kB] Get: 180 http://deb.debian.org/debian bullseye/main amd64 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get: 181 http://deb.debian.org/debian bullseye/main amd64 libsyntax-perl all 0.004-1.1 [6548 B] Get: 182 http://deb.debian.org/debian bullseye/main amd64 libsyntax-keyword-junction-perl all 0.003008-1.1 [11.2 kB] Get: 183 http://deb.debian.org/debian bullseye/main amd64 libmoose-autobox-perl all 0.16-1 [52.5 kB] Get: 184 http://deb.debian.org/debian bullseye/main amd64 libaliased-perl all 0.34-1.1 [14.1 kB] Get: 185 http://deb.debian.org/debian bullseye/main amd64 libmoosex-lazyrequire-perl all 0.11-1.1 [8928 B] Get: 186 http://deb.debian.org/debian bullseye/main amd64 libmoosex-setonce-perl all 0.200002-1.1 [6344 B] Get: 187 http://deb.debian.org/debian bullseye/main amd64 libcarp-clan-perl all 6.08-1 [15.6 kB] Get: 188 http://deb.debian.org/debian bullseye/main amd64 libsub-exporter-formethods-perl all 0.100052-1 [7598 B] Get: 189 http://deb.debian.org/debian bullseye/main amd64 libmoosex-types-perl all 0.50-1 [54.2 kB] Get: 190 http://deb.debian.org/debian bullseye/main amd64 libmoosex-types-perl-perl all 0.101343-1.1 [7612 B] Get: 191 http://deb.debian.org/debian bullseye/main amd64 libpath-tiny-perl all 0.118-1 [53.5 kB] Get: 192 http://deb.debian.org/debian bullseye/main amd64 libmodule-path-perl all 0.19-1.1 [12.3 kB] Get: 193 http://deb.debian.org/debian bullseye/main amd64 libclone-perl amd64 0.45-1+b1 [15.4 kB] Get: 194 http://deb.debian.org/debian bullseye/main amd64 libtask-weaken-perl all 1.06-1 [9252 B] Get: 195 http://deb.debian.org/debian bullseye/main amd64 libppi-perl all 1.270-1 [317 kB] Get: 196 http://deb.debian.org/debian bullseye/main amd64 libperl-prereqscanner-perl all 1.023-1 [35.8 kB] Get: 197 http://deb.debian.org/debian bullseye/main amd64 libfile-slurp-tiny-perl all 0.004-1 [7288 B] Get: 198 http://deb.debian.org/debian bullseye/main amd64 libperl-version-perl all 1.013-2 [28.0 kB] Get: 199 http://deb.debian.org/debian bullseye/main amd64 libtext-template-perl all 1.59-1 [54.3 kB] Get: 200 http://deb.debian.org/debian bullseye/main amd64 libsoftware-license-perl all 0.103014-2 [113 kB] Get: 201 http://deb.debian.org/debian bullseye/main amd64 libterm-encoding-perl all 0.03-1 [5300 B] Get: 202 http://deb.debian.org/debian bullseye/main amd64 libyaml-tiny-perl all 1.73-1 [32.3 kB] Get: 203 http://deb.debian.org/debian bullseye/main amd64 libdist-zilla-perl all 6.017-1 [342 kB] Get: 204 http://deb.debian.org/debian bullseye/main amd64 dh-dist-zilla all 1.4.1 [17.9 kB] Get: 205 http://deb.debian.org/debian bullseye/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get: 206 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 207 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get: 208 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1+deb11u1 [418 kB] Get: 209 http://deb.debian.org/debian bullseye/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 210 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 211 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get: 212 http://deb.debian.org/debian bullseye/main amd64 fontconfig amd64 2.13.1-4.2 [417 kB] Get: 213 http://deb.debian.org/debian bullseye/main amd64 libarray-utils-perl all 0.5-1.1 [5796 B] Get: 214 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3 [153 kB] Get: 215 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 216 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get: 217 http://deb.debian.org/debian bullseye/main amd64 libpixman-1-0 amd64 0.40.0-1.1~deb11u1 [543 kB] Get: 218 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 219 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 220 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 221 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1 [311 kB] Get: 222 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1 [772 kB] Get: 223 http://deb.debian.org/debian bullseye/main amd64 libxcb-render0 amd64 1.14-3 [111 kB] Get: 224 http://deb.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get: 225 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get: 226 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 227 http://deb.debian.org/debian bullseye/main amd64 libcairo2 amd64 1.16.0-5 [694 kB] Get: 228 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get: 229 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get: 230 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get: 231 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 232 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 233 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 234 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 235 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u7 [346 kB] Get: 236 http://deb.debian.org/debian bullseye/main amd64 libdatrie1 amd64 0.2.13-1 [42.7 kB] Get: 237 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 238 http://deb.debian.org/debian bullseye/main amd64 libpod-eventual-perl all 0.094001-1.1 [12.6 kB] Get: 239 http://deb.debian.org/debian bullseye/main amd64 libstring-truncate-perl all 1.100602-1.1 [9760 B] Get: 240 http://deb.debian.org/debian bullseye/main amd64 libpod-elemental-perl all 0.103005-1 [61.9 kB] Get: 241 http://deb.debian.org/debian bullseye/main amd64 libpod-elemental-perlmunger-perl all 0.200006-1.1 [10.4 kB] Get: 242 http://deb.debian.org/debian bullseye/main amd64 libpod-weaver-perl all 4.015-1 [64.6 kB] Get: 243 http://deb.debian.org/debian bullseye/main amd64 libdist-zilla-plugin-podweaver-perl all 4.008-1.1 [9096 B] Get: 244 http://deb.debian.org/debian bullseye/main amd64 libenv-path-perl all 0.19-2 [19.5 kB] Get: 245 http://deb.debian.org/debian bullseye/main amd64 libfile-grep-perl all 0.02-1.1 [7904 B] Get: 246 http://deb.debian.org/debian bullseye/main amd64 libfile-slurper-perl all 0.012-1 [8344 B] Get: 247 http://deb.debian.org/debian bullseye/main amd64 libfindbin-libs-perl all 2.190.02-1 [30.3 kB] Get: 248 http://deb.debian.org/debian bullseye/main amd64 libfribidi0 amd64 1.0.8-2+deb11u1 [64.9 kB] Get: 249 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 250 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1 [1370 kB] Get: 251 http://deb.debian.org/debian bullseye/main amd64 libheap-perl all 0.80-3 [34.2 kB] Get: 252 http://deb.debian.org/debian bullseye/main amd64 libset-object-perl amd64 1.41-1 [40.1 kB] Get: 253 http://deb.debian.org/debian bullseye/main amd64 libgraph-perl all 1:0.9716-2 [109 kB] Get: 254 http://deb.debian.org/debian bullseye/main amd64 libspiffy-perl all 0.46-1 [25.7 kB] Get: 255 http://deb.debian.org/debian bullseye/main amd64 libio-all-perl all 0.87-1 [66.7 kB] Get: 256 http://deb.debian.org/debian bullseye/main amd64 libparse-yapp-perl all 1.21-2 [46.9 kB] Get: 257 http://deb.debian.org/debian bullseye/main amd64 libxml-parser-perl amd64 2.46-2 [206 kB] Get: 258 http://deb.debian.org/debian bullseye/main amd64 libxml-writer-perl all 0.900-1 [29.9 kB] Get: 259 http://deb.debian.org/debian bullseye/main amd64 libgraph-readwrite-perl all 2.09-1.1 [44.9 kB] Get: 260 http://deb.debian.org/debian bullseye/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 261 http://deb.debian.org/debian bullseye/main amd64 libharfbuzz0b amd64 2.7.4-1 [1471 kB] Get: 262 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get: 263 http://deb.debian.org/debian bullseye/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get: 264 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 265 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get: 266 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3 [2166 kB] Get: 267 http://deb.debian.org/debian bullseye/main amd64 liblmdb0 amd64 0.9.24-1 [45.0 kB] Get: 268 http://deb.debian.org/debian bullseye/main amd64 liblog-log4perl-perl all 1.54-1 [378 kB] Get: 269 http://deb.debian.org/debian bullseye/main amd64 libmbedcrypto3 amd64 2.16.9-0.1 [219 kB] Get: 270 http://deb.debian.org/debian bullseye/main amd64 libmbedx509-0 amd64 2.16.9-0.1 [109 kB] Get: 271 http://deb.debian.org/debian bullseye/main amd64 libmbedtls12 amd64 2.16.9-0.1 [139 kB] Get: 272 http://deb.debian.org/debian bullseye/main amd64 libthai-data all 0.1.28-3 [170 kB] Get: 273 http://deb.debian.org/debian bullseye/main amd64 libthai0 amd64 0.1.28-3 [54.2 kB] Get: 274 http://deb.debian.org/debian bullseye/main amd64 libpango-1.0-0 amd64 1.46.2-3 [191 kB] Get: 275 http://deb.debian.org/debian bullseye/main amd64 libpangoft2-1.0-0 amd64 1.46.2-3 [62.2 kB] Get: 276 http://deb.debian.org/debian bullseye/main amd64 libpangocairo-1.0-0 amd64 1.46.2-3 [50.6 kB] Get: 277 http://deb.debian.org/debian bullseye/main amd64 libpaper1 amd64 1.1.28+b1 [21.6 kB] Get: 278 http://deb.debian.org/debian bullseye/main amd64 libpaper-utils amd64 1.1.28+b1 [18.3 kB] Get: 279 http://deb.debian.org/debian bullseye/main amd64 libsensors-config all 1:3.6.0-7 [32.3 kB] Get: 280 http://deb.debian.org/debian bullseye/main amd64 libsensors5 amd64 1:3.6.0-7 [52.3 kB] Get: 281 http://deb.debian.org/debian bullseye/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 282 http://deb.debian.org/debian bullseye/main amd64 libtcl8.6 amd64 8.6.11+dfsg-1 [1018 kB] Get: 283 http://deb.debian.org/debian bullseye/main amd64 libtest-file-perl all 1.444-1 [24.2 kB] Get: 284 http://deb.debian.org/debian bullseye/main amd64 libtest-files-perl all 0.15-1 [12.0 kB] Get: 285 http://deb.debian.org/debian bullseye/main amd64 libtest-output-perl all 1.033-1 [16.8 kB] Get: 286 http://deb.debian.org/debian bullseye/main amd64 libtext-csv-perl all 2.00-1 [105 kB] Get: 287 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1 [258 kB] Get: 288 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1+deb11u4 [290 kB] Get: 289 http://deb.debian.org/debian bullseye/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get: 290 http://deb.debian.org/debian bullseye/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get: 291 http://deb.debian.org/debian bullseye/main amd64 libtk8.6 amd64 8.6.11-2 [780 kB] Get: 292 http://deb.debian.org/debian bullseye/main amd64 libxt6 amd64 1:1.2.0-1 [189 kB] Get: 293 http://deb.debian.org/debian bullseye/main amd64 mafft amd64 7.475-1 [1051 kB] Get: 294 http://deb.debian.org/debian bullseye/main amd64 mcl amd64 1:14-137+ds-9+b1 [586 kB] Get: 295 http://deb.debian.org/debian bullseye/main amd64 ncbi-data all 6.1.20170106+dfsg1-9 [3556 kB] Get: 296 http://deb.debian.org/debian bullseye/main amd64 ncbi-blast+ amd64 2.11.0+ds-1 [11.3 MB] Get: 297 http://deb.debian.org/debian bullseye/main amd64 sysstat amd64 12.5.2-2 [603 kB] Get: 298 http://deb.debian.org/debian bullseye/main amd64 parallel all 20161222-1.1 [306 kB] Get: 299 http://deb.debian.org/debian bullseye/main amd64 prank amd64 0.0.170427+dfsg-3 [395 kB] Get: 300 http://deb.debian.org/debian bullseye/main amd64 zip amd64 3.0-12 [232 kB] Get: 301 http://deb.debian.org/debian bullseye/main amd64 unzip amd64 6.0-26+deb11u1 [172 kB] Get: 302 http://deb.debian.org/debian bullseye/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 303 http://deb.debian.org/debian bullseye/main amd64 r-base-core amd64 4.0.4-1 [25.1 MB] Fetched 101 MB in 7s (13.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19707 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. 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Setting up libio-stringy-perl (2.111-3) ... Setting up libhtml-tagset-perl (3.20-4) ... Setting up libtest-file-perl (1.444-1) ... Setting up unzip (6.0-26+deb11u1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libfile-slurp-tiny-perl (0.004-1) ... Setting up libheap-perl (0.80-3) ... Setting up liblwp-mediatypes-perl (6.04-1) ... Setting up x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libtry-tiny-perl (0.30-1) ... Setting up libsensors-config (1:3.6.0-7) ... Setting up libnghttp2-14:amd64 (1.43.0-1) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up perl-openssl-defaults:amd64 (5) ... Setting up gettext-base (0.21-4) ... Setting up libclass-singleton-perl (1.6-1) ... Setting up libencode-locale-perl (1.05-1.1) ... Setting up libfindbin-libs-perl (2.190.02-1) ... 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Setting up libbsd0:amd64 (0.11.3-1) ... Setting up libautobox-perl (3.0.1-1+b3) ... Setting up libelf1:amd64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... 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 (2.30.0+dfsg-1) ... Setting up liburi-perl (5.08-1) ... Setting up libprocps8:amd64 (2:3.3.17-5) ... Setting up prank (0.0.170427+dfsg-3) ... Setting up libtext-csv-perl (2.00-1) ... Setting up libnet-ssleay-perl (1.88-3+b1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libhttp-date-perl (6.05-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.9.0-3) ... 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 libxcb1:amd64 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libfile-listing-perl (6.14-1) ... Setting up libtool (2.4.6-15) ... Setting up libxcb-render0:amd64 (1.14-3) ... Setting up libmbedx509-0:amd64 (2.16.9-0.1) ... Setting up liblist-moreutils-perl (0.430-2) ... Setting up libtest-warn-perl (0.36-1) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libmbedtls12:amd64 (2.16.9-0.1) ... Setting up libtest-differences-perl (0.67-1) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up libnet-http-perl (6.20-1) ... Setting up m4 (1.4.18-5) ... Setting up libxcb-shm0:amd64 (1.14-3) ... Setting up libexception-class-perl (1.44-1) ... Setting up libio-all-perl (0.87-1) ... Setting up libclass-c3-perl (0.35-1) ... Setting up libgraph-perl (1:0.9716-2) ... Setting up libdevel-callchecker-perl (0.008-1+b2) ... Setting up libtest-files-perl (0.15-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libthai0:amd64 (0.1.28-3) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libtest-exception-perl (0.43-1) ... Setting up libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Setting up libppi-perl (1.270-1) ... Setting up libdata-optlist-perl (0.110-1.1) ... Setting up ucf (3.0043) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libhtml-parser-perl (3.75-1+b1) ... Setting up procps (2:3.3.17-5) ... Setting up libcurl4:amd64 (7.74.0-1.3+deb11u7) ... Setting up libx11-6:amd64 (2:1.7.2-1) ... Setting up libharfbuzz0b:amd64 (2.7.4-1) ... Setting up libmro-compat-perl (0.13-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up sysstat (12.5.2-2) ... 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 (2.069-1) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libsub-exporter-perl (0.987-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up libhttp-message-perl (6.28-1) ... Setting up libeval-closure-perl (0.14-1) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libstring-truncate-perl (1.100602-1.1) ... Setting up libpaper1:amd64 (1.1.28+b1) ... Creating config file /etc/papersize with new version Setting up libstring-flogger-perl (1.101245-2) ... Setting up libhttp-negotiate-perl (6.01-1) ... Setting up libparams-validationcompiler-perl (0.30-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libtest-most-perl (0.37-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-2) ... Setting up libparams-classify-perl (0.015-1+b3) ... Setting up libxext6:amd64 (2:1.3.3-1.1) ... Setting up libsub-exporter-formethods-perl (0.100052-1) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libmixin-linewise-perl (0.108-1.1) ... Setting up libconfig-ini-perl (1:0.025-1.1) ... Setting up dh-autoreconf (20) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libdist-checkconflicts-perl (0.11-1.1) ... Setting up libtest-output-perl (1.033-1) ... Setting up libxt6:amd64 (1:1.2.0-1) ... Setting up libstring-formatter-perl (0.102084-1.1) ... Setting up parallel (20161222-1.1) ... Setting up libdata-section-perl (0.200007-1) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up libsub-exporter-globexporter-perl (0.005-1) ... Setting up libstring-rewriteprefix-perl (0.008-1) ... Setting up python3.9 (3.9.2-1) ... Setting up bioperl (1.7.7-2) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.2-2) ... Setting up libmodule-implementation-perl (0.09-1.1) ... Setting up libpackage-stash-perl (0.39-1) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libmoo-perl (2.004004-1) ... Setting up libtk8.6:amd64 (8.6.11-2) ... Setting up libpango-1.0-0:amd64 (1.46.2-3) ... Setting up debhelper (13.3.4) ... Setting up libpod-eventual-perl (0.094001-1.1) ... Setting up python3 (3.9.2-3) ... Setting up libmodule-runtime-conflicts-perl (0.003-1.1) ... Setting up libcairo2:amd64 (1.16.0-5) ... Setting up libsoftware-license-perl (0.103014-2) ... Setting up libclass-load-perl (0.25-1) ... Setting up libstring-errf-perl (0.008-1.1) ... Setting up ncbi-blast+ (2.11.0+ds-1) ... Setting up libspecio-perl (0.47-1) ... Setting up libpackage-deprecationmanager-perl (0.17-1.1) ... Setting up libdevel-overloadinfo-perl (0.005-1) ... Setting up libclass-load-xs-perl (0.10-1+b5) ... Setting up libpangoft2-1.0-0:amd64 (1.46.2-3) ... Setting up libparams-validate-perl:amd64 (1.30-1+b1) ... Setting up libb-hooks-endofscope-perl (0.24-1.1) ... Setting up libpangocairo-1.0-0:amd64 (1.46.2-3) ... Setting up libthrowable-perl (0.200013-1.1) ... Setting up libmoose-perl (2.2014-2) ... Setting up r-base-core (4.0.4-1) ... Creating config file /etc/R/Renviron with new version Setting up libnamespace-clean-perl (0.27-1) ... Setting up libmoosex-setonce-perl (0.200002-1.1) ... Setting up libsyntax-perl (0.004-1.1) ... Setting up libgetopt-long-descriptive-perl (0.105-1) ... Setting up librole-identifiable-perl (0.007-1) ... Setting up libnamespace-autoclean-perl (0.29-1) ... Setting up libdatetime-locale-perl (1:1.31-1) ... Setting up libmoosex-role-parameterized-perl (1.11-1) ... Setting up libapp-cmd-perl (0.331-1) ... Setting up librole-hasmessage-perl (0.006-1.1) ... Setting up libperl-prereqscanner-perl (1.023-1) ... Setting up libdatetime-timezone-perl (1:2.47-1+2023c) ... Setting up libmoosex-types-perl (0.50-1) ... Setting up libmoosex-oneargnew-perl (0.005-1) ... Setting up libmoosex-lazyrequire-perl (0.11-1.1) ... Setting up libsyntax-keyword-junction-perl (0.003008-1.1) ... Setting up liblog-dispatch-perl (2.70-1) ... Setting up libconfig-mvp-perl (2.200012-1) ... Setting up libdatetime-perl:amd64 (2:1.54-1) ... Setting up libpod-elemental-perl (0.103005-1) ... Setting up libmoose-autobox-perl (0.16-1) ... Setting up libmoosex-types-perl-perl (0.101343-1.1) ... Setting up libconfig-mvp-reader-ini-perl (2.101463-1.1) ... Setting up liblog-dispatch-array-perl (1.003-1) ... Setting up libpod-elemental-perlmunger-perl (0.200006-1.1) ... Setting up liblog-dispatchouli-perl (2.022-1) ... Setting up libpod-weaver-perl (4.015-1) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up libwww-perl (6.52-1) ... Setting up libcpan-uploader-perl (0.103015-1) ... Setting up libdist-zilla-perl (6.017-1) ... Setting up libdist-zilla-plugin-podweaver-perl (4.008-1.1) ... Setting up libxml-parser-perl:amd64 (2.46-2) ... Setting up dh-dist-zilla (1.4.1) ... Setting up libgraph-readwrite-perl (2.09-1.1) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/roary-3.13.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../roary_3.13.0+dfsg-1_source.changes dpkg-buildpackage: info: source package roary dpkg-buildpackage: info: source version 3.13.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with dist-zilla dh_dzil_clean dh_clean debian/rules build dh build --with dist-zilla dh_update_autotools_config dh_autoreconf debian/rules override_dh_dzil_build make[1]: Entering directory '/build/roary-3.13.0+dfsg' mv bin/create_pan_genome_plots.R bin/create_pan_genome_plots dh_dzil_build -- [DZ] beginning to build Bio-Roary [DZ] writing Bio-Roary in .build/debian-build [DZ] built in .build/debian-build make[1]: Leaving directory '/build/roary-3.13.0+dfsg' dh_auto_configure -D .build/debian-build cd .build/debian-build && perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -fdebug-prefix-map=/build/roary-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/build/roary-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro" Warning: prerequisite Digest::MD5::File 0 not found. Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::Roary Writing MYMETA.yml and MYMETA.json dh_auto_build -D .build/debian-build cd .build/debian-build && make -j15 make[1]: Entering directory '/build/roary-3.13.0+dfsg/.build/debian-build' cp lib/Bio/Roary/AccessoryBinaryFasta.pm blib/lib/Bio/Roary/AccessoryBinaryFasta.pm cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.pm cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm cp lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm cp lib/Bio/Roary/AnnotateGroups.pm blib/lib/Bio/Roary/AnnotateGroups.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/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm cp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.pm cp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm cp lib/Bio/Roary/CommandLine/AssemblyStatistics.pm blib/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm cp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm cp lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm blib/lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm cp lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm blib/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm cp lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm cp lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.pm cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.pm cp lib/Bio/Roary/AccessoryClustering.pm blib/lib/Bio/Roary/AccessoryClustering.pm cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm cp lib/Bio/Roary/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm cp lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.pm cp lib/Bio/Roary/Output/EMBLHeaderCommon.pm blib/lib/Bio/Roary/Output/EMBLHeaderCommon.pm cp lib/Bio/Roary/GeneNamesFromGFF.pm blib/lib/Bio/Roary/GeneNamesFromGFF.pm cp lib/Bio/Roary/External/Mafft.pm blib/lib/Bio/Roary/External/Mafft.pm cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pm cp lib/Bio/Roary/External/Mcl.pm blib/lib/Bio/Roary/External/Mcl.pm cp lib/Bio/Roary/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pm cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.pm cp lib/Bio/Roary/JobRunner/Parallel.pm blib/lib/Bio/Roary/JobRunner/Parallel.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/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/GroupMultifasta.pm blib/lib/Bio/Roary/Output/GroupMultifasta.pm cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm cp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm cp lib/Bio/Roary/UniqueGenesPerSample.pm blib/lib/Bio/Roary/UniqueGenesPerSample.pm cp lib/Bio/Roary/PresenceAbsenceMatrix.pm blib/lib/Bio/Roary/PresenceAbsenceMatrix.pm cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm cp lib/Bio/Roary/ReorderSpreadsheet.pm blib/lib/Bio/Roary/ReorderSpreadsheet.pm cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm cp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm cp lib/Bio/Roary/SpreadsheetRole.pm blib/lib/Bio/Roary/SpreadsheetRole.pm cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm cp lib/Bio/Roary/SequenceLengths.pm blib/lib/Bio/Roary/SequenceLengths.pm cp lib/Bio/Roary/SampleOrder.pm blib/lib/Bio/Roary/SampleOrder.pm cp lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm cp lib/Bio/Roary/Output/QueryGroups.pm blib/lib/Bio/Roary/Output/QueryGroups.pm cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm cp bin/create_pan_genome blib/script/create_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- 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 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 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_post_analysis cp bin/pan_genome_reorder_spreadsheet blib/script/pan_genome_reorder_spreadsheet cp bin/parallel_all_against_all_blastp blib/script/parallel_all_against_all_blastp "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_reorder_spreadsheet "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/parallel_all_against_all_blastp cp bin/protein_alignment_from_nucleotides blib/script/protein_alignment_from_nucleotides "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/protein_alignment_from_nucleotides cp bin/query_pan_genome blib/script/query_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/query_pan_genome cp bin/roary blib/script/roary "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary cp bin/roary-create_pan_genome_plots.R blib/script/roary-create_pan_genome_plots.R cp bin/roary-pan_genome_reorder_spreadsheet blib/script/roary-pan_genome_reorder_spreadsheet "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-create_pan_genome_plots.R "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-pan_genome_reorder_spreadsheet cp bin/roary-query_pan_genome blib/script/roary-query_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-query_pan_genome cp bin/roary-unique_genes_per_sample blib/script/roary-unique_genes_per_sample "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-unique_genes_per_sample cp bin/transfer_annotation_to_groups blib/script/transfer_annotation_to_groups "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/transfer_annotation_to_groups Manifying 16 pod documents Manifying 26 pod documents Manifying 28 pod documents Manifying 25 pod documents make[1]: Leaving directory '/build/roary-3.13.0+dfsg/.build/debian-build' debian/rules override_dh_auto_test make[1]: Entering directory '/build/roary-3.13.0+dfsg' # Hmmm, seems the test is not automatically run anyway by the build system dh_auto_test || true make[1]: Leaving directory '/build/roary-3.13.0+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with dist-zilla dh_testroot dh_prep dh_auto_install -D .build/debian-build cd .build/debian-build && make -j15 install DESTDIR=/build/roary-3.13.0\+dfsg/debian/roary AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/roary-3.13.0+dfsg/.build/debian-build' Manifying 16 pod documents Manifying 26 pod documents Manifying 28 pod documents Manifying 25 pod documents Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SortFasta.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PrepareInputFiles.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SampleOrder.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SequenceLengths.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReformatInputGFFs.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SpreadsheetRole.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SplitGroups.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParallelAllAgainstAllBlast.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PostAnalysis.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReorderSpreadsheet.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParseGFFAnnotationRole.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PresenceAbsenceMatrix.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/UniqueGenesPerSample.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/LookupGeneFiles.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterFullClusters.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/MergeMultifastaAlignments.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/InflateClusters.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFF.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupStatistics.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/IterativeCdhit.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFFs.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GeneNamesFromGFF.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterUnknownsFromFasta.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupLabels.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/OrderGenes.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryClustering.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Exceptions.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ClustersRole.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnalyseGroups.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/BedFromGFFRole.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ChunkFastaFile.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ContigsToGeneIDsFromGFF.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AssemblyStatistics.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnnotateGroups.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CombinedProteome.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryBinaryFasta.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/QC/Report.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Parallel.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Role.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Local.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastas.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/QueryGroups.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaNucleotide.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastasNucleotide.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaProtein.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/NumberOfGroups.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupMultifasta.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/DifferenceBetweenSets.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/BlastIdentityFrequency.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EMBLHeaderCommon.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EmblGroups.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Fasttree.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/IterativeCdhit.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Prank.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/PostAnalysis.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mcl.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mafft.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/GeneAlignmentFromNucleotides.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Makeblastdb.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/CheckTools.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Cdhit.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Blastp.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/CreatePanGenome.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/UniqueGenesPerSample.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryCoreAlignment.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/AssemblyStatistics.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryPostAnalysis.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Roary.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/QueryRoary.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/IterativeCdhit.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Common.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/transfer_annotation_to_groups.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-unique_genes_per_sample.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-query_pan_genome.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-pan_genome_reorder_spreadsheet.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/query_pan_genome.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/protein_alignment_from_nucleotides.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/parallel_all_against_all_blastp.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_reorder_spreadsheet.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_post_analysis.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_core_alignment.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_assembly_statistics.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/iterative_cdhit.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/extract_proteome_from_gff.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome_plots.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::UniqueGenesPerSample.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SpreadsheetRole.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SplitGroups.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SortFasta.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SequenceLengths.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SampleOrder.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReorderSpreadsheet.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReformatInputGFFs.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::QC::Report.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PresenceAbsenceMatrix.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PrepareInputFiles.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PostAnalysis.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ParseGFFAnnotationRole.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ParallelAllAgainstAllBlast.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::QueryGroups.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::NumberOfGroups.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastasNucleotide.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastas.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaProtein.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaNucleotide.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupMultifasta.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::EmblGroups.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::EMBLHeaderCommon.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::DifferenceBetweenSets.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::BlastIdentityFrequency.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::OrderGenes.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::MergeMultifastaAlignments.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::LookupGeneFiles.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Role.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Parallel.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Local.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::IterativeCdhit.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::InflateClusters.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GroupStatistics.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GroupLabels.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GeneNamesFromGFF.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::FilterUnknownsFromFasta.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::FilterFullClusters.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFFs.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFF.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractCoreGenesFromSpreadsheet.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Prank.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::PostAnalysis.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Mcl.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Makeblastdb.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Mafft.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::IterativeCdhit.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::GeneAlignmentFromNucleotides.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Fasttree.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::CheckTools.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Cdhit.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Blastp.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Exceptions.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ContigsToGeneIDsFromGFF.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::UniqueGenesPerSample.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::TransferAnnotationToGroups.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryReorderSpreadsheet.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryPostAnalysis.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryCoreAlignment.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Roary.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::QueryRoary.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::IterativeCdhit.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::GeneAlignmentFromNucleotides.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ExtractProteomeFromGff.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::CreatePanGenome.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Common.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::AssemblyStatistics.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CombinedProteome.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ClustersRole.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ChunkFastaFile.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::BedFromGFFRole.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AssemblyStatistics.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnnotateGroups.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnalyseGroups.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AccessoryClustering.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AccessoryBinaryFasta.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-pan_genome_reorder_spreadsheet Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/transfer_annotation_to_groups Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/protein_alignment_from_nucleotides Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-create_pan_genome_plots.R Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-unique_genes_per_sample Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-query_pan_genome Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_reorder_spreadsheet Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/parallel_all_against_all_blastp Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_post_analysis Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_core_alignment Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_assembly_statistics Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/iterative_cdhit Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/extract_proteome_from_gff Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/query_pan_genome Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/create_pan_genome_plots Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/create_pan_genome make[1]: Leaving directory '/build/roary-3.13.0+dfsg/.build/debian-build' dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'roary' in '../roary_3.13.0+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../roary_3.13.0+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1239721 and its subdirectories I: Current time: Fri Aug 4 06:44:52 -12 2023 I: pbuilder-time-stamp: 1691174692 Fri Aug 4 18:44:53 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Fri Aug 4 18:44:53 UTC 2023 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Fri Aug 4 18:46:14 UTC 2023 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Fri Aug 4 18:46:15 UTC 2023 I: roary_3.13.0+dfsg-1_amd64.changes: Format: 1.8 Date: Fri, 08 Nov 2019 14:37:07 +0100 Source: roary Binary: roary Architecture: all Version: 3.13.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.13.0+dfsg-1) unstable; urgency=medium . * New upstream release. * Use debhelper 12. * Bump Standards-Version. * Update source lintian override location and tags. Checksums-Sha1: 8cc9418190667ef56b4d0565bea001bf5246b487 184560 roary_3.13.0+dfsg-1_all.deb 20654ae608210bacb7eb575300c021e44dabb5bd 14396 roary_3.13.0+dfsg-1_amd64.buildinfo Checksums-Sha256: da57b495ddbe2a0949142ba6c5d0c8643e5d66c97c092d858664935d5fadabaf 184560 roary_3.13.0+dfsg-1_all.deb 5d45fca1273c67d75a105f7345901c8e5ea36338ba97588fb1e8e9cb32addbaa 14396 roary_3.13.0+dfsg-1_amd64.buildinfo Files: 0a7ad9c46eea4885c3e60a42c6bb954f 184560 science optional roary_3.13.0+dfsg-1_all.deb 3ed9290055b4af3329ef8274e6bba313 14396 science optional roary_3.13.0+dfsg-1_amd64.buildinfo Fri Aug 4 18:46:16 UTC 2023 I: diffoscope 243 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.wCwejBai/roary_3.13.0+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.wCwejBai/roary_3.13.0+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.wCwejBai/roary_3.13.0+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.wCwejBai/b1/roary_3.13.0+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.wCwejBai/b2/roary_3.13.0+dfsg-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.293s) 0.293s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.021s) 0.021s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Fri Aug 4 18:46:28 UTC 2023 I: diffoscope 243 found no differences in the changes files, and a .buildinfo file also exists. Fri Aug 4 18:46:28 UTC 2023 I: roary from bullseye built successfully and reproducibly on amd64. Fri Aug 4 18:46:29 UTC 2023 I: Submitting .buildinfo files to external archives: Fri Aug 4 18:46:29 UTC 2023 I: Submitting 16K b1/roary_3.13.0+dfsg-1_amd64.buildinfo.asc Fri Aug 4 18:46:31 UTC 2023 I: Submitting 16K b2/roary_3.13.0+dfsg-1_amd64.buildinfo.asc Fri Aug 4 18:46:32 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Aug 4 18:46:32 UTC 2023 I: Done submitting .buildinfo files. Fri Aug 4 18:46:32 UTC 2023 I: Removing signed roary_3.13.0+dfsg-1_amd64.buildinfo.asc files: removed './b1/roary_3.13.0+dfsg-1_amd64.buildinfo.asc' removed './b2/roary_3.13.0+dfsg-1_amd64.buildinfo.asc'