Diff of the two buildlogs: -- --- b1/build.log 2024-04-30 17:57:50.380335667 +0000 +++ b2/build.log 2024-04-30 18:05:19.033192593 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 30 05:48:05 -12 2024 -I: pbuilder-time-stamp: 1714499285 +I: Current time: Tue Jun 3 14:20:54 +14 2025 +I: pbuilder-time-stamp: 1748910054 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -47,52 +47,84 @@ dpkg-source: info: applying adjust-muscle-test.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/76464/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/783320/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 3 00:21 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/783320/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/783320/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='d151531fd1544d7da406657d1da58368' - 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='76464' - PS1='# ' - PS2='> ' + INVOCATION_ID=ea195305d0124837a94601a082cecb27 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=783320 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.P36OAyXm/pbuilderrc_pHJC --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.P36OAyXm/b1 --logfile b1/build.log bioperl-run_1.7.3-11.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://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.P36OAyXm/pbuilderrc_0VjU --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.P36OAyXm/b2 --logfile b2/build.log bioperl-run_1.7.3-11.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 22 12:43 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/76464/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 27 17:46 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/783320/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -105,7 +137,7 @@ Depends: debhelper-compat (= 13), libmodule-build-perl, perl, bioperl (>= 1.7.4), libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, libfile-sort-perl, libtest-most-perl, libarray-compare-perl, libtree-dagnode-perl, libbio-cluster-perl, libbio-featureio-perl, libconfig-any-perl, libbio-tools-run-alignment-clustalw-perl, libbio-eutilities-perl, libbio-tools-run-remoteblast-perl, amap-align, bedtools, bedtools-test, ncbi-blast+-legacy, clustalw, emboss, exonerate, hmmer, hyphy-pt | hyphy-mpi, infernal, kalign, mafft, muscle, ncoils, phyml, primer3, probcons, python3-pybedtools, raxml, samtools, sim4, tigr-glimmer, wise, fasttree, lagan, pal2nal, pftools, libwww-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 ... 19901 files and directories currently installed.) +(Reading database ... 19725 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: @@ -211,11 +243,11 @@ 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: - amap-align{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bioperl{a} bsdextrautils{a} clustalw{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} emboss{a} emboss-data{a} emboss-lib{a} exonerate{a} fasttree{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} hmmer{a} infernal{a} intltool-debian{a} kalign{a} lagan{a} libabsl20230802{a} libalgorithm-diff-perl{a} libaom3{a} libarchive-zip-perl{a} libarray-compare-perl{a} libavif16{a} libb-hooks-op-check-perl{a} libbio-perl-perl{a} libbio-perl-run-perl{a} libbio-tools-run-alignment-clustalw-perl{a} libbrotli1{a} libbsd0{a} libcapture-tiny-perl{a} libclass-data-inheritable-perl{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libconfig-any-perl{a} libdata-stag-perl{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-stacktrace-perl{a} libdivsufsort3{a} libdynaloader-functions-perl{a} libelf1t64{a} libencode-locale-perl{a} libexception-class-perl{a} libexpat1{a} libexporter-tiny-perl{a} libfile-slurp-perl{a} libfile-slurp-tiny-perl{a} libfile-sort-perl{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libgav1-1{a} libgd3{a} libgfortran5{a} libglib2.0-0t64{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhpdf-2.3.0{a} libhttp-date-perl{a} libhttp-message-perl{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-string-perl{a} libipc-run-perl{a} libjbig0{a} libjpeg62-turbo{a} libldap-2.5-0{a} liblerc4{a} liblwp-mediatypes-perl{a} libmagic-mgc{a} libmagic1t64{a} libmariadb3{a} libmodule-build-perl{a} libmodule-pluggable-perl{a} libmodule-runtime-perl{a} libmoo-perl{a} libparams-classify-perl{a} libpipeline1{a} libpng16-16t64{a} libpq5{a} librav1e0{a} librole-tiny-perl{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsub-override-perl{a} libsub-quote-perl{a} libsub-uplevel-perl{a} libsvtav1enc1d1{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-diff-perl{a} libtiff6{a} libtimedate-perl{a} libtool{a} libtree-dagnode-perl{a} libtype-tiny-perl{a} libuchardet0{a} liburi-perl{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} libxpm4{a} libyuv0{a} m4{a} mafft{a} man-db{a} mariadb-common{a} muscle{a} mysql-common{a} ncoils{a} pal2nal{a} pftools{a} po-debconf{a} primer3{a} probcons{a} raxml{a} sensible-utils{a} sim4{a} tigr-glimmer{a} wise{a} wise-data{a} + amap-align{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bioperl{a} bsdextrautils{a} clustalw{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} emboss{a} emboss-data{a} emboss-lib{a} exonerate{a} fasttree{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} hmmer{a} infernal{a} intltool-debian{a} kalign{a} lagan{a} libabsl20230802{a} libalgorithm-diff-perl{a} libaom3{a} libarchive-zip-perl{a} libarray-compare-perl{a} libavif16{a} libb-hooks-op-check-perl{a} libbio-perl-perl{a} libbio-perl-run-perl{a} libbio-tools-run-alignment-clustalw-perl{a} libbrotli1{a} libbsd0{a} libcapture-tiny-perl{a} libclass-data-inheritable-perl{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcom-err2{a} libconfig-any-perl{a} libdata-stag-perl{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-stacktrace-perl{a} libdivsufsort3{a} libdynaloader-functions-perl{a} libelf1t64{a} libencode-locale-perl{a} libexception-class-perl{a} libexpat1{a} libexporter-tiny-perl{a} libfile-slurp-perl{a} libfile-slurp-tiny-perl{a} libfile-sort-perl{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libgav1-1{a} libgd3{a} libgfortran5{a} libglib2.0-0t64{a} libgssapi-krb5-2{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhpdf-2.3.0{a} libhttp-date-perl{a} libhttp-message-perl{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-string-perl{a} libipc-run-perl{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblerc4{a} liblwp-mediatypes-perl{a} libmagic-mgc{a} libmagic1t64{a} libmariadb3{a} libmodule-build-perl{a} libmodule-pluggable-perl{a} libmodule-runtime-perl{a} libmoo-perl{a} libparams-classify-perl{a} libpipeline1{a} libpng16-16t64{a} libpq5{a} librav1e0{a} librole-tiny-perl{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsub-override-perl{a} libsub-quote-perl{a} libsub-uplevel-perl{a} libsvtav1enc1d1{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-diff-perl{a} libtiff6{a} libtimedate-perl{a} libtool{a} libtree-dagnode-perl{a} libtype-tiny-perl{a} libuchardet0{a} liburi-perl{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} libxpm4{a} libyuv0{a} m4{a} mafft{a} man-db{a} mariadb-common{a} muscle{a} mysql-common{a} ncoils{a} pal2nal{a} pftools{a} po-debconf{a} primer3{a} probcons{a} raxml{a} sensible-utils{a} sim4{a} tigr-glimmer{a} wise{a} wise-data{a} The following packages are RECOMMENDED but will NOT be installed: - bioperl-run curl dialign libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libcache-cache-perl libconfig-general-perl libconfig-tiny-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libgd-perl libglib2.0-data libgraph-perl libgraphviz-perl libheif-plugin-aomenc libheif-plugin-x265 libhtml-parser-perl libhtml-tableextract-perl libio-compress-brotli-perl libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libmodule-signature-perl libnamespace-clean-perl libpod-readme-perl libpostscript-perl libref-util-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsoftware-license-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl libtype-tiny-xs-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-writer-perl libxstring-perl libyaml-libyaml-perl libyaml-perl libyaml-syck-perl lynx paml perl-doc perl-tk ruby shared-mime-info wget xdg-user-dirs -0 packages upgraded, 149 newly installed, 0 to remove and 0 not upgraded. -Need to get 146 MB of archives. After unpacking 799 MB will be used. + bioperl-run curl dialign krb5-locales libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libcache-cache-perl libconfig-general-perl libconfig-tiny-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libgd-perl libglib2.0-data libgraph-perl libgraphviz-perl libheif-plugin-aomenc libheif-plugin-x265 libhtml-parser-perl libhtml-tableextract-perl libio-compress-brotli-perl libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libmodule-signature-perl libnamespace-clean-perl libpod-readme-perl libpostscript-perl libref-util-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsoftware-license-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl libtype-tiny-xs-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-writer-perl libxstring-perl libyaml-libyaml-perl libyaml-perl libyaml-syck-perl lynx paml perl-doc perl-tk ruby shared-mime-info wget xdg-user-dirs +0 packages upgraded, 155 newly installed, 0 to remove and 0 not upgraded. +Need to get 147 MB of archives. After unpacking 801 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: libxml-twig-perl but it is not installable Depends: libbio-cluster-perl but it is not installable @@ -359,13 +391,13 @@ The following NEW packages will be installed: - amap-align{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bedtools-test{a} bioperl{a} bsdextrautils{a} ca-certificates{a} clustalw{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} emboss{a} emboss-data{a} emboss-lib{a} exonerate{a} fasttree{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} hmmer{a} hyphy-common{a} hyphy-mpi{a} ibverbs-providers{a} infernal{a} intltool-debian{a} kalign{a} lagan{a} libabsl20230802{a} libalgorithm-diff-perl{a} libamd-comgr2{a} libamdhip64-5{a} libaom3{a} libarchive-zip-perl{a} libarray-compare-perl{a} libavif16{a} libb-hooks-op-check-perl{a} libbio-asn1-entrezgene-perl{a} libbio-cluster-perl{a} libbio-eutilities-perl{a} libbio-featureio-perl{a} libbio-perl-perl{a} libbio-perl-run-perl{a} libbio-tools-run-alignment-clustalw-perl{a} libbio-tools-run-remoteblast-perl{a} libbio-variation-perl{a} libblis4-serial{a} libbrotli1{a} libbsd0{a} libcapture-tiny-perl{a} libcbor0.10{a} libclass-data-inheritable-perl{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libconfig-any-perl{a} libcurl3t64-gnutls{a} libdata-stag-perl{a} libdav1d7{a} libdb5.3t64{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-stacktrace-perl{a} libdivsufsort3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libdynaloader-functions-perl{a} libedit2{a} libelf1t64{a} libencode-locale-perl{a} libevent-core-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexception-class-perl{a} libexpat1{a} libexporter-tiny-perl{a} libfabric1{a} libfido2-1{a} libfile-listing-perl{a} libfile-slurp-perl{a} libfile-slurp-tiny-perl{a} libfile-sort-perl{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libgav1-1{a} libgd3{a} libgfortran5{a} libglib2.0-0t64{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhpdf-2.3.0{a} libhsa-runtime64-1{a} libhsakmt1{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhts3{a} libhtscodecs2{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhwloc-plugins{a} libhwloc15{a} libibverbs1{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libio-string-perl{a} libipc-run-perl{a} libjbig0{a} libjpeg62-turbo{a} liblapack3{a} libldap-2.5-0{a} liblerc4{a} libllvm17t64{a} liblmdb0{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmariadb3{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libmodule-build-perl{a} libmodule-pluggable-perl{a} libmodule-runtime-perl{a} libmoo-perl{a} libmunge2{a} libncurses6{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libnl-3-200{a} libnl-route-3-200{a} libnuma1{a} libopenmpi3{a} libparams-classify-perl{a} libpciaccess0{a} libpipeline1{a} libpmix2{a} libpng16-16t64{a} libpq5{a} libpsl5t64{a} libpsm-infinipath1{a} libpsm2-2{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} librav1e0{a} librdmacm1t64{a} libreadline8t64{a} librole-tiny-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libssl3t64{a} libsub-override-perl{a} libsub-quote-perl{a} libsub-uplevel-perl{a} libsvtav1enc1d1{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-csv-perl{a} libtext-diff-perl{a} libtiff6{a} libtimedate-perl{a} libtool{a} libtree-dagnode-perl{a} libtry-tiny-perl{a} libtype-tiny-perl{a} libuchardet0{a} libucx0{a} liburi-perl{a} libwebp7{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml-dom-perl{a} libxml-dom-xpath-perl{a} libxml-namespacesupport-perl{a} libxml-parser-perl{a} libxml-perl{a} libxml-regexp-perl{a} libxml-sax-base-perl{a} libxml-sax-expat-perl{a} libxml-sax-perl{a} libxml-simple-perl{a} libxml-twig-perl{a} libxml-writer-perl{a} libxml-xpathengine-perl{a} libxml2{a} libxnvctrl0{a} libxpm4{a} libyuv0{a} libz3-4{a} m4{a} mafft{a} man-db{a} mariadb-common{a} media-types{a} muscle{a} mysql-common{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} ncoils{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} pal2nal{a} perl-openssl-defaults{a} pftools{a} phyml{a} po-debconf{a} primer3{a} probcons{a} python3{a} python3-minimal{a} python3-numpy{a} python3-pkg-resources{a} python3-pybedtools{a} python3-pysam{a} python3-six{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} raxml{a} readline-common{a} samtools{a} sensible-utils{a} sim4{a} tigr-glimmer{a} tzdata{a} ucf{a} wise{a} wise-data{a} + amap-align{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bedtools-test{a} bioperl{a} bsdextrautils{a} ca-certificates{a} clustalw{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} emboss{a} emboss-data{a} emboss-lib{a} exonerate{a} fasttree{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} hmmer{a} hyphy-common{a} hyphy-mpi{a} ibverbs-providers{a} infernal{a} intltool-debian{a} kalign{a} lagan{a} libabsl20230802{a} libalgorithm-diff-perl{a} libamd-comgr2{a} libamdhip64-5{a} libaom3{a} libarchive-zip-perl{a} libarray-compare-perl{a} libavif16{a} libb-hooks-op-check-perl{a} libbio-asn1-entrezgene-perl{a} libbio-cluster-perl{a} libbio-eutilities-perl{a} libbio-featureio-perl{a} libbio-perl-perl{a} libbio-perl-run-perl{a} libbio-tools-run-alignment-clustalw-perl{a} libbio-tools-run-remoteblast-perl{a} libbio-variation-perl{a} libblis4-serial{a} libbrotli1{a} libbsd0{a} libcapture-tiny-perl{a} libcbor0.10{a} libclass-data-inheritable-perl{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcom-err2{a} libconfig-any-perl{a} libcurl3t64-gnutls{a} libdata-stag-perl{a} libdav1d7{a} libdb5.3t64{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-stacktrace-perl{a} libdivsufsort3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libdynaloader-functions-perl{a} libedit2{a} libelf1t64{a} libencode-locale-perl{a} libevent-core-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexception-class-perl{a} libexpat1{a} libexporter-tiny-perl{a} libfabric1{a} libfido2-1{a} libfile-listing-perl{a} libfile-slurp-perl{a} libfile-slurp-tiny-perl{a} libfile-sort-perl{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libgav1-1{a} libgd3{a} libgfortran5{a} libglib2.0-0t64{a} libgssapi-krb5-2{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhpdf-2.3.0{a} libhsa-runtime64-1{a} libhsakmt1{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhts3{a} libhtscodecs2{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhwloc-plugins{a} libhwloc15{a} libibverbs1{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libio-string-perl{a} libipc-run-perl{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap-2.5-0{a} liblerc4{a} libllvm17t64{a} liblmdb0{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmariadb3{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libmodule-build-perl{a} libmodule-pluggable-perl{a} libmodule-runtime-perl{a} libmoo-perl{a} libmunge2{a} libncurses6{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libnl-3-200{a} libnl-route-3-200{a} libnuma1{a} libopenmpi3{a} libparams-classify-perl{a} libpciaccess0{a} libpipeline1{a} libpmix2{a} libpng16-16t64{a} libpq5{a} libpsl5t64{a} libpsm-infinipath1{a} libpsm2-2{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} librav1e0{a} librdmacm1t64{a} libreadline8t64{a} librole-tiny-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libssl3t64{a} libsub-override-perl{a} libsub-quote-perl{a} libsub-uplevel-perl{a} libsvtav1enc1d1{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-csv-perl{a} libtext-diff-perl{a} libtiff6{a} libtimedate-perl{a} libtool{a} libtree-dagnode-perl{a} libtry-tiny-perl{a} libtype-tiny-perl{a} libuchardet0{a} libucx0{a} liburi-perl{a} libwebp7{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml-dom-perl{a} libxml-dom-xpath-perl{a} libxml-namespacesupport-perl{a} libxml-parser-perl{a} libxml-perl{a} libxml-regexp-perl{a} libxml-sax-base-perl{a} libxml-sax-expat-perl{a} libxml-sax-perl{a} libxml-simple-perl{a} libxml-twig-perl{a} libxml-writer-perl{a} libxml-xpathengine-perl{a} libxml2{a} libxnvctrl0{a} libxpm4{a} libyuv0{a} libz3-4{a} m4{a} mafft{a} man-db{a} mariadb-common{a} media-types{a} muscle{a} mysql-common{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} ncoils{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} pal2nal{a} perl-openssl-defaults{a} pftools{a} phyml{a} po-debconf{a} primer3{a} probcons{a} python3{a} python3-minimal{a} python3-numpy{a} python3-pkg-resources{a} python3-pybedtools{a} python3-pysam{a} python3-six{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} raxml{a} readline-common{a} samtools{a} sensible-utils{a} sim4{a} tigr-glimmer{a} tzdata{a} ucf{a} wise{a} wise-data{a} The following packages will be REMOVED: libdb5.3{a} libssl3{a} The following packages are RECOMMENDED but will NOT be installed: - bioperl-run curl dialign libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libcache-cache-perl libconfig-general-perl libconfig-tiny-perl libconvert-binary-c-perl libdata-dump-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libgd-perl libglib2.0-data libgpm2 libgraph-perl libgraphviz-perl libheif-plugin-aomenc libheif-plugin-x265 libhtml-form-perl libhtml-format-perl libhtml-tableextract-perl libhttp-daemon-perl libio-compress-brotli-perl libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libmldbm-perl libmodule-signature-perl libnamespace-clean-perl libpod-readme-perl libpostscript-perl libref-util-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsoftware-license-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl libtext-csv-xs-perl libtext-iconv-perl libtie-ixhash-perl libtype-tiny-xs-perl libxml-libxml-perl libxml-libxslt-perl libxml-sax-writer-perl libxstring-perl libyaml-libyaml-perl libyaml-perl libyaml-syck-perl lynx paml perl-doc perl-tk publicsuffix ruby shared-mime-info wget xauth xdg-user-dirs -0 packages upgraded, 267 newly installed, 2 to remove and 0 not upgraded. -Need to get 290 MB of archives. After unpacking 1410 MB will be used. + bioperl-run curl dialign krb5-locales libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libcache-cache-perl libconfig-general-perl libconfig-tiny-perl libconvert-binary-c-perl libdata-dump-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libgd-perl libglib2.0-data libgpm2 libgraph-perl libgraphviz-perl libheif-plugin-aomenc libheif-plugin-x265 libhtml-form-perl libhtml-format-perl libhtml-tableextract-perl libhttp-daemon-perl libio-compress-brotli-perl libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libmldbm-perl libmodule-signature-perl libnamespace-clean-perl libpod-readme-perl libpostscript-perl libref-util-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsoftware-license-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl libtext-csv-xs-perl libtext-iconv-perl libtie-ixhash-perl libtype-tiny-xs-perl libxml-libxml-perl libxml-libxslt-perl libxml-sax-writer-perl libxstring-perl libyaml-libyaml-perl libyaml-perl libyaml-syck-perl lynx paml perl-doc perl-tk publicsuffix ruby shared-mime-info wget xauth xdg-user-dirs +0 packages upgraded, 273 newly installed, 2 to remove and 0 not upgraded. +Need to get 290 MB of archives. After unpacking 1412 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-7 [697 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libssl3t64 amd64 3.2.1-3 [2244 kB] @@ -400,266 +432,271 @@ Get: 31 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libcbor0.10 amd64 0.10.2-1.1 [27.8 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libfido2-1 amd64 1.14.0-1+b2 [77.7 kB] -Get: 34 http://deb.debian.org/debian trixie/main amd64 openssh-client amd64 1:9.6p1-4 [975 kB] -Get: 35 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] -Get: 36 http://deb.debian.org/debian trixie/main amd64 amap-align amd64 2.2+git20080214.600fc29+dfsg-2 [132 kB] -Get: 37 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] -Get: 38 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] -Get: 39 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] -Get: 40 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] -Get: 41 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] -Get: 42 http://deb.debian.org/debian trixie/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] -Get: 43 http://deb.debian.org/debian trixie/main amd64 bedtools-test all 2.31.1+dfsg-2 [10.9 MB] -Get: 44 http://deb.debian.org/debian trixie/main amd64 libio-string-perl all 1.08-4 [12.1 kB] -Get: 45 http://deb.debian.org/debian trixie/main amd64 libdata-stag-perl all 0.14-3 [448 kB] -Get: 46 http://deb.debian.org/debian trixie/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] -Get: 47 http://deb.debian.org/debian trixie/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] -Get: 48 http://deb.debian.org/debian trixie/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] -Get: 49 http://deb.debian.org/debian trixie/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] -Get: 50 http://deb.debian.org/debian trixie/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB] -Get: 51 http://deb.debian.org/debian trixie/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] -Get: 52 http://deb.debian.org/debian trixie/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] -Get: 53 http://deb.debian.org/debian trixie/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] -Get: 54 http://deb.debian.org/debian trixie/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB] -Get: 55 http://deb.debian.org/debian trixie/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] -Get: 56 http://deb.debian.org/debian trixie/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] -Get: 57 http://deb.debian.org/debian trixie/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] -Get: 58 http://deb.debian.org/debian trixie/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] -Get: 59 http://deb.debian.org/debian trixie/main amd64 bioperl all 1.7.8-1 [246 kB] -Get: 60 http://deb.debian.org/debian trixie/main amd64 clustalw amd64 2.1+lgpl-7 [282 kB] -Get: 61 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] -Get: 62 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] -Get: 63 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] -Get: 64 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] -Get: 65 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] -Get: 66 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] -Get: 67 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] -Get: 68 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] -Get: 69 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] -Get: 70 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] -Get: 71 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] -Get: 72 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] -Get: 73 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] -Get: 74 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] -Get: 75 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] -Get: 76 http://deb.debian.org/debian trixie/main amd64 libaom3 amd64 3.8.2-2 [1869 kB] -Get: 77 http://deb.debian.org/debian trixie/main amd64 libdav1d7 amd64 1.4.1-1 [547 kB] -Get: 78 http://deb.debian.org/debian trixie/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB] -Get: 79 http://deb.debian.org/debian trixie/main amd64 libgav1-1 amd64 0.19.0-2+b1 [351 kB] -Get: 80 http://deb.debian.org/debian trixie/main amd64 librav1e0 amd64 0.7.1-2 [900 kB] -Get: 81 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.3.2-0.4+b1 [108 kB] -Get: 82 http://deb.debian.org/debian trixie/main amd64 libsvtav1enc1d1 amd64 1.7.0+dfsg-2+b1 [2169 kB] -Get: 83 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] -Get: 84 http://deb.debian.org/debian trixie/main amd64 libyuv0 amd64 0.0~git202401110.af6ac82-1 [169 kB] -Get: 85 http://deb.debian.org/debian trixie/main amd64 libavif16 amd64 1.0.4-2 [106 kB] -Get: 86 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] -Get: 87 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] -Get: 88 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] -Get: 89 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] -Get: 90 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] -Get: 91 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] -Get: 92 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] -Get: 93 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-dav1d amd64 1.17.6-1+b2 [9856 B] -Get: 94 http://deb.debian.org/debian trixie/main amd64 libde265-0 amd64 1.0.15-1+b1 [187 kB] -Get: 95 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-libde265 amd64 1.17.6-1+b2 [13.1 kB] -Get: 96 http://deb.debian.org/debian trixie/main amd64 libheif1 amd64 1.17.6-1+b2 [284 kB] -Get: 97 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] -Get: 98 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] -Get: 99 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] -Get: 100 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.3.2-0.4+b1 [308 kB] -Get: 101 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] -Get: 102 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] -Get: 103 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] -Get: 104 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.15-1 [144 kB] -Get: 105 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] -Get: 106 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] -Get: 107 http://deb.debian.org/debian trixie/main amd64 libxpm4 amd64 1:3.5.17-1+b1 [56.1 kB] -Get: 108 http://deb.debian.org/debian trixie/main amd64 libgd3 amd64 2.3.3-9+b3 [125 kB] -Get: 109 http://deb.debian.org/debian trixie/main amd64 libhpdf-2.3.0 amd64 2.3.0+dfsg-1+b2 [346 kB] -Get: 110 http://deb.debian.org/debian trixie/main amd64 mysql-common all 5.8+1.1.0 [6636 B] -Get: 111 http://deb.debian.org/debian trixie/main amd64 mariadb-common all 1:10.11.6-2 [25.2 kB] -Get: 112 http://deb.debian.org/debian trixie/main amd64 libmariadb3 amd64 1:10.11.6-2 [174 kB] -Get: 113 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4+b1 [19.7 kB] -Get: 114 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4+b1 [57.0 kB] -Get: 115 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5+b3 [184 kB] -Get: 116 http://deb.debian.org/debian trixie/main amd64 libpq5 amd64 16.2-1 [216 kB] -Get: 117 http://deb.debian.org/debian trixie/main amd64 emboss-lib amd64 6.6.0+dfsg-15 [2874 kB] -Get: 118 http://deb.debian.org/debian trixie/main amd64 emboss-data all 6.6.0+dfsg-15 [61.1 MB] -Get: 119 http://deb.debian.org/debian trixie/main amd64 emboss amd64 6.6.0+dfsg-15 [1072 kB] -Get: 120 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.78.4-7 [1455 kB] -Get: 121 http://deb.debian.org/debian trixie/main amd64 exonerate amd64 2.4.0-5+b1 [1963 kB] -Get: 122 http://deb.debian.org/debian trixie/main amd64 fasttree amd64 2.1.11-2 [181 kB] -Get: 123 http://deb.debian.org/debian trixie/main amd64 libdivsufsort3 amd64 2.0.1-6 [45.6 kB] -Get: 124 http://deb.debian.org/debian trixie/main amd64 hmmer amd64 3.4+dfsg-2 [1062 kB] -Get: 125 http://deb.debian.org/debian trixie/main amd64 hyphy-common all 2.5.59+dfsg-1 [602 kB] -Get: 126 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.59.0-1 [74.3 kB] -Get: 127 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] -Get: 128 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] -Get: 129 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] -Get: 130 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.7.1-3 [432 kB] -Get: 131 http://deb.debian.org/debian trixie/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [132 kB] -Get: 132 http://deb.debian.org/debian trixie/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [54.1 kB] -Get: 133 http://deb.debian.org/debian trixie/main amd64 libnl-3-200 amd64 3.7.0-0.3 [59.0 kB] -Get: 134 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [181 kB] -Get: 135 http://deb.debian.org/debian trixie/main amd64 libibverbs1 amd64 50.0-2+b1 [61.7 kB] -Get: 136 http://deb.debian.org/debian trixie/main amd64 ibverbs-providers amd64 50.0-2+b1 [342 kB] -Get: 137 http://deb.debian.org/debian trixie/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] -Get: 138 http://deb.debian.org/debian trixie/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] -Get: 139 http://deb.debian.org/debian trixie/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] -Get: 140 http://deb.debian.org/debian trixie/main amd64 librdmacm1t64 amd64 50.0-2+b1 [70.2 kB] -Get: 141 http://deb.debian.org/debian trixie/main amd64 libfabric1 amd64 1.17.0-3+b1 [628 kB] -Get: 142 http://deb.debian.org/debian trixie/main amd64 libhwloc15 amd64 2.10.0-1+b1 [161 kB] -Get: 143 http://deb.debian.org/debian trixie/main amd64 libmunge2 amd64 0.5.15-4 [19.8 kB] -Get: 144 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] -Get: 145 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] -Get: 146 http://deb.debian.org/debian trixie/main amd64 libxnvctrl0 amd64 535.171.04-1 [13.8 kB] -Get: 147 http://deb.debian.org/debian trixie/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b1 [40.3 kB] -Get: 148 http://deb.debian.org/debian trixie/main amd64 libhwloc-plugins amd64 2.10.0-1+b1 [18.0 kB] -Get: 149 http://deb.debian.org/debian trixie/main amd64 libpmix2 amd64 5.0.1-4+b1 [645 kB] -Get: 150 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] -Get: 151 http://deb.debian.org/debian trixie/main amd64 libllvm17t64 amd64 1:17.0.6-11 [23.7 MB] -Get: 152 http://deb.debian.org/debian trixie/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b1 [13.0 MB] -Get: 153 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.120-2 [7688 B] -Get: 154 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] -Get: 155 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] -Get: 156 http://deb.debian.org/debian trixie/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] -Get: 157 http://deb.debian.org/debian trixie/main amd64 libhsa-runtime64-1 amd64 5.7.1-2 [504 kB] -Get: 158 http://deb.debian.org/debian trixie/main amd64 libamdhip64-5 amd64 5.7.1-3 [8760 kB] -Get: 159 http://deb.debian.org/debian trixie/main amd64 libucx0 amd64 1.16.0+ds-5 [1109 kB] -Get: 160 http://deb.debian.org/debian trixie/main amd64 libopenmpi3 amd64 4.1.6-5 [2427 kB] -Get: 161 http://deb.debian.org/debian trixie/main amd64 hyphy-mpi amd64 2.5.59+dfsg-1 [1607 kB] -Get: 162 http://deb.debian.org/debian trixie/main amd64 infernal amd64 1.1.5-2 [5914 kB] -Get: 163 http://deb.debian.org/debian trixie/main amd64 kalign amd64 1:3.4.0-1 [138 kB] -Get: 164 http://deb.debian.org/debian trixie/main amd64 lagan amd64 2.0-10 [184 kB] -Get: 165 http://deb.debian.org/debian trixie/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] -Get: 166 http://deb.debian.org/debian trixie/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b2 [36.3 kB] -Get: 167 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b2 [10.7 kB] -Get: 168 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] -Get: 169 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.008-2+b1 [15.1 kB] -Get: 170 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b2 [22.4 kB] -Get: 171 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] -Get: 172 http://deb.debian.org/debian trixie/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] -Get: 173 http://deb.debian.org/debian trixie/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] -Get: 174 http://deb.debian.org/debian trixie/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] -Get: 175 http://deb.debian.org/debian trixie/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] -Get: 176 http://deb.debian.org/debian trixie/main amd64 libexporter-tiny-perl all 1.006002-1 [38.7 kB] -Get: 177 http://deb.debian.org/debian trixie/main amd64 libtype-tiny-perl all 2.004000-1 [357 kB] -Get: 178 http://deb.debian.org/debian trixie/main amd64 libarray-compare-perl all 3.0.8-1 [14.9 kB] -Get: 179 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.28-1 [98.6 kB] -Get: 180 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] -Get: 181 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] -Get: 182 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] -Get: 183 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] -Get: 184 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] -Get: 185 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.81-1+b1 [99.0 kB] -Get: 186 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] -Get: 187 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.46-1+b1 [13.8 kB] -Get: 188 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] -Get: 189 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] -Get: 190 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] -Get: 191 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] -Get: 192 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] -Get: 193 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] -Get: 194 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-1 [338 kB] -Get: 195 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB] -Get: 196 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] -Get: 197 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] -Get: 198 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] -Get: 199 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] -Get: 200 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB] -Get: 201 http://deb.debian.org/debian trixie/main amd64 libxml-parser-perl amd64 2.47-1+b1 [199 kB] -Get: 202 http://deb.debian.org/debian trixie/main amd64 libxml-twig-perl all 1:3.52-3 [177 kB] -Get: 203 http://deb.debian.org/debian trixie/main amd64 libxml-writer-perl all 0.900-2 [26.8 kB] -Get: 204 http://deb.debian.org/debian trixie/main amd64 libbio-variation-perl all 1.7.5-3 [72.6 kB] -Get: 205 http://deb.debian.org/debian trixie/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] -Get: 206 http://deb.debian.org/debian trixie/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] -Get: 207 http://deb.debian.org/debian trixie/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] -Get: 208 http://deb.debian.org/debian trixie/main amd64 libbio-cluster-perl all 1.7.3-6 [53.3 kB] -Get: 209 http://deb.debian.org/debian trixie/main amd64 libbio-asn1-entrezgene-perl all 1.730-3 [46.3 kB] -Get: 210 http://deb.debian.org/debian trixie/main amd64 libtext-csv-perl all 2.04-1 [112 kB] -Get: 211 http://deb.debian.org/debian trixie/main amd64 libxml-sax-expat-perl all 0.51-2 [11.1 kB] -Get: 212 http://deb.debian.org/debian trixie/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] -Get: 213 http://deb.debian.org/debian trixie/main amd64 libbio-eutilities-perl all 1.77-2 [124 kB] -Get: 214 http://deb.debian.org/debian trixie/main amd64 libfile-slurp-tiny-perl all 0.004-2 [7592 B] -Get: 215 http://deb.debian.org/debian trixie/main amd64 libtree-dagnode-perl all 1.32-1 [61.7 kB] -Get: 216 http://deb.debian.org/debian trixie/main amd64 libxml-perl all 0.08-4 [93.0 kB] -Get: 217 http://deb.debian.org/debian trixie/main amd64 libxml-regexp-perl all 0.04-1.1 [7500 B] -Get: 218 http://deb.debian.org/debian trixie/main amd64 libxml-dom-perl all 1.46-2 [152 kB] -Get: 219 http://deb.debian.org/debian trixie/main amd64 libxml-xpathengine-perl all 0.14-2 [33.5 kB] -Get: 220 http://deb.debian.org/debian trixie/main amd64 libxml-dom-xpath-perl all 0.14-4 [9352 B] -Get: 221 http://deb.debian.org/debian trixie/main amd64 libbio-featureio-perl all 1.6.905-2 [53.2 kB] -Get: 222 http://deb.debian.org/debian trixie/main amd64 libio-pty-perl amd64 1:1.20-1 [34.1 kB] -Get: 223 http://deb.debian.org/debian trixie/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] -Get: 224 http://deb.debian.org/debian trixie/main amd64 libfile-sort-perl all 1.01-3 [21.3 kB] -Get: 225 http://deb.debian.org/debian trixie/main amd64 libbio-perl-run-perl all 1.7.3-11 [528 kB] -Get: 226 http://deb.debian.org/debian trixie/main amd64 libbio-tools-run-alignment-clustalw-perl all 1.7.4-4 [24.5 kB] -Get: 227 http://deb.debian.org/debian trixie/main amd64 libbio-tools-run-remoteblast-perl all 1.7.3-3 [17.5 kB] -Get: 228 http://deb.debian.org/debian trixie/main amd64 libblis4-serial amd64 0.9.0-1+b2 [5282 kB] -Get: 229 http://deb.debian.org/debian trixie/main amd64 libmodule-pluggable-perl all 5.2-5 [23.0 kB] -Get: 230 http://deb.debian.org/debian trixie/main amd64 libconfig-any-perl all 0.33-1 [31.0 kB] -Get: 231 http://deb.debian.org/debian trixie/main amd64 libfile-slurp-perl all 9999.32-2 [26.7 kB] -Get: 232 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] -Get: 233 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] -Get: 234 http://deb.debian.org/debian trixie/main amd64 libhts3 amd64 1.19+ds-1 [447 kB] -Get: 235 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] -Get: 236 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] -Get: 237 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] -Get: 238 http://deb.debian.org/debian trixie/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] -Get: 239 http://deb.debian.org/debian trixie/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] -Get: 240 http://deb.debian.org/debian trixie/main amd64 libmodule-build-perl all 0.423400-2 [252 kB] -Get: 241 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.4+20240414-1 [104 kB] -Get: 242 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.3-1 [1951 kB] -Get: 243 http://deb.debian.org/debian trixie/main amd64 mafft amd64 7.505-1 [1078 kB] -Get: 244 http://deb.debian.org/debian trixie/main amd64 muscle amd64 1:5.1.0-1 [297 kB] -Get: 245 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] -Get: 246 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.12.0+ds-4+b1 [12.5 MB] -Get: 247 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+-legacy all 2.12.0+ds-4 [8956 B] -Get: 248 http://deb.debian.org/debian trixie/main amd64 ncoils amd64 2002-9 [22.2 kB] -Get: 249 http://deb.debian.org/debian trixie/main amd64 openmpi-common all 4.1.6-5 [168 kB] -Get: 250 http://deb.debian.org/debian trixie/main amd64 openmpi-bin amd64 4.1.6-5 [226 kB] -Get: 251 http://deb.debian.org/debian trixie/main amd64 pal2nal all 14.1-3 [17.8 kB] -Get: 252 http://deb.debian.org/debian trixie/main amd64 pftools amd64 3.2.12-1 [24.8 MB] -Get: 253 http://deb.debian.org/debian trixie/main amd64 phyml amd64 3:3.3.20220408-3 [1103 kB] -Get: 254 http://deb.debian.org/debian trixie/main amd64 primer3 amd64 2.6.1-4 [202 kB] -Get: 255 http://deb.debian.org/debian trixie/main amd64 probcons amd64 1.12-14 [119 kB] -Get: 256 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] -Get: 257 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.3-1 [659 kB] -Get: 258 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.24.2-2 [6299 kB] -Get: 259 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.22.0+ds-1+b1 [4110 kB] -Get: 260 http://deb.debian.org/debian trixie/main amd64 python3-six all 1.16.0-6 [16.3 kB] -Get: 261 http://deb.debian.org/debian trixie/main amd64 python3-pybedtools amd64 0.9.1-1+b1 [12.3 MB] -Get: 262 http://deb.debian.org/debian trixie/main amd64 raxml amd64 8.2.13+dfsg-1 [1480 kB] -Get: 263 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.19.2-1 [645 kB] -Get: 264 http://deb.debian.org/debian trixie/main amd64 sim4 amd64 0.0.20121010-8 [359 kB] -Get: 265 http://deb.debian.org/debian trixie/main amd64 tigr-glimmer amd64 3.02b-6+b1 [283 kB] -Get: 266 http://deb.debian.org/debian trixie/main amd64 wise-data all 2.4.1-24 [76.0 kB] -Get: 267 http://deb.debian.org/debian trixie/main amd64 wise amd64 2.4.1-24 [1041 kB] -Fetched 290 MB in 12s (25.1 MB/s) +Get: 34 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.20.1-5+b1 [33.2 kB] +Get: 35 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.0-2.4 [20.2 kB] +Get: 36 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.20.1-5+b1 [80.0 kB] +Get: 37 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] +Get: 38 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.20.1-5+b1 [333 kB] +Get: 39 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.20.1-5+b1 [135 kB] +Get: 40 http://deb.debian.org/debian trixie/main amd64 openssh-client amd64 1:9.6p1-4 [975 kB] +Get: 41 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] +Get: 42 http://deb.debian.org/debian trixie/main amd64 amap-align amd64 2.2+git20080214.600fc29+dfsg-2 [132 kB] +Get: 43 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] +Get: 44 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] +Get: 45 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] +Get: 46 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] +Get: 47 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] +Get: 48 http://deb.debian.org/debian trixie/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] +Get: 49 http://deb.debian.org/debian trixie/main amd64 bedtools-test all 2.31.1+dfsg-2 [10.9 MB] +Get: 50 http://deb.debian.org/debian trixie/main amd64 libio-string-perl all 1.08-4 [12.1 kB] +Get: 51 http://deb.debian.org/debian trixie/main amd64 libdata-stag-perl all 0.14-3 [448 kB] +Get: 52 http://deb.debian.org/debian trixie/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] +Get: 53 http://deb.debian.org/debian trixie/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] +Get: 54 http://deb.debian.org/debian trixie/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] +Get: 55 http://deb.debian.org/debian trixie/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] +Get: 56 http://deb.debian.org/debian trixie/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB] +Get: 57 http://deb.debian.org/debian trixie/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] +Get: 58 http://deb.debian.org/debian trixie/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] +Get: 59 http://deb.debian.org/debian trixie/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] +Get: 60 http://deb.debian.org/debian trixie/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB] +Get: 61 http://deb.debian.org/debian trixie/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] +Get: 62 http://deb.debian.org/debian trixie/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] +Get: 63 http://deb.debian.org/debian trixie/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] +Get: 64 http://deb.debian.org/debian trixie/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] +Get: 65 http://deb.debian.org/debian trixie/main amd64 bioperl all 1.7.8-1 [246 kB] +Get: 66 http://deb.debian.org/debian trixie/main amd64 clustalw amd64 2.1+lgpl-7 [282 kB] +Get: 67 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] +Get: 68 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] +Get: 69 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] +Get: 70 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] +Get: 71 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] +Get: 72 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] +Get: 73 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] +Get: 74 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] +Get: 75 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] +Get: 76 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] +Get: 77 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] +Get: 78 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] +Get: 79 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] +Get: 80 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] +Get: 81 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] +Get: 82 http://deb.debian.org/debian trixie/main amd64 libaom3 amd64 3.8.2-2 [1869 kB] +Get: 83 http://deb.debian.org/debian trixie/main amd64 libdav1d7 amd64 1.4.1-1 [547 kB] +Get: 84 http://deb.debian.org/debian trixie/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB] +Get: 85 http://deb.debian.org/debian trixie/main amd64 libgav1-1 amd64 0.19.0-2+b1 [351 kB] +Get: 86 http://deb.debian.org/debian trixie/main amd64 librav1e0 amd64 0.7.1-2 [900 kB] +Get: 87 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.3.2-0.4+b1 [108 kB] +Get: 88 http://deb.debian.org/debian trixie/main amd64 libsvtav1enc1d1 amd64 1.7.0+dfsg-2+b1 [2169 kB] +Get: 89 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] +Get: 90 http://deb.debian.org/debian trixie/main amd64 libyuv0 amd64 0.0~git202401110.af6ac82-1 [169 kB] +Get: 91 http://deb.debian.org/debian trixie/main amd64 libavif16 amd64 1.0.4-2 [106 kB] +Get: 92 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] +Get: 93 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] +Get: 94 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] +Get: 95 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] +Get: 96 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] +Get: 97 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] +Get: 98 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] +Get: 99 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-dav1d amd64 1.17.6-1+b2 [9856 B] +Get: 100 http://deb.debian.org/debian trixie/main amd64 libde265-0 amd64 1.0.15-1+b1 [187 kB] +Get: 101 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-libde265 amd64 1.17.6-1+b2 [13.1 kB] +Get: 102 http://deb.debian.org/debian trixie/main amd64 libheif1 amd64 1.17.6-1+b2 [284 kB] +Get: 103 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] +Get: 104 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] +Get: 105 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] +Get: 106 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.3.2-0.4+b1 [308 kB] +Get: 107 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] +Get: 108 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] +Get: 109 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] +Get: 110 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.15-1 [144 kB] +Get: 111 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] +Get: 112 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] +Get: 113 http://deb.debian.org/debian trixie/main amd64 libxpm4 amd64 1:3.5.17-1+b1 [56.1 kB] +Get: 114 http://deb.debian.org/debian trixie/main amd64 libgd3 amd64 2.3.3-9+b3 [125 kB] +Get: 115 http://deb.debian.org/debian trixie/main amd64 libhpdf-2.3.0 amd64 2.3.0+dfsg-1+b2 [346 kB] +Get: 116 http://deb.debian.org/debian trixie/main amd64 mysql-common all 5.8+1.1.0 [6636 B] +Get: 117 http://deb.debian.org/debian trixie/main amd64 mariadb-common all 1:10.11.6-2 [25.2 kB] +Get: 118 http://deb.debian.org/debian trixie/main amd64 libmariadb3 amd64 1:10.11.6-2 [174 kB] +Get: 119 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4+b1 [19.7 kB] +Get: 120 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4+b1 [57.0 kB] +Get: 121 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5+b3 [184 kB] +Get: 122 http://deb.debian.org/debian trixie/main amd64 libpq5 amd64 16.2-1 [216 kB] +Get: 123 http://deb.debian.org/debian trixie/main amd64 emboss-lib amd64 6.6.0+dfsg-15 [2874 kB] +Get: 124 http://deb.debian.org/debian trixie/main amd64 emboss-data all 6.6.0+dfsg-15 [61.1 MB] +Get: 125 http://deb.debian.org/debian trixie/main amd64 emboss amd64 6.6.0+dfsg-15 [1072 kB] +Get: 126 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.78.4-7 [1455 kB] +Get: 127 http://deb.debian.org/debian trixie/main amd64 exonerate amd64 2.4.0-5+b1 [1963 kB] +Get: 128 http://deb.debian.org/debian trixie/main amd64 fasttree amd64 2.1.11-2 [181 kB] +Get: 129 http://deb.debian.org/debian trixie/main amd64 libdivsufsort3 amd64 2.0.1-6 [45.6 kB] +Get: 130 http://deb.debian.org/debian trixie/main amd64 hmmer amd64 3.4+dfsg-2 [1062 kB] +Get: 131 http://deb.debian.org/debian trixie/main amd64 hyphy-common all 2.5.59+dfsg-1 [602 kB] +Get: 132 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.59.0-1 [74.3 kB] +Get: 133 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] +Get: 134 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] +Get: 135 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] +Get: 136 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.7.1-3 [432 kB] +Get: 137 http://deb.debian.org/debian trixie/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [132 kB] +Get: 138 http://deb.debian.org/debian trixie/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [54.1 kB] +Get: 139 http://deb.debian.org/debian trixie/main amd64 libnl-3-200 amd64 3.7.0-0.3 [59.0 kB] +Get: 140 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [181 kB] +Get: 141 http://deb.debian.org/debian trixie/main amd64 libibverbs1 amd64 50.0-2+b1 [61.7 kB] +Get: 142 http://deb.debian.org/debian trixie/main amd64 ibverbs-providers amd64 50.0-2+b1 [342 kB] +Get: 143 http://deb.debian.org/debian trixie/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] +Get: 144 http://deb.debian.org/debian trixie/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] +Get: 145 http://deb.debian.org/debian trixie/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] +Get: 146 http://deb.debian.org/debian trixie/main amd64 librdmacm1t64 amd64 50.0-2+b1 [70.2 kB] +Get: 147 http://deb.debian.org/debian trixie/main amd64 libfabric1 amd64 1.17.0-3+b1 [628 kB] +Get: 148 http://deb.debian.org/debian trixie/main amd64 libhwloc15 amd64 2.10.0-1+b1 [161 kB] +Get: 149 http://deb.debian.org/debian trixie/main amd64 libmunge2 amd64 0.5.15-4 [19.8 kB] +Get: 150 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] +Get: 151 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] +Get: 152 http://deb.debian.org/debian trixie/main amd64 libxnvctrl0 amd64 535.171.04-1 [13.8 kB] +Get: 153 http://deb.debian.org/debian trixie/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b1 [40.3 kB] +Get: 154 http://deb.debian.org/debian trixie/main amd64 libhwloc-plugins amd64 2.10.0-1+b1 [18.0 kB] +Get: 155 http://deb.debian.org/debian trixie/main amd64 libpmix2 amd64 5.0.1-4+b1 [645 kB] +Get: 156 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] +Get: 157 http://deb.debian.org/debian trixie/main amd64 libllvm17t64 amd64 1:17.0.6-11 [23.7 MB] +Get: 158 http://deb.debian.org/debian trixie/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b1 [13.0 MB] +Get: 159 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.120-2 [7688 B] +Get: 160 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] +Get: 161 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] +Get: 162 http://deb.debian.org/debian trixie/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] +Get: 163 http://deb.debian.org/debian trixie/main amd64 libhsa-runtime64-1 amd64 5.7.1-2 [504 kB] +Get: 164 http://deb.debian.org/debian trixie/main amd64 libamdhip64-5 amd64 5.7.1-3 [8760 kB] +Get: 165 http://deb.debian.org/debian trixie/main amd64 libucx0 amd64 1.16.0+ds-5 [1109 kB] +Get: 166 http://deb.debian.org/debian trixie/main amd64 libopenmpi3 amd64 4.1.6-5 [2427 kB] +Get: 167 http://deb.debian.org/debian trixie/main amd64 hyphy-mpi amd64 2.5.59+dfsg-1 [1607 kB] +Get: 168 http://deb.debian.org/debian trixie/main amd64 infernal amd64 1.1.5-2 [5914 kB] +Get: 169 http://deb.debian.org/debian trixie/main amd64 kalign amd64 1:3.4.0-1 [138 kB] +Get: 170 http://deb.debian.org/debian trixie/main amd64 lagan amd64 2.0-10 [184 kB] +Get: 171 http://deb.debian.org/debian trixie/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] +Get: 172 http://deb.debian.org/debian trixie/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b2 [36.3 kB] +Get: 173 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b2 [10.7 kB] +Get: 174 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] +Get: 175 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.008-2+b1 [15.1 kB] +Get: 176 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b2 [22.4 kB] +Get: 177 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] +Get: 178 http://deb.debian.org/debian trixie/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] +Get: 179 http://deb.debian.org/debian trixie/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] +Get: 180 http://deb.debian.org/debian trixie/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] +Get: 181 http://deb.debian.org/debian trixie/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] +Get: 182 http://deb.debian.org/debian trixie/main amd64 libexporter-tiny-perl all 1.006002-1 [38.7 kB] +Get: 183 http://deb.debian.org/debian trixie/main amd64 libtype-tiny-perl all 2.004000-1 [357 kB] +Get: 184 http://deb.debian.org/debian trixie/main amd64 libarray-compare-perl all 3.0.8-1 [14.9 kB] +Get: 185 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.28-1 [98.6 kB] +Get: 186 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] +Get: 187 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] +Get: 188 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] +Get: 189 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] +Get: 190 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] +Get: 191 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.81-1+b1 [99.0 kB] +Get: 192 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] +Get: 193 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.46-1+b1 [13.8 kB] +Get: 194 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] +Get: 195 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] +Get: 196 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] +Get: 197 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] +Get: 198 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] +Get: 199 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] +Get: 200 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-1 [338 kB] +Get: 201 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB] +Get: 202 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] +Get: 203 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] +Get: 204 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] +Get: 205 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] +Get: 206 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB] +Get: 207 http://deb.debian.org/debian trixie/main amd64 libxml-parser-perl amd64 2.47-1+b1 [199 kB] +Get: 208 http://deb.debian.org/debian trixie/main amd64 libxml-twig-perl all 1:3.52-3 [177 kB] +Get: 209 http://deb.debian.org/debian trixie/main amd64 libxml-writer-perl all 0.900-2 [26.8 kB] +Get: 210 http://deb.debian.org/debian trixie/main amd64 libbio-variation-perl all 1.7.5-3 [72.6 kB] +Get: 211 http://deb.debian.org/debian trixie/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] +Get: 212 http://deb.debian.org/debian trixie/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] +Get: 213 http://deb.debian.org/debian trixie/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] +Get: 214 http://deb.debian.org/debian trixie/main amd64 libbio-cluster-perl all 1.7.3-6 [53.3 kB] +Get: 215 http://deb.debian.org/debian trixie/main amd64 libbio-asn1-entrezgene-perl all 1.730-3 [46.3 kB] +Get: 216 http://deb.debian.org/debian trixie/main amd64 libtext-csv-perl all 2.04-1 [112 kB] +Get: 217 http://deb.debian.org/debian trixie/main amd64 libxml-sax-expat-perl all 0.51-2 [11.1 kB] +Get: 218 http://deb.debian.org/debian trixie/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] +Get: 219 http://deb.debian.org/debian trixie/main amd64 libbio-eutilities-perl all 1.77-2 [124 kB] +Get: 220 http://deb.debian.org/debian trixie/main amd64 libfile-slurp-tiny-perl all 0.004-2 [7592 B] +Get: 221 http://deb.debian.org/debian trixie/main amd64 libtree-dagnode-perl all 1.32-1 [61.7 kB] +Get: 222 http://deb.debian.org/debian trixie/main amd64 libxml-perl all 0.08-4 [93.0 kB] +Get: 223 http://deb.debian.org/debian trixie/main amd64 libxml-regexp-perl all 0.04-1.1 [7500 B] +Get: 224 http://deb.debian.org/debian trixie/main amd64 libxml-dom-perl all 1.46-2 [152 kB] +Get: 225 http://deb.debian.org/debian trixie/main amd64 libxml-xpathengine-perl all 0.14-2 [33.5 kB] +Get: 226 http://deb.debian.org/debian trixie/main amd64 libxml-dom-xpath-perl all 0.14-4 [9352 B] +Get: 227 http://deb.debian.org/debian trixie/main amd64 libbio-featureio-perl all 1.6.905-2 [53.2 kB] +Get: 228 http://deb.debian.org/debian trixie/main amd64 libio-pty-perl amd64 1:1.20-1 [34.1 kB] +Get: 229 http://deb.debian.org/debian trixie/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] +Get: 230 http://deb.debian.org/debian trixie/main amd64 libfile-sort-perl all 1.01-3 [21.3 kB] +Get: 231 http://deb.debian.org/debian trixie/main amd64 libbio-perl-run-perl all 1.7.3-11 [528 kB] +Get: 232 http://deb.debian.org/debian trixie/main amd64 libbio-tools-run-alignment-clustalw-perl all 1.7.4-4 [24.5 kB] +Get: 233 http://deb.debian.org/debian trixie/main amd64 libbio-tools-run-remoteblast-perl all 1.7.3-3 [17.5 kB] +Get: 234 http://deb.debian.org/debian trixie/main amd64 libblis4-serial amd64 0.9.0-1+b2 [5282 kB] +Get: 235 http://deb.debian.org/debian trixie/main amd64 libmodule-pluggable-perl all 5.2-5 [23.0 kB] +Get: 236 http://deb.debian.org/debian trixie/main amd64 libconfig-any-perl all 0.33-1 [31.0 kB] +Get: 237 http://deb.debian.org/debian trixie/main amd64 libfile-slurp-perl all 9999.32-2 [26.7 kB] +Get: 238 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] +Get: 239 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] +Get: 240 http://deb.debian.org/debian trixie/main amd64 libhts3 amd64 1.19+ds-1 [447 kB] +Get: 241 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] +Get: 242 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] +Get: 243 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] +Get: 244 http://deb.debian.org/debian trixie/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] +Get: 245 http://deb.debian.org/debian trixie/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] +Get: 246 http://deb.debian.org/debian trixie/main amd64 libmodule-build-perl all 0.423400-2 [252 kB] +Get: 247 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.4+20240414-1 [104 kB] +Get: 248 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.3-1 [1951 kB] +Get: 249 http://deb.debian.org/debian trixie/main amd64 mafft amd64 7.505-1 [1078 kB] +Get: 250 http://deb.debian.org/debian trixie/main amd64 muscle amd64 1:5.1.0-1 [297 kB] +Get: 251 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] +Get: 252 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.12.0+ds-4+b1 [12.5 MB] +Get: 253 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+-legacy all 2.12.0+ds-4 [8956 B] +Get: 254 http://deb.debian.org/debian trixie/main amd64 ncoils amd64 2002-9 [22.2 kB] +Get: 255 http://deb.debian.org/debian trixie/main amd64 openmpi-common all 4.1.6-5 [168 kB] +Get: 256 http://deb.debian.org/debian trixie/main amd64 openmpi-bin amd64 4.1.6-5 [226 kB] +Get: 257 http://deb.debian.org/debian trixie/main amd64 pal2nal all 14.1-3 [17.8 kB] +Get: 258 http://deb.debian.org/debian trixie/main amd64 pftools amd64 3.2.12-1 [24.8 MB] +Get: 259 http://deb.debian.org/debian trixie/main amd64 phyml amd64 3:3.3.20220408-3 [1103 kB] +Get: 260 http://deb.debian.org/debian trixie/main amd64 primer3 amd64 2.6.1-4 [202 kB] +Get: 261 http://deb.debian.org/debian trixie/main amd64 probcons amd64 1.12-14 [119 kB] +Get: 262 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] +Get: 263 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.3-1 [659 kB] +Get: 264 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.24.2-2 [6299 kB] +Get: 265 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.22.0+ds-1+b1 [4110 kB] +Get: 266 http://deb.debian.org/debian trixie/main amd64 python3-six all 1.16.0-6 [16.3 kB] +Get: 267 http://deb.debian.org/debian trixie/main amd64 python3-pybedtools amd64 0.9.1-1+b1 [12.3 MB] +Get: 268 http://deb.debian.org/debian trixie/main amd64 raxml amd64 8.2.13+dfsg-1 [1480 kB] +Get: 269 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.19.2-1 [645 kB] +Get: 270 http://deb.debian.org/debian trixie/main amd64 sim4 amd64 0.0.20121010-8 [359 kB] +Get: 271 http://deb.debian.org/debian trixie/main amd64 tigr-glimmer amd64 3.02b-6+b1 [283 kB] +Get: 272 http://deb.debian.org/debian trixie/main amd64 wise-data all 2.4.1-24 [76.0 kB] +Get: 273 http://deb.debian.org/debian trixie/main amd64 wise amd64 2.4.1-24 [1041 kB] +Fetched 290 MB in 37s (7761 kB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: libperl5.38:amd64 depends on libdb5.3. libpam-modules:amd64 depends on libdb5.3. -(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 ... 19901 files and directories currently installed.) +(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 ... 19725 files and directories currently installed.) Removing libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Selecting previously unselected package libdb5.3t64:amd64. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19894 files and directories currently installed.) +(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 ... 19718 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-7_amd64.deb ... Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-7) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-7) ... dpkg: libssl3:amd64: dependency problems, but removing anyway as you requested: - libkrb5-3:amd64 depends on libssl3 (>= 3.0.0). coreutils depends on libssl3 (>= 3.0.0). -(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 ... 19900 files and directories currently installed.) +(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 ... 19724 files and directories currently installed.) Removing libssl3:amd64 (3.1.5-1) ... Selecting previously unselected package libssl3t64:amd64. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19887 files and directories currently installed.) +(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 ... 19711 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.2.1-3_amd64.deb ... Unpacking libssl3t64:amd64 (3.2.1-3) ... Setting up libssl3t64:amd64 (3.2.1-3) ... Selecting previously unselected package libpython3.11-minimal:amd64. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19902 files and directories currently installed.) +(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 ... 19726 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. @@ -672,7 +709,7 @@ Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20218 files and directories currently installed.) +(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 ... 20042 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. @@ -705,7 +742,7 @@ Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21210 files and directories currently installed.) +(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 ... 21034 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:amd64. @@ -762,710 +799,728 @@ Selecting previously unselected package libfido2-1:amd64. Preparing to unpack .../018-libfido2-1_1.14.0-1+b2_amd64.deb ... Unpacking libfido2-1:amd64 (1.14.0-1+b2) ... +Selecting previously unselected package libkrb5support0:amd64. +Preparing to unpack .../019-libkrb5support0_1.20.1-5+b1_amd64.deb ... +Unpacking libkrb5support0:amd64 (1.20.1-5+b1) ... +Selecting previously unselected package libcom-err2:amd64. +Preparing to unpack .../020-libcom-err2_1.47.0-2.4_amd64.deb ... +Unpacking libcom-err2:amd64 (1.47.0-2.4) ... +Selecting previously unselected package libk5crypto3:amd64. +Preparing to unpack .../021-libk5crypto3_1.20.1-5+b1_amd64.deb ... +Unpacking libk5crypto3:amd64 (1.20.1-5+b1) ... +Selecting previously unselected package libkeyutils1:amd64. +Preparing to unpack .../022-libkeyutils1_1.6.3-3_amd64.deb ... +Unpacking libkeyutils1:amd64 (1.6.3-3) ... +Selecting previously unselected package libkrb5-3:amd64. +Preparing to unpack .../023-libkrb5-3_1.20.1-5+b1_amd64.deb ... +Unpacking libkrb5-3:amd64 (1.20.1-5+b1) ... +Selecting previously unselected package libgssapi-krb5-2:amd64. +Preparing to unpack .../024-libgssapi-krb5-2_1.20.1-5+b1_amd64.deb ... +Unpacking libgssapi-krb5-2:amd64 (1.20.1-5+b1) ... Selecting previously unselected package openssh-client. -Preparing to unpack .../019-openssh-client_1%3a9.6p1-4_amd64.deb ... +Preparing to unpack .../025-openssh-client_1%3a9.6p1-4_amd64.deb ... Unpacking openssh-client (1:9.6p1-4) ... Selecting previously unselected package ucf. -Preparing to unpack .../020-ucf_3.0043+nmu1_all.deb ... +Preparing to unpack .../026-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package amap-align. -Preparing to unpack .../021-amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.deb ... +Preparing to unpack .../027-amap-align_2.2+git20080214.600fc29+dfsg-2_amd64.deb ... Unpacking amap-align (2.2+git20080214.600fc29+dfsg-2) ... Selecting previously unselected package m4. -Preparing to unpack .../022-m4_1.4.19-4_amd64.deb ... +Preparing to unpack .../028-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. -Preparing to unpack .../023-autoconf_2.71-3_all.deb ... +Preparing to unpack .../029-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. -Preparing to unpack .../024-autotools-dev_20220109.1_all.deb ... +Preparing to unpack .../030-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. -Preparing to unpack .../025-automake_1%3a1.16.5-1.3_all.deb ... +Preparing to unpack .../031-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. -Preparing to unpack .../026-autopoint_0.21-14_all.deb ... +Preparing to unpack .../032-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... 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Selecting previously unselected package libfile-listing-perl. -Preparing to unpack .../168-libfile-listing-perl_6.16-1_all.deb ... +Preparing to unpack .../174-libfile-listing-perl_6.16-1_all.deb ... Unpacking libfile-listing-perl (6.16-1) ... Selecting previously unselected package libhtml-tagset-perl. -Preparing to unpack .../169-libhtml-tagset-perl_3.24-1_all.deb ... +Preparing to unpack .../175-libhtml-tagset-perl_3.24-1_all.deb ... Unpacking libhtml-tagset-perl (3.24-1) ... Selecting previously unselected package libhtml-parser-perl:amd64. -Preparing to unpack .../170-libhtml-parser-perl_3.81-1+b1_amd64.deb ... +Preparing to unpack .../176-libhtml-parser-perl_3.81-1+b1_amd64.deb ... Unpacking libhtml-parser-perl:amd64 (3.81-1+b1) ... Selecting previously unselected package libhtml-tree-perl. -Preparing to unpack .../171-libhtml-tree-perl_5.07-3_all.deb ... +Preparing to unpack .../177-libhtml-tree-perl_5.07-3_all.deb ... Unpacking libhtml-tree-perl (5.07-3) ... Selecting previously unselected package libclone-perl:amd64. -Preparing to unpack .../172-libclone-perl_0.46-1+b1_amd64.deb ... +Preparing to unpack .../178-libclone-perl_0.46-1+b1_amd64.deb ... Unpacking libclone-perl:amd64 (0.46-1+b1) ... Selecting previously unselected package libio-html-perl. -Preparing to unpack .../173-libio-html-perl_1.004-3_all.deb ... +Preparing to unpack .../179-libio-html-perl_1.004-3_all.deb ... Unpacking libio-html-perl (1.004-3) ... Selecting previously unselected package liblwp-mediatypes-perl. -Preparing to unpack .../174-liblwp-mediatypes-perl_6.04-2_all.deb ... +Preparing to unpack .../180-liblwp-mediatypes-perl_6.04-2_all.deb ... Unpacking liblwp-mediatypes-perl (6.04-2) ... Selecting previously unselected package libhttp-message-perl. -Preparing to unpack .../175-libhttp-message-perl_6.45-1_all.deb ... +Preparing to unpack .../181-libhttp-message-perl_6.45-1_all.deb ... Unpacking libhttp-message-perl (6.45-1) ... 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Unpacking libnet-ssleay-perl:amd64 (1.94-1) ... Selecting previously unselected package libio-socket-ssl-perl. -Preparing to unpack .../180-libio-socket-ssl-perl_2.085-1_all.deb ... +Preparing to unpack .../186-libio-socket-ssl-perl_2.085-1_all.deb ... Unpacking libio-socket-ssl-perl (2.085-1) ... Selecting previously unselected package libnet-http-perl. -Preparing to unpack .../181-libnet-http-perl_6.23-1_all.deb ... +Preparing to unpack .../187-libnet-http-perl_6.23-1_all.deb ... Unpacking libnet-http-perl (6.23-1) ... Selecting previously unselected package liblwp-protocol-https-perl. -Preparing to unpack .../182-liblwp-protocol-https-perl_6.14-1_all.deb ... +Preparing to unpack .../188-liblwp-protocol-https-perl_6.14-1_all.deb ... Unpacking liblwp-protocol-https-perl (6.14-1) ... Selecting previously unselected package libtry-tiny-perl. -Preparing to unpack .../183-libtry-tiny-perl_0.31-2_all.deb ... +Preparing to unpack .../189-libtry-tiny-perl_0.31-2_all.deb ... Unpacking libtry-tiny-perl (0.31-2) ... Selecting previously unselected package libwww-robotrules-perl. -Preparing to unpack .../184-libwww-robotrules-perl_6.02-1_all.deb ... +Preparing to unpack .../190-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. -Preparing to unpack .../185-libwww-perl_6.77-1_all.deb ... +Preparing to unpack .../191-libwww-perl_6.77-1_all.deb ... Unpacking libwww-perl (6.77-1) ... Selecting previously unselected package libxml-parser-perl. -Preparing to unpack .../186-libxml-parser-perl_2.47-1+b1_amd64.deb ... +Preparing to unpack .../192-libxml-parser-perl_2.47-1+b1_amd64.deb ... Unpacking libxml-parser-perl (2.47-1+b1) ... Selecting previously unselected package libxml-twig-perl. -Preparing to unpack .../187-libxml-twig-perl_1%3a3.52-3_all.deb ... +Preparing to unpack .../193-libxml-twig-perl_1%3a3.52-3_all.deb ... Unpacking libxml-twig-perl (1:3.52-3) ... Selecting previously unselected package libxml-writer-perl. -Preparing to unpack .../188-libxml-writer-perl_0.900-2_all.deb ... +Preparing to unpack .../194-libxml-writer-perl_0.900-2_all.deb ... Unpacking libxml-writer-perl (0.900-2) ... Selecting previously unselected package libbio-variation-perl. -Preparing to unpack .../189-libbio-variation-perl_1.7.5-3_all.deb ... +Preparing to unpack .../195-libbio-variation-perl_1.7.5-3_all.deb ... Unpacking libbio-variation-perl (1.7.5-3) ... Selecting previously unselected package libxml-namespacesupport-perl. -Preparing to unpack .../190-libxml-namespacesupport-perl_1.12-2_all.deb ... +Preparing to unpack .../196-libxml-namespacesupport-perl_1.12-2_all.deb ... Unpacking libxml-namespacesupport-perl (1.12-2) ... Selecting previously unselected package libxml-sax-base-perl. -Preparing to unpack .../191-libxml-sax-base-perl_1.09-3_all.deb ... +Preparing to unpack .../197-libxml-sax-base-perl_1.09-3_all.deb ... 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Unpacking libtext-csv-perl (2.04-1) ... Selecting previously unselected package libxml-sax-expat-perl. -Preparing to unpack .../196-libxml-sax-expat-perl_0.51-2_all.deb ... +Preparing to unpack .../202-libxml-sax-expat-perl_0.51-2_all.deb ... Unpacking libxml-sax-expat-perl (0.51-2) ... Selecting previously unselected package libxml-simple-perl. -Preparing to unpack .../197-libxml-simple-perl_2.25-2_all.deb ... +Preparing to unpack .../203-libxml-simple-perl_2.25-2_all.deb ... Unpacking libxml-simple-perl (2.25-2) ... Selecting previously unselected package libbio-eutilities-perl. -Preparing to unpack .../198-libbio-eutilities-perl_1.77-2_all.deb ... +Preparing to unpack .../204-libbio-eutilities-perl_1.77-2_all.deb ... Unpacking libbio-eutilities-perl (1.77-2) ... Selecting previously unselected package libfile-slurp-tiny-perl. -Preparing to unpack .../199-libfile-slurp-tiny-perl_0.004-2_all.deb ... +Preparing to unpack .../205-libfile-slurp-tiny-perl_0.004-2_all.deb ... Unpacking libfile-slurp-tiny-perl (0.004-2) ... Selecting previously unselected package libtree-dagnode-perl. -Preparing to unpack .../200-libtree-dagnode-perl_1.32-1_all.deb ... +Preparing to unpack .../206-libtree-dagnode-perl_1.32-1_all.deb ... Unpacking libtree-dagnode-perl (1.32-1) ... Selecting previously unselected package libxml-perl. -Preparing to unpack .../201-libxml-perl_0.08-4_all.deb ... +Preparing to unpack .../207-libxml-perl_0.08-4_all.deb ... Unpacking libxml-perl (0.08-4) ... Selecting previously unselected package libxml-regexp-perl. -Preparing to unpack .../202-libxml-regexp-perl_0.04-1.1_all.deb ... +Preparing to unpack .../208-libxml-regexp-perl_0.04-1.1_all.deb ... Unpacking libxml-regexp-perl (0.04-1.1) ... Selecting previously unselected package libxml-dom-perl. -Preparing to unpack .../203-libxml-dom-perl_1.46-2_all.deb ... +Preparing to unpack .../209-libxml-dom-perl_1.46-2_all.deb ... Unpacking libxml-dom-perl (1.46-2) ... Selecting previously unselected package libxml-xpathengine-perl. -Preparing to unpack .../204-libxml-xpathengine-perl_0.14-2_all.deb ... +Preparing to unpack .../210-libxml-xpathengine-perl_0.14-2_all.deb ... Unpacking libxml-xpathengine-perl (0.14-2) ... Selecting previously unselected package libxml-dom-xpath-perl. -Preparing to unpack .../205-libxml-dom-xpath-perl_0.14-4_all.deb ... +Preparing to unpack .../211-libxml-dom-xpath-perl_0.14-4_all.deb ... Unpacking libxml-dom-xpath-perl (0.14-4) ... Selecting previously unselected package libbio-featureio-perl. -Preparing to unpack .../206-libbio-featureio-perl_1.6.905-2_all.deb ... +Preparing to unpack .../212-libbio-featureio-perl_1.6.905-2_all.deb ... Unpacking libbio-featureio-perl (1.6.905-2) ... Selecting previously unselected package libio-pty-perl. -Preparing to unpack .../207-libio-pty-perl_1%3a1.20-1_amd64.deb ... +Preparing to unpack .../213-libio-pty-perl_1%3a1.20-1_amd64.deb ... Unpacking libio-pty-perl (1:1.20-1) ... Selecting previously unselected package libipc-run-perl. -Preparing to unpack .../208-libipc-run-perl_20231003.0-2_all.deb ... +Preparing to unpack .../214-libipc-run-perl_20231003.0-2_all.deb ... Unpacking libipc-run-perl (20231003.0-2) ... Selecting previously unselected package libfile-sort-perl. -Preparing to unpack .../209-libfile-sort-perl_1.01-3_all.deb ... +Preparing to unpack .../215-libfile-sort-perl_1.01-3_all.deb ... Unpacking libfile-sort-perl (1.01-3) ... Selecting previously unselected package libbio-perl-run-perl. -Preparing to unpack .../210-libbio-perl-run-perl_1.7.3-11_all.deb ... +Preparing to unpack .../216-libbio-perl-run-perl_1.7.3-11_all.deb ... Unpacking libbio-perl-run-perl (1.7.3-11) ... Selecting previously unselected package libbio-tools-run-alignment-clustalw-perl. -Preparing to unpack .../211-libbio-tools-run-alignment-clustalw-perl_1.7.4-4_all.deb ... +Preparing to unpack .../217-libbio-tools-run-alignment-clustalw-perl_1.7.4-4_all.deb ... Unpacking libbio-tools-run-alignment-clustalw-perl (1.7.4-4) ... Selecting previously unselected package libbio-tools-run-remoteblast-perl. -Preparing to unpack .../212-libbio-tools-run-remoteblast-perl_1.7.3-3_all.deb ... +Preparing to unpack .../218-libbio-tools-run-remoteblast-perl_1.7.3-3_all.deb ... Unpacking libbio-tools-run-remoteblast-perl (1.7.3-3) ... Selecting previously unselected package libblis4-serial:amd64. -Preparing to unpack .../213-libblis4-serial_0.9.0-1+b2_amd64.deb ... +Preparing to unpack .../219-libblis4-serial_0.9.0-1+b2_amd64.deb ... Unpacking libblis4-serial:amd64 (0.9.0-1+b2) ... Selecting previously unselected package libmodule-pluggable-perl. -Preparing to unpack .../214-libmodule-pluggable-perl_5.2-5_all.deb ... +Preparing to unpack .../220-libmodule-pluggable-perl_5.2-5_all.deb ... Unpacking libmodule-pluggable-perl (5.2-5) ... Selecting previously unselected package libconfig-any-perl. -Preparing to unpack .../215-libconfig-any-perl_0.33-1_all.deb ... +Preparing to unpack .../221-libconfig-any-perl_0.33-1_all.deb ... Unpacking libconfig-any-perl (0.33-1) ... Selecting previously unselected package libfile-slurp-perl. -Preparing to unpack .../216-libfile-slurp-perl_9999.32-2_all.deb ... +Preparing to unpack .../222-libfile-slurp-perl_9999.32-2_all.deb ... Unpacking libfile-slurp-perl (9999.32-2) ... Selecting previously unselected package libgfortran5:amd64. -Preparing to unpack .../217-libgfortran5_14-20240330-1_amd64.deb ... +Preparing to unpack .../223-libgfortran5_14-20240330-1_amd64.deb ... Unpacking libgfortran5:amd64 (14-20240330-1) ... Selecting previously unselected package libhtscodecs2:amd64. -Preparing to unpack .../218-libhtscodecs2_1.6.0-1+b1_amd64.deb ... +Preparing to unpack .../224-libhtscodecs2_1.6.0-1+b1_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.6.0-1+b1) ... Selecting previously unselected package libhts3:amd64. -Preparing to unpack .../219-libhts3_1.19+ds-1_amd64.deb ... +Preparing to unpack .../225-libhts3_1.19+ds-1_amd64.deb ... Unpacking libhts3:amd64 (1.19+ds-1) ... Selecting previously unselected package liblapack3:amd64. -Preparing to unpack .../220-liblapack3_3.12.0-3_amd64.deb ... +Preparing to unpack .../226-liblapack3_3.12.0-3_amd64.deb ... Unpacking liblapack3:amd64 (3.12.0-3) ... Selecting previously unselected package liblmdb0:amd64. -Preparing to unpack .../221-liblmdb0_0.9.31-1+b1_amd64.deb ... +Preparing to unpack .../227-liblmdb0_0.9.31-1+b1_amd64.deb ... Unpacking liblmdb0:amd64 (0.9.31-1+b1) ... Selecting previously unselected package libmbedcrypto7t64:amd64. -Preparing to unpack .../222-libmbedcrypto7t64_2.28.8-1_amd64.deb ... +Preparing to unpack .../228-libmbedcrypto7t64_2.28.8-1_amd64.deb ... Unpacking libmbedcrypto7t64:amd64 (2.28.8-1) ... Selecting previously unselected package libmbedx509-1t64:amd64. -Preparing to unpack .../223-libmbedx509-1t64_2.28.8-1_amd64.deb ... +Preparing to unpack .../229-libmbedx509-1t64_2.28.8-1_amd64.deb ... Unpacking libmbedx509-1t64:amd64 (2.28.8-1) ... Selecting previously unselected package libmbedtls14t64:amd64. -Preparing to unpack .../224-libmbedtls14t64_2.28.8-1_amd64.deb ... +Preparing to unpack .../230-libmbedtls14t64_2.28.8-1_amd64.deb ... Unpacking libmbedtls14t64:amd64 (2.28.8-1) ... Selecting previously unselected package libmodule-build-perl. -Preparing to unpack .../225-libmodule-build-perl_0.423400-2_all.deb ... +Preparing to unpack .../231-libmodule-build-perl_0.423400-2_all.deb ... Adding 'diversion of /usr/bin/config_data to /usr/bin/config_data.diverted by libmodule-build-perl' Adding 'diversion of /usr/share/man/man1/config_data.1.gz to /usr/share/man/man1/config_data.diverted.1.gz by libmodule-build-perl' Unpacking libmodule-build-perl (0.423400-2) ... Selecting previously unselected package libncurses6:amd64. -Preparing to unpack .../226-libncurses6_6.4+20240414-1_amd64.deb ... +Preparing to unpack .../232-libncurses6_6.4+20240414-1_amd64.deb ... Unpacking libncurses6:amd64 (6.4+20240414-1) ... Selecting previously unselected package libpython3.12-stdlib:amd64. -Preparing to unpack .../227-libpython3.12-stdlib_3.12.3-1_amd64.deb ... +Preparing to unpack .../233-libpython3.12-stdlib_3.12.3-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.3-1) ... Selecting previously unselected package mafft. -Preparing to unpack .../228-mafft_7.505-1_amd64.deb ... +Preparing to unpack .../234-mafft_7.505-1_amd64.deb ... Unpacking mafft (7.505-1) ... Selecting previously unselected package muscle. -Preparing to unpack .../229-muscle_1%3a5.1.0-1_amd64.deb ... +Preparing to unpack .../235-muscle_1%3a5.1.0-1_amd64.deb ... Unpacking muscle (1:5.1.0-1) ... Selecting previously unselected package ncbi-data. -Preparing to unpack .../230-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... +Preparing to unpack .../236-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... Selecting previously unselected package ncbi-blast+. -Preparing to unpack .../231-ncbi-blast+_2.12.0+ds-4+b1_amd64.deb ... +Preparing to unpack .../237-ncbi-blast+_2.12.0+ds-4+b1_amd64.deb ... Unpacking ncbi-blast+ (2.12.0+ds-4+b1) ... Selecting previously unselected package ncbi-blast+-legacy. -Preparing to unpack .../232-ncbi-blast+-legacy_2.12.0+ds-4_all.deb ... +Preparing to unpack .../238-ncbi-blast+-legacy_2.12.0+ds-4_all.deb ... Unpacking ncbi-blast+-legacy (2.12.0+ds-4) ... Selecting previously unselected package ncoils. -Preparing to unpack .../233-ncoils_2002-9_amd64.deb ... +Preparing to unpack .../239-ncoils_2002-9_amd64.deb ... Unpacking ncoils (2002-9) ... 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Selecting previously unselected package python3-pybedtools. -Preparing to unpack .../246-python3-pybedtools_0.9.1-1+b1_amd64.deb ... +Preparing to unpack .../252-python3-pybedtools_0.9.1-1+b1_amd64.deb ... Unpacking python3-pybedtools (0.9.1-1+b1) ... Selecting previously unselected package raxml. -Preparing to unpack .../247-raxml_8.2.13+dfsg-1_amd64.deb ... +Preparing to unpack .../253-raxml_8.2.13+dfsg-1_amd64.deb ... Unpacking raxml (8.2.13+dfsg-1) ... Selecting previously unselected package samtools. -Preparing to unpack .../248-samtools_1.19.2-1_amd64.deb ... +Preparing to unpack .../254-samtools_1.19.2-1_amd64.deb ... Unpacking samtools (1.19.2-1) ... Selecting previously unselected package sim4. -Preparing to unpack .../249-sim4_0.0.20121010-8_amd64.deb ... +Preparing to unpack .../255-sim4_0.0.20121010-8_amd64.deb ... Unpacking sim4 (0.0.20121010-8) ... Selecting previously unselected package tigr-glimmer. -Preparing to unpack .../250-tigr-glimmer_3.02b-6+b1_amd64.deb ... +Preparing to unpack .../256-tigr-glimmer_3.02b-6+b1_amd64.deb ... Unpacking tigr-glimmer (3.02b-6+b1) ... Selecting previously unselected package wise-data. -Preparing to unpack .../251-wise-data_2.4.1-24_all.deb ... +Preparing to unpack .../257-wise-data_2.4.1-24_all.deb ... Unpacking wise-data (2.4.1-24) ... Selecting previously unselected package wise. -Preparing to unpack .../252-wise_2.4.1-24_amd64.deb ... +Preparing to unpack .../258-wise_2.4.1-24_amd64.deb ... Unpacking wise (2.4.1-24) ... Setting up libhtscodecs2:amd64 (1.6.0-1+b1) ... Setting up media-types (10.1.0) ... @@ -1479,6 +1534,7 @@ Setting up mysql-common (5.8+1.1.0) ... update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libxau6:amd64 (1:1.0.9-1+b1) ... +Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libfile-slurp-perl (9999.32-2) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-4+b1) ... @@ -1517,6 +1573,7 @@ update-alternatives: using /usr/lib/x86_64-linux-gnu/blis-serial/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up ncoils (2002-9) ... Setting up libsvtav1enc1d1:amd64 (1.7.0+dfsg-2+b1) ... +Setting up libcom-err2:amd64 (1.47.0-2.4) ... Setting up hyphy-common (2.5.59+dfsg-1) ... Setting up file (1:5.45-3) ... Setting up muscle (1:5.1.0-1) ... @@ -1525,12 +1582,13 @@ Setting up librav1e0:amd64 (0.7.1-2) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libmodule-build-perl (0.423400-2) ... +Setting up libkrb5support0:amd64 (1.20.1-5+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b1) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Apr 30 17:50:53 UTC 2024. -Universal Time is now: Tue Apr 30 17:50:53 UTC 2024. +Local time is now: Tue Jun 3 00:24:35 UTC 2025. +Universal Time is now: Tue Jun 3 00:24:35 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up mariadb-common (1:10.11.6-2) ... @@ -1565,6 +1623,7 @@ Setting up fonts-dejavu-core (2.37-8) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up wise-data (2.4.1-24) ... +Setting up libk5crypto3:amd64 (1.20.1-5+b1) ... Setting up amap-align (2.2+git20080214.600fc29+dfsg-2) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-4+b1) ... Setting up libgfortran5:amd64 (14-20240330-1) ... @@ -1597,6 +1656,7 @@ Setting up libsub-quote-perl (2.006008-1) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b2) ... +Setting up libkrb5-3:amd64 (1.20.1-5+b1) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... @@ -1656,6 +1716,7 @@ Setting up libllvm17t64:amd64 (1:17.0.6-11) ... Setting up libtest-exception-perl (0.43-3) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... +Setting up libgssapi-krb5-2:amd64 (1.20.1-5+b1) ... Setting up libgav1-1:amd64 (0.19.0-2+b1) ... Setting up ucf (3.0043+nmu1) ... Setting up libreadline8t64:amd64 (8.2-4) ... @@ -1769,7 +1830,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/bioperl-run-1.7.3/ && 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 > ../bioperl-run_1.7.3-11_source.changes +I: user script /srv/workspace/pbuilder/783320/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/783320/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/bioperl-run-1.7.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../bioperl-run_1.7.3-11_source.changes dpkg-buildpackage: info: source package bioperl-run dpkg-buildpackage: info: source version 1.7.3-11 dpkg-buildpackage: info: source distribution unstable @@ -1835,7 +1900,7 @@ gapOpen[] = { 0.01993141696 0.01993141696 } gapExtend[] = { 0.7943345308 0.7943345308 } -Loading sequence file: /tmp/TW0hCdFdZM +Loading sequence file: /tmp/OdI9uP3RqG Computing posterior matrices Building DAG Starting the sequence annealing process @@ -1877,7 +1942,7 @@ ok 11 - can return output format for command 'annotate' ok 12 - result claims to be in correct format for command 'annotate' ok 13 - can return output file for command 'annotate' -ok 14 - file format of '/tmp/7HiZ59NQrU/sBx1sYxL0F.bed' consistent with claim for 'annotate' +ok 14 - file format of '/tmp/oIEqNRC3nh/4htOXbrP8g.bed' consistent with claim for 'annotate' ok 15 - can set want to IO object for command 'annotate' ok 16 - can get the basic object result for command 'annotate' ok 17 - 'returned object is correct for command 'annotate'' isa 'Bio::Root::IO' @@ -1914,7 +1979,7 @@ ok 48 - can return output format for command 'overlap' ok 49 - result claims to be in correct format for command 'overlap' ok 50 - can return output file for command 'overlap' -ok 51 - file format of '/tmp/TBdAO689VW/9s_59418fo.bed' consistent with claim for 'overlap' +ok 51 - file format of '/tmp/pmm7mw0aMG/5UFb7xMXsx.bed' consistent with claim for 'overlap' ok 52 - can set want to IO object for command 'overlap' ok 53 - can get the basic object result for command 'overlap' ok 54 - 'returned object is correct for command 'overlap'' isa 'Bio::Root::IO' @@ -1932,7 +1997,7 @@ ok 66 - can return output format for command 'bam_to_bed' ok 67 - result claims to be in correct format for command 'bam_to_bed' ok 68 - can return output file for command 'bam_to_bed' -ok 69 - file format of '/tmp/un7ErnSpcX/fTNsfAGiak.bed' consistent with claim for 'bam_to_bed' +ok 69 - file format of '/tmp/aZgIkFQgDM/yLPGGN6t_T.bed' consistent with claim for 'bam_to_bed' ok 70 - can set want to IO object for command 'bam_to_bed' ok 71 - can get the basic object result for command 'bam_to_bed' ok 72 - 'returned object is correct for command 'bam_to_bed'' isa 'Bio::Root::IO' @@ -1967,7 +2032,7 @@ ok 101 - can return output format for command 'pair_to_pair' ok 102 - result claims to be in correct format for command 'pair_to_pair' ok 103 - can return output file for command 'pair_to_pair' -ok 104 - file format of '/tmp/V8QXXlTFKP/riyCYdq0t0.bedpe' consistent with claim for 'pair_to_pair' +ok 104 - file format of '/tmp/_pmahjUp5s/Qqx2mDKtUT.bedpe' consistent with claim for 'pair_to_pair' ok 105 - can set want to IO object for command 'pair_to_pair' ok 106 - can get the basic object result for command 'pair_to_pair' ok 107 - 'returned object is correct for command 'pair_to_pair'' isa 'Bio::Root::IO' @@ -2047,7 +2112,7 @@ ok 181 - can return output format for command 'group_by' ok 182 - result claims to be in correct format for command 'group_by' ok 183 - can return output file for command 'group_by' -ok 184 - file format of '/tmp/sxIoymkQeG/Lgk4C4iaow.bed' consistent with claim for 'group_by' +ok 184 - file format of '/tmp/6FdmP0WT_j/Wluj1B2lsr.bed' consistent with claim for 'group_by' ok 185 - can set want to IO object for command 'group_by' ok 186 - can get the basic object result for command 'group_by' ok 187 - 'returned object is correct for command 'group_by'' isa 'Bio::Root::IO' @@ -2065,7 +2130,7 @@ ok 199 - can return output format for command 'shuffle' ok 200 - result claims to be in correct format for command 'shuffle' ok 201 - can return output file for command 'shuffle' -ok 202 - file format of '/tmp/qPe33rddiQ/oJaXXUjYQJ.bed' consistent with claim for 'shuffle' +ok 202 - file format of '/tmp/qrHLS7OtB5/kRhui1Ye8K.bed' consistent with claim for 'shuffle' ok 203 - can set want to IO object for command 'shuffle' ok 204 - can get the basic object result for command 'shuffle' ok 205 - 'returned object is correct for command 'shuffle'' isa 'Bio::Root::IO' @@ -2083,7 +2148,7 @@ ok 217 - can return output format for command 'b12_to_b6' ok 218 - result claims to be in correct format for command 'b12_to_b6' ok 219 - can return output file for command 'b12_to_b6' -ok 220 - file format of '/tmp/4rfb6d4PCE/bzZie_pDMx.bed' consistent with claim for 'b12_to_b6' +ok 220 - file format of '/tmp/2WagkZZVVY/BoOXF1bZiQ.bed' consistent with claim for 'b12_to_b6' ok 221 - can set want to IO object for command 'b12_to_b6' ok 222 - can get the basic object result for command 'b12_to_b6' ok 223 - 'returned object is correct for command 'b12_to_b6'' isa 'Bio::Root::IO' @@ -2123,7 +2188,7 @@ ok 253 - can return output format for command 'slop' ok 254 - result claims to be in correct format for command 'slop' ok 255 - can return output file for command 'slop' -ok 256 - file format of '/tmp/VG8H_j57Bx/lXM743FsmS.bed' consistent with claim for 'slop' +ok 256 - file format of '/tmp/OwU3epxWGK/trR5WvNcNd.bed' consistent with claim for 'slop' ok 257 - can set want to IO object for command 'slop' ok 258 - can get the basic object result for command 'slop' ok 259 - 'returned object is correct for command 'slop'' isa 'Bio::Root::IO' @@ -2141,7 +2206,7 @@ ok 271 - can return output format for command 'closest' ok 272 - result claims to be in correct format for command 'closest' ok 273 - can return output file for command 'closest' -ok 274 - file format of '/tmp/XfsiVJC9dS/yRtFgERqg8.bedpe' consistent with claim for 'closest' +ok 274 - file format of '/tmp/juMMT0z84D/5_UFZ6YX6F.bedpe' consistent with claim for 'closest' ok 275 - can set want to IO object for command 'closest' ok 276 - can get the basic object result for command 'closest' ok 277 - 'returned object is correct for command 'closest'' isa 'Bio::Root::IO' @@ -2176,7 +2241,7 @@ ok 306 - can return output format for command 'sort' ok 307 - result claims to be in correct format for command 'sort' ok 308 - can return output file for command 'sort' -ok 309 - file format of '/tmp/U3m47lFA1R/aC7OzUQsfe.bed' consistent with claim for 'sort' +ok 309 - file format of '/tmp/_Aq_YoKMEQ/5Epn8ibmQk.bed' consistent with claim for 'sort' ok 310 - can set want to IO object for command 'sort' ok 311 - can get the basic object result for command 'sort' ok 312 - 'returned object is correct for command 'sort'' isa 'Bio::Root::IO' @@ -2194,7 +2259,7 @@ ok 324 - can return output format for command 'complement' ok 325 - result claims to be in correct format for command 'complement' ok 326 - can return output file for command 'complement' -ok 327 - file format of '/tmp/PIFBtVb3hw/Y080bFEypp.bed' consistent with claim for 'complement' +ok 327 - file format of '/tmp/omIG1sgUWx/coqri6yM0W.bed' consistent with claim for 'complement' ok 328 - can set want to IO object for command 'complement' ok 329 - can get the basic object result for command 'complement' ok 330 - 'returned object is correct for command 'complement'' isa 'Bio::Root::IO' @@ -2230,7 +2295,7 @@ ok 360 - can return output format for command 'subtract' ok 361 - result claims to be in correct format for command 'subtract' ok 362 - can return output file for command 'subtract' -ok 363 - file format of '/tmp/S7Bu3PguZt/2EMcfIJWnG.bed' consistent with claim for 'subtract' +ok 363 - file format of '/tmp/l0yOWtsOkN/rN5p5CVkyq.bed' consistent with claim for 'subtract' ok 364 - can set want to IO object for command 'subtract' ok 365 - can get the basic object result for command 'subtract' ok 366 - 'returned object is correct for command 'subtract'' isa 'Bio::Root::IO' @@ -2252,7 +2317,7 @@ ok 378 - can return output format for command 'coverage' ok 379 - result claims to be in correct format for command 'coverage' ok 380 - can return output file for command 'coverage' -ok 381 - file format of '/tmp/yKRIPZfb9C/Dsbhq1kP6z.bed' consistent with claim for 'coverage' +ok 381 - file format of '/tmp/zdyXxqFElB/8TYmSg0vmS.bed' consistent with claim for 'coverage' ok 382 - can set want to IO object for command 'coverage' ok 383 - can get the basic object result for command 'coverage' ok 384 - 'returned object is correct for command 'coverage'' isa 'Bio::Root::IO' @@ -2274,7 +2339,7 @@ ok 396 - can return output format for command 'merge' ok 397 - result claims to be in correct format for command 'merge' ok 398 - can return output file for command 'merge' -ok 399 - file format of '/tmp/P08SCMXkia/IqtEurw5US.bed' consistent with claim for 'merge' +ok 399 - file format of '/tmp/Gh8eCWH3w9/R6z9zCs3nU.bed' consistent with claim for 'merge' ok 400 - can set want to IO object for command 'merge' ok 401 - can get the basic object result for command 'merge' ok 402 - 'returned object is correct for command 'merge'' isa 'Bio::Root::IO' @@ -2292,7 +2357,7 @@ ok 414 - can return output format for command 'window' ok 415 - result claims to be in correct format for command 'window' ok 416 - can return output file for command 'window' -ok 417 - file format of '/tmp/blZAxOlZs8/qyCbGpj652.bedpe' consistent with claim for 'window' +ok 417 - file format of '/tmp/IKJSOFBjYQ/87PnQEFugn.bedpe' consistent with claim for 'window' ok 418 - can set want to IO object for command 'window' ok 419 - can get the basic object result for command 'window' ok 420 - 'returned object is correct for command 'window'' isa 'Bio::Root::IO' @@ -2916,15 +2981,15 @@ Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795 -[2024-04-30 05:56:06] : LOG : Detected protein sequences. -[2024-04-30 05:56:06] : LOG : Read 7 sequences from standard input. -[2024-04-30 05:56:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -[2024-04-30 05:56:06] : LOG : Calculating pairwise distances -[2024-04-30 05:56:06] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 -[2024-04-30 05:56:06] : LOG : Building guide tree. -[2024-04-30 05:56:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -[2024-04-30 05:56:06] : LOG : Aligning -[2024-04-30 05:56:06] : LOG : CPU Time: 0.05u 00:00:00.05 Elapsed: 00:00:00.00 +[2025-06-03 14:27:47] : LOG : Detected protein sequences. +[2025-06-03 14:27:47] : LOG : Read 7 sequences from standard input. +[2025-06-03 14:27:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2025-06-03 14:27:47] : LOG : Calculating pairwise distances +[2025-06-03 14:27:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2025-06-03 14:27:47] : LOG : Building guide tree. +[2025-06-03 14:27:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2025-06-03 14:27:47] : LOG : Aligning +[2025-06-03 14:27:47] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 ok 5 ok 6 @@ -2943,15 +3008,15 @@ Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795 -[2024-04-30 05:56:06] : LOG : Detected protein sequences. -[2024-04-30 05:56:06] : LOG : Read 7 sequences from standard input. -[2024-04-30 05:56:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -[2024-04-30 05:56:06] : LOG : Calculating pairwise distances -[2024-04-30 05:56:06] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -[2024-04-30 05:56:06] : LOG : Building guide tree. -[2024-04-30 05:56:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -[2024-04-30 05:56:06] : LOG : Aligning -[2024-04-30 05:56:06] : LOG : CPU Time: 0.07u 00:00:00.06 Elapsed: 00:00:00.00 +[2025-06-03 14:27:47] : LOG : Detected protein sequences. +[2025-06-03 14:27:47] : LOG : Read 7 sequences from standard input. +[2025-06-03 14:27:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2025-06-03 14:27:47] : LOG : Calculating pairwise distances +[2025-06-03 14:27:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2025-06-03 14:27:47] : LOG : Building guide tree. +[2025-06-03 14:27:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2025-06-03 14:27:47] : LOG : Aligning +[2025-06-03 14:27:47] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 ok 7 ok # Required executable for Bio::Tools::Run::Phylo::LVB is not present @@ -3411,7 +3476,7 @@ gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } -Loading sequence file: /tmp/WmTMhgrq0s +Loading sequence file: /tmp/KslrF_BtZE Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) @@ -3424,7 +3489,7 @@ gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } -Loading sequence file: /tmp/tiawU6kYTF +Loading sequence file: /tmp/TQWW4w8Mu8 Computing posterior matrix: (1) CYS1_DICDI vs. (2) ALEU_HORVU -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (3) CATH_HUMAN -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (4) CATH_RAT -- done. @@ -3460,7 +3525,7 @@ gapOpen[] = { 0.01386300847 0.01386300847 0.006556313485 0.006556313485 } gapExtend[] = { 0.360332042 0.360332042 0.7831901312 0.7831901312 } -Loading sequence file: /tmp/_WrbetEwgY +Loading sequence file: /tmp/aIVzuXDWBZ Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) @@ -3923,7 +3988,7 @@ t/BEDTools.t (Wstat: 0 Tests: 423 Failed: 0) TODO passed: 20, 57, 75, 88, 110, 155, 190, 208, 226 262, 280, 315, 333, 405 -Files=60, Tests=1652, 362 wallclock secs ( 0.44 usr 0.23 sys + 288.23 cusr 21.26 csys = 310.16 CPU) +Files=60, Tests=1652, 192 wallclock secs ( 0.37 usr 0.08 sys + 179.66 cusr 10.80 csys = 190.91 CPU) Result: PASS mv t.skip/* t rm -rf t.skip @@ -3933,211 +3998,211 @@ dh_auto_install /usr/bin/perl Build install --destdir /build/reproducible-path/bioperl-run-1.7.3/debian/tmp --create_packlist 0 Building BioPerl-Run -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_panalysis.pl.1p Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_papplmaker.pl.1p -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_neighbor.pl.1p +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_panalysis.pl.1p Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_multi_hmmsearch.pl.1p +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_neighbor.pl.1p Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_protdist.pl.1p -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/tRNAscanSE.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Coil.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Seg.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/TribeMCL.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Profile.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primate.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSApplication.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSacd.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/FootPrinter.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RNAMotif.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/ESoap.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/GQueryAdaptor.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/LinkAdaptor.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/DocSumAdaptor.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/Result.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/ESoap/WSDL.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Mdust.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Hmmer.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Signalp.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genemark.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/ERPIN.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Prints.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Glimmer.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Tmhmm.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Eponine.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Vista.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primer3.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Simprot.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSApplication.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Promoterwise.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Prints.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Infernal.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Profile.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Eponine.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RNAMotif.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primate.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Seg.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/FootPrinter.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Glimmer.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Coil.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSacd.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/tRNAscanSE.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genewise.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/MCS.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genemark.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Match.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Ensembl.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneWUBlast.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primer3.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RepeatMasker.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Pseudowise.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genscan.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Signalp.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Simprot.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Hmmer.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RepeatMasker.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneNCBIBlast.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Raxml.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Vista.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneWUBlast.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/TribeMCL.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Pseudowise.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Tmhmm.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Ensembl.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Match.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Analysis/soap.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/AnalysisFactory/soap.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Sim4.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probalign.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MSAProbs.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Pal2Nal.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Gmap.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Kalign.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Blat.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Muscle.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/StandAloneFasta.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probcons.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Proda.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Exonerate.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Lagan.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/DBA.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Amap.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MAFFT.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools/Config.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus/Config.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phyml.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Gerp.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/QuickTree.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Semphy.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Gerp.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/LVB.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/FastTree.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/LVB.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/SLR.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Raxml.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Molphy/ProtML.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/REL.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Base.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/FEL.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Base.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/REL.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhastCons.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Njtree/Best.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Base.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Base.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Consense.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Njtree/Best.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhastCons.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Analysis/soap.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/AnalysisFactory/soap.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools/Config.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools/Config.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus/Config.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Lagan.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Gmap.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MAFFT.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probalign.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Amap.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Muscle.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Sim4.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/DBA.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Proda.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Pal2Nal.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/StandAloneFasta.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Kalign.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Exonerate.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Blat.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MSAProbs.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probcons.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Factory/EMBOSS.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/ESoap.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/LinkAdaptor.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/DocSumAdaptor.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/Result.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/GQueryAdaptor.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/ESoap/WSDL.pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Primer3.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Molphy::ProtML.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Amap.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::SeqBoot.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::FEL.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::tRNAscanSE.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtDist.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::BatchFile.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Njtree::Best.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Neighbor.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::SLR.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Exonerate.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Semphy.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::EMBOSSacd.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phast::PhyloFit.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::GQueryAdaptor.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Muscle.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Ensembl.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Probalign.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Promoterwise.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Prints.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genemark.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::LVB.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Simprot.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Hmmer.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::DocSumAdaptor.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneNCBIBlast.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus::BlastMethods.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::LinkAdaptor.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Samtools.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genewise.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Prints.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Match.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::FootPrinter.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Ensembl.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Lagan.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Pal2Nal.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::QuickTree.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::ESoap.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genscan.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Kalign.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BlastPlus.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Glimmer.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Samtools.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Mdust.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::BatchFile.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BEDTools.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Raxml.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::MCS.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Analysis::soap.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::tRNAscanSE.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Primate.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor::species.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Factory::EMBOSS.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Profile.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Lagan.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor::seq.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::EMBOSSApplication.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BEDTools::Config.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Proda.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Gmap.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus::BlastMethods.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Molphy::ProtML.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genemark.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::RNAMotif.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Eponine.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::SLAC.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Primer3.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Njtree::Best.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::QuickTree.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::DBA.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Vista.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BEDTools.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Seg.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BEDTools::Config.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlast.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Base.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::Modeltest.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawGram.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Tmhmm.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor::species.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BlastPlus.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneWUBlast.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::RNAMotif.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtPars.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Match.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::TribeMCL.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Semphy.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::GQueryAdaptor.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::LinkAdaptor.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Probcons.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::AnalysisFactory::soap.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlast.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Signalp.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Mdust.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::MAFFT.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::MSAProbs.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Vista.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::PhylipConf.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::ERPIN.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Blat.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::Result.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtDist.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Consense.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::EMBOSSApplication.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::DocSumAdaptor.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawTree.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Neighbor.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::MSAProbs.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Samtools::Config.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Promoterwise.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Exonerate.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Sim4.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtPars.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::FEL.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Profile.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::RepeatMasker.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::EMBOSSacd.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Signalp.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawGram.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneWUBlast.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::StandAloneFasta.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Analysis::soap.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Gerp.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Coil.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::REL.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Amap.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Eponine.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phast::PhastCons.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::FastTree.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genscan.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phyml.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::SLR.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::PhylipConf.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::REL.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Sim4.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::ESoap.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Pal2Nal.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Factory::EMBOSS.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Probcons.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::ESoap::WSDL.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Muscle.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::FastTree.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::RepeatMasker.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::Base.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Samtools::Config.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::AnalysisFactory::soap.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::StandAloneFasta.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Primate.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::FootPrinter.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Pseudowise.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::SLAC.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Coil.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Glimmer.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Seg.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawTree.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Hmmer.3pm +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::Result.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Infernal.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::MAFFT.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::Modeltest.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::ERPIN.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Proda.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneNCBIBlast.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phast::PhastCons.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::LVB.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phast::PhyloFit.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::Base.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::SeqBoot.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Base.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_papplmaker.pl -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_panalysis.pl Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_protdist.pl -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_multi_hmmsearch.pl +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_panalysis.pl Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_neighbor.pl +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_multi_hmmsearch.pl dh_install dh_installdocs dh_installchangelogs @@ -4153,8 +4218,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libbio-perl-run-perl' in '../libbio-perl-run-perl_1.7.3-11_all.deb'. dpkg-deb: building package 'bioperl-run' in '../bioperl-run_1.7.3-11_all.deb'. +dpkg-deb: building package 'libbio-perl-run-perl' in '../libbio-perl-run-perl_1.7.3-11_all.deb'. dpkg-genbuildinfo --build=binary -O../bioperl-run_1.7.3-11_amd64.buildinfo dpkg-genchanges --build=binary -O../bioperl-run_1.7.3-11_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -4162,12 +4227,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/783320/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/783320/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/76464 and its subdirectories -I: Current time: Tue Apr 30 05:57:49 -12 2024 -I: pbuilder-time-stamp: 1714499869 +I: removing directory /srv/workspace/pbuilder/783320 and its subdirectories +I: Current time: Tue Jun 3 14:28:18 +14 2025 +I: pbuilder-time-stamp: 1748910498