Thu May 9 17:40:40 UTC 2024 I: starting to build bioperl-run/trixie/armhf on jenkins on '2024-05-09 17:40' Thu May 9 17:40:40 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_13/2972/console.log Thu May 9 17:40:41 UTC 2024 I: Downloading source for trixie/bioperl-run=1.7.3-11 --2024-05-09 17:40:41-- http://deb.debian.org/debian/pool/main/b/bioperl-run/bioperl-run_1.7.3-11.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3199 (3.1K) [text/prs.lines.tag] Saving to: ‘bioperl-run_1.7.3-11.dsc’ 0K ... 100% 420M=0s 2024-05-09 17:40:41 (420 MB/s) - ‘bioperl-run_1.7.3-11.dsc’ saved [3199/3199] Thu May 9 17:40:41 UTC 2024 I: bioperl-run_1.7.3-11.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bioperl-run Binary: bioperl-run, libbio-perl-run-perl Architecture: all Version: 1.7.3-11 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Étienne Mollier Homepage: https://metacpan.org/release/BioPerl-Run Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/bioperl-run Vcs-Git: https://salsa.debian.org/med-team/bioperl-run.git Testsuite: autopkgtest-pkg-perl Build-Depends: debhelper-compat (= 13), libmodule-build-perl Build-Depends-Indep: 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 [any-amd64], libbio-eutilities-perl, libbio-tools-run-remoteblast-perl, amap-align, bedtools [any-amd64], bedtools-test, ncbi-blast+-legacy, clustalw [any-amd64], emboss [any-amd64 arm64 mips64el ppc64el riscv64], exonerate, hmmer [any-amd64 any-i386 powerpc ppc64], hyphy-pt | hyphy-mpi [any-amd64], infernal [any-amd64 any-i386], kalign, mafft, muscle, ncoils, phyml, primer3, probcons, python3-pybedtools [any-amd64], raxml, samtools [any-amd64], sim4, tigr-glimmer [any-amd64 arm64 mips64el ppc64el riscv64], wise, fasttree, lagan, pal2nal, pftools [any-amd64], libwww-perl Package-List: bioperl-run deb science optional arch=all libbio-perl-run-perl deb perl optional arch=all Checksums-Sha1: 930b52695705a503be1583d42d637e84e0d71ee8 4872163 bioperl-run_1.7.3.orig.tar.gz ff8069cbc672292aa8d3a080424c69a9ce3dc97c 19640 bioperl-run_1.7.3-11.debian.tar.xz Checksums-Sha256: 04f11b3a931f625bf80770c3aec1b57658b41cde54573132b58b6179adda7c65 4872163 bioperl-run_1.7.3.orig.tar.gz 0e87a3cc2f7208cf19dad2e639cb4fd93932557d6f70fd9d10ebb711a2a216c9 19640 bioperl-run_1.7.3-11.debian.tar.xz Files: e582f2dc591b947348670ce1479da109 4872163 bioperl-run_1.7.3.orig.tar.gz 50d0a107ea24fbb78c0c3f8fa63f7a81 19640 bioperl-run_1.7.3-11.debian.tar.xz Dgit: 0604168ee401c98a652249254a15606a29342506 debian archive/debian/1.7.3-11 https://git.dgit.debian.org/bioperl-run -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmYtWiQUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoWBA//VO/jDM+f6C4oDonAfNL6HksrTAGm HPCkMjRTqmDEVG9wwUVFibRjART2XA7zObtiaPv6H4nNXnBQPTYSKM3MwD+FCDC0 j5MlMp1oy2gJ/Bz5rwOzRdNnPeytLeGIK0gNP6kjnijUpmIt3m7id8YTR5JqG3rD clHSTz1xJyqTKjmOiV6uKxNLZzu/nXdwliH8Enf85VQfcCZYDHc6E/UDoS8jDaod /6RDPQC09410TSUrGMfFthIfuL9woVis3vLO8IxdQzldCICICrq/USM11wq5xKTO ojQ1inSbh4nY3lzA8INfBJtVjVxSa2BSu6LuCVqxIiZTMqfqJ1dmQKGVayrxCYvw wY8qSkHdzMbwVaO3Xz5TtBpDbdc8o2AU9vPh+w5ceq8AlUTkOsGeaWPIpXHjotmk 8AMbNuXXiJvm9RVZGmM4nUsPqQgurL9gniEO0a58tv1sIz1Mv3SXMGy3tPK2dwpz X0en9tbhgCnRxfOT96yWmegJJWgXCA9J36ar/5CorvCeCDgE+3RnMXNvXB13y4eV E20ZHXfzoNlGeVAh+H8PjWRXNKDT7peuPl12X2NgLXkZxZvaMZZc93eGWCQIKII7 lennChj/LURfyVrUU/e/EbQ2EbLK8E18b4C7Ql9vG7z7Wvdqu3MnsmmN/FHUHwvh HSgqAPNF7Mlz2pw= =T4q5 -----END PGP SIGNATURE----- Thu May 9 17:40:41 UTC 2024 I: Checking whether the package is not for us Thu May 9 17:40:41 UTC 2024 I: Starting 1st build on remote node ff64a-armhf-rb.debian.net. Thu May 9 17:40:41 UTC 2024 I: Preparing to do remote build '1' on ff64a-armhf-rb.debian.net. Thu May 9 17:52:33 UTC 2024 I: Deleting $TMPDIR on ff64a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu May 9 05:40:49 -12 2024 I: pbuilder-time-stamp: 1715276449 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bioperl-run_1.7.3-11.dsc] I: copying [./bioperl-run_1.7.3.orig.tar.gz] I: copying [./bioperl-run_1.7.3-11.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Apr 27 20:03:48 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bioperl-run_1.7.3-11.dsc: no acceptable signature found dpkg-source: info: extracting bioperl-run in bioperl-run-1.7.3 dpkg-source: info: unpacking bioperl-run_1.7.3.orig.tar.gz dpkg-source: info: unpacking bioperl-run_1.7.3-11.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Extract_version_from_BEDTools_properly.patch dpkg-source: info: applying skip_tests_for_RemoteBlast_rpsblast.patch dpkg-source: info: applying skip_tests_for_RemoteBlast.patch dpkg-source: info: applying kalign-input-via-piping.patch dpkg-source: info: applying kalign-version-regex.patch dpkg-source: info: applying skip_tests_for_wise.patch dpkg-source: info: applying skip_tests_for_phylip.patch dpkg-source: info: applying skip_tests_for_phyml.patch dpkg-source: info: applying skip_tests_for_infernal.patch dpkg-source: info: applying skip_tests_for_ncbi-blast+.patch dpkg-source: info: applying hyphy.patch dpkg-source: info: applying remove_tests_for_ensembl.patch dpkg-source: info: applying skip_tests_for_soap.patch dpkg-source: info: applying get-overlap.patch dpkg-source: info: applying alternate-data.patch dpkg-source: info: applying skip-test-for-kalign.patch dpkg-source: info: applying fix-whatis-entries.patch dpkg-source: info: applying unscramble-erpin.patch dpkg-source: info: applying fix-pod-conversion.patch 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/2135/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='2ed8db36dfc54ffbbffe9093f07e5a69' 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='2135' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.3wdGQBcw/pbuilderrc_93C2 --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.3wdGQBcw/b1 --logfile b1/build.log bioperl-run_1.7.3-11.dsc' SUDO_GID='114' SUDO_UID='109' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux ff64a 6.1.0-21-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 9 11:26 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2135/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-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-eutilities-perl, libbio-tools-run-remoteblast-perl, amap-align, bedtools-test, ncbi-blast+-legacy, exonerate, hyphy-pt, kalign, mafft, muscle, ncoils, phyml, primer3, probcons, raxml, sim4, wise, fasttree, lagan, pal2nal, 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 ... 19445 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libmodule-build-perl; however: Package libmodule-build-perl is not installed. pbuilder-satisfydepends-dummy depends on bioperl (>= 1.7.4); however: Package bioperl is not installed. pbuilder-satisfydepends-dummy depends on libalgorithm-diff-perl; however: Package libalgorithm-diff-perl is not installed. pbuilder-satisfydepends-dummy depends on libipc-run-perl; however: Package libipc-run-perl is not installed. pbuilder-satisfydepends-dummy depends on libio-string-perl; however: Package libio-string-perl is not installed. pbuilder-satisfydepends-dummy depends on libxml-twig-perl; however: Package libxml-twig-perl is not installed. pbuilder-satisfydepends-dummy depends on libfile-sort-perl; however: Package libfile-sort-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-most-perl; however: Package libtest-most-perl is not installed. pbuilder-satisfydepends-dummy depends on libarray-compare-perl; however: Package libarray-compare-perl is not installed. pbuilder-satisfydepends-dummy depends on libtree-dagnode-perl; however: Package libtree-dagnode-perl is not installed. pbuilder-satisfydepends-dummy depends on libbio-cluster-perl; however: Package libbio-cluster-perl is not installed. pbuilder-satisfydepends-dummy depends on libbio-featureio-perl; however: Package libbio-featureio-perl is not installed. pbuilder-satisfydepends-dummy depends on libconfig-any-perl; however: Package libconfig-any-perl is not installed. pbuilder-satisfydepends-dummy depends on libbio-eutilities-perl; however: Package libbio-eutilities-perl is not installed. pbuilder-satisfydepends-dummy depends on libbio-tools-run-remoteblast-perl; however: Package libbio-tools-run-remoteblast-perl is not installed. pbuilder-satisfydepends-dummy depends on amap-align; however: Package amap-align is not installed. pbuilder-satisfydepends-dummy depends on bedtools-test; however: Package bedtools-test is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+-legacy; however: Package ncbi-blast+-legacy is not installed. pbuilder-satisfydepends-dummy depends on exonerate; however: Package exonerate is not installed. pbuilder-satisfydepends-dummy depends on hyphy-pt; however: Package hyphy-pt is not installed. pbuilder-satisfydepends-dummy depends on kalign; however: Package kalign is not installed. pbuilder-satisfydepends-dummy depends on mafft; however: Package mafft is not installed. pbuilder-satisfydepends-dummy depends on muscle; however: Package muscle is not installed. pbuilder-satisfydepends-dummy depends on ncoils; however: Package ncoils is not installed. pbuilder-satisfydepends-dummy depends on phyml; however: Package phyml is not installed. pbuilder-satisfydepends-dummy depends on primer3; however: Package primer3 is not installed. pbuilder-satisfydepends-dummy depends on probcons; however: Package probcons is not installed. pbuilder-satisfydepends-dummy depends on raxml; however: Package raxml is not installed. pbuilder-satisfydepends-dummy depends on sim4; however: Package sim4 is not installed. pbuilder-satisfydepends-dummy depends on wise; however: Package wise is not installed. pbuilder-satisfydepends-dummy depends on fasttree; however: Package fasttree is not installed. pbuilder-satisfydepends-dummy depends on lagan; however: Package lagan is not installed. pbuilder-satisfydepends-dummy depends on pal2nal; however: Package pal2nal is not installed. pbuilder-satisfydepends-dummy depends on libwww-perl; however: Package libwww-perl is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: amap-align{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools-test{a} bioperl{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} exonerate{a} fasttree{a} file{a} gettext{a} gettext-base{a} groff-base{a} hyphy-common{a} hyphy-pt{a} intltool-debian{a} kalign{a} lagan{a} libalgorithm-diff-perl{a} libarchive-zip-perl{a} libarray-compare-perl{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-tools-run-remoteblast-perl{a} libbio-variation-perl{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} libdebhelper-perl{a} libdevel-callchecker-perl{a} libdevel-stacktrace-perl{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-tiny-perl{a} libfile-sort-perl{a} libfile-stripnondeterminism-perl{a} libglib2.0-0t64{a} libgssapi-krb5-2{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} 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} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblmdb0{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libmodule-build-perl{a} libmodule-pluggable-perl{a} libmodule-runtime-perl{a} libmoo-perl{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libnl-3-200{a} libnl-route-3-200{a} libopenmpi3t64{a} libparams-classify-perl{a} libpciaccess0{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} librdmacm1t64{a} libreadline8t64{a} librole-tiny-perl{a} librtmp1{a} libssh2-1t64{a} libsub-override-perl{a} libsub-quote-perl{a} libsub-uplevel-perl{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} libtimedate-perl{a} libtool{a} libtree-dagnode-perl{a} libtry-tiny-perl{a} libtype-tiny-perl{a} libuchardet0{a} liburi-perl{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-libxml-perl{a} libxml-namespacesupport-perl{a} libxml-parser-perl{a} libxml-perl{a} libxml-regexp-perl{a} libxml-sax-base-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} m4{a} mafft{a} man-db{a} media-types{a} muscle{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} phyml{a} po-debconf{a} primer3{a} probcons{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} raxml{a} readline-common{a} sensible-utils{a} sim4{a} tzdata{a} ucf{a} wise{a} wise-data{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run curl ibverbs-providers krb5-locales libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libbio-perl-run-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 libgraph-perl libgraphviz-perl libhtml-form-perl libhtml-format-perl libhtml-tableextract-perl libhttp-daemon-perl libio-compress-brotli-perl 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 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-libxslt-perl libxml-sax-expat-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, 191 newly installed, 0 to remove and 0 not upgraded. Need to get 76.3 MB of archives. After unpacking 292 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf libpython3.11-minimal armhf 3.11.9-1 [805 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.6.2-1 [83.5 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf python3.11-minimal armhf 3.11.9-1 [1600 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf python3-minimal armhf 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libreadline8t64 armhf 8.2-4 [145 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf libpython3.11-stdlib armhf 3.11.9-1 [1704 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf python3.11 armhf 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf libpython3-stdlib armhf 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main armhf python3 armhf 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf openssl armhf 3.2.1-3 [1326 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf ca-certificates all 20240203 [158 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-4 [1090 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40-8 [85.6 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.1-1 [1375 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libbsd0 armhf 0.12.2-1 [127 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf libedit2 armhf 3.1-20230828-1+b1 [77.6 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf libcbor0.10 armhf 0.10.2-1.1 [23.9 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf libfido2-1 armhf 1.14.0-1+b2 [70.4 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf libkrb5support0 armhf 1.20.1-6+b1 [30.6 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libcom-err2 armhf 1.47.1~rc2-1 [21.8 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf libk5crypto3 armhf 1.20.1-6+b1 [75.5 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libkeyutils1 armhf 1.6.3-3 [7908 B] Get: 34 http://deb.debian.org/debian trixie/main armhf libkrb5-3 armhf 1.20.1-6+b1 [290 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf libgssapi-krb5-2 armhf 1.20.1-6+b1 [112 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf openssh-client armhf 1:9.7p1-4 [870 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf ucf all 3.0043+nmu1 [55.2 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf amap-align armhf 2.2+git20080214.600fc29+dfsg-2 [110 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf bedtools-test all 2.31.1+dfsg-2 [10.9 MB] Get: 45 http://deb.debian.org/debian trixie/main armhf libio-string-perl all 1.08-4 [12.1 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf libdata-stag-perl all 0.14-3 [448 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf libclass-data-inheritable-perl all 0.08-3 [8588 B] Get: 49 http://deb.debian.org/debian trixie/main armhf libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf libexception-class-perl all 1.45-1 [34.6 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf libtest-deep-perl all 1.204-1 [52.9 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libcapture-tiny-perl all 0.48-2 [24.6 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf libtext-diff-perl all 1.45-2 [27.2 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf libtest-differences-perl all 0.71-1 [17.9 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf libtest-exception-perl all 0.43-3 [16.9 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf libtest-warn-perl all 0.37-2 [14.5 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf libtest-most-perl all 0.38-1 [25.1 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf bioperl all 1.7.8-1 [246 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 68 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.191-1+b1 [183 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 70 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b3 [598 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 76 http://deb.debian.org/debian trixie/main armhf libglib2.0-0t64 armhf 2.80.1-1 [1314 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf exonerate armhf 2.4.0-5+b1 [1661 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf fasttree armhf 2.1.11-2 [169 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf hyphy-common all 2.5.60+dfsg-1 [604 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.61.0-1+b1 [64.1 kB] Get: 82 http://deb.debian.org/debian trixie/main armhf libpsl5t64 armhf 0.21.2-1.1 [55.6 kB] Get: 83 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b4 [53.2 kB] Get: 84 http://deb.debian.org/debian trixie/main armhf libssh2-1t64 armhf 1.11.0-4.1+b2 [198 kB] Get: 85 http://deb.debian.org/debian trixie/main armhf libcurl3t64-gnutls armhf 8.7.1-3 [384 kB] Get: 86 http://deb.debian.org/debian trixie/main armhf hyphy-pt armhf 2.5.60+dfsg-1 [762 kB] Get: 87 http://deb.debian.org/debian trixie/main armhf kalign armhf 1:3.4.0-1 [78.7 kB] Get: 88 http://deb.debian.org/debian trixie/main armhf lagan armhf 2.0-10 [166 kB] Get: 89 http://deb.debian.org/debian trixie/main armhf libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 90 http://deb.debian.org/debian trixie/main armhf libclass-xsaccessor-perl armhf 1.19-4+b3 [35.4 kB] Get: 91 http://deb.debian.org/debian trixie/main armhf libb-hooks-op-check-perl armhf 0.22-3+b1 [10.2 kB] Get: 92 http://deb.debian.org/debian trixie/main armhf libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 93 http://deb.debian.org/debian trixie/main armhf libdevel-callchecker-perl armhf 0.009-1 [15.7 kB] Get: 94 http://deb.debian.org/debian trixie/main armhf libparams-classify-perl armhf 0.015-2+b3 [21.3 kB] Get: 95 http://deb.debian.org/debian trixie/main armhf libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 96 http://deb.debian.org/debian trixie/main armhf libimport-into-perl all 1.002005-2 [11.3 kB] Get: 97 http://deb.debian.org/debian trixie/main armhf librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 98 http://deb.debian.org/debian trixie/main armhf libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 99 http://deb.debian.org/debian trixie/main armhf libmoo-perl all 2.005005-1 [58.0 kB] Get: 100 http://deb.debian.org/debian trixie/main armhf libexporter-tiny-perl all 1.006002-1 [38.7 kB] Get: 101 http://deb.debian.org/debian trixie/main armhf libtype-tiny-perl all 2.004000-1 [357 kB] Get: 102 http://deb.debian.org/debian trixie/main armhf libarray-compare-perl all 3.0.8-1 [14.9 kB] Get: 103 http://deb.debian.org/debian trixie/main armhf liburi-perl all 5.28-1 [98.6 kB] Get: 104 http://deb.debian.org/debian trixie/main armhf libencode-locale-perl all 1.05-3 [12.9 kB] Get: 105 http://deb.debian.org/debian trixie/main armhf libtimedate-perl all 2.3300-2 [39.3 kB] Get: 106 http://deb.debian.org/debian trixie/main armhf libhttp-date-perl all 6.06-1 [10.7 kB] Get: 107 http://deb.debian.org/debian trixie/main armhf libfile-listing-perl all 6.16-1 [12.4 kB] Get: 108 http://deb.debian.org/debian trixie/main armhf libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 109 http://deb.debian.org/debian trixie/main armhf libhtml-parser-perl armhf 3.82-1 [95.6 kB] Get: 110 http://deb.debian.org/debian trixie/main armhf libhtml-tree-perl all 5.07-3 [211 kB] Get: 111 http://deb.debian.org/debian trixie/main armhf libclone-perl armhf 0.46-1+b2 [13.1 kB] Get: 112 http://deb.debian.org/debian trixie/main armhf libio-html-perl all 1.004-3 [16.2 kB] Get: 113 http://deb.debian.org/debian trixie/main armhf liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 114 http://deb.debian.org/debian trixie/main armhf libhttp-message-perl all 6.45-1 [82.0 kB] Get: 115 http://deb.debian.org/debian trixie/main armhf libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 116 http://deb.debian.org/debian trixie/main armhf libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 117 http://deb.debian.org/debian trixie/main armhf perl-openssl-defaults armhf 7+b2 [6708 B] Get: 118 http://deb.debian.org/debian trixie/main armhf libnet-ssleay-perl armhf 1.94-1+b1 [319 kB] Get: 119 http://deb.debian.org/debian trixie/main armhf libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 120 http://deb.debian.org/debian trixie/main armhf libnet-http-perl all 6.23-1 [23.9 kB] Get: 121 http://deb.debian.org/debian trixie/main armhf liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 122 http://deb.debian.org/debian trixie/main armhf libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 123 http://deb.debian.org/debian trixie/main armhf libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 124 http://deb.debian.org/debian trixie/main armhf libwww-perl all 6.77-1 [183 kB] Get: 125 http://deb.debian.org/debian trixie/main armhf libxml-parser-perl armhf 2.47-1+b2 [196 kB] Get: 126 http://deb.debian.org/debian trixie/main armhf libxml-twig-perl all 1:3.52-3 [177 kB] Get: 127 http://deb.debian.org/debian trixie/main armhf libxml-writer-perl all 0.900-2 [26.8 kB] Get: 128 http://deb.debian.org/debian trixie/main armhf libbio-variation-perl all 1.7.5-3 [72.6 kB] Get: 129 http://deb.debian.org/debian trixie/main armhf libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get: 130 http://deb.debian.org/debian trixie/main armhf libxml-sax-base-perl all 1.09-3 [20.6 kB] Get: 131 http://deb.debian.org/debian trixie/main armhf libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get: 132 http://deb.debian.org/debian trixie/main armhf libbio-cluster-perl all 1.7.3-6 [53.3 kB] Get: 133 http://deb.debian.org/debian trixie/main armhf libbio-asn1-entrezgene-perl all 1.730-3 [46.3 kB] Get: 134 http://deb.debian.org/debian trixie/main armhf libtext-csv-perl all 2.04-1 [112 kB] Get: 135 http://deb.debian.org/debian trixie/main armhf libxml-libxml-perl armhf 2.0207+dfsg+really+2.0134-1+b4 [297 kB] Get: 136 http://deb.debian.org/debian trixie/main armhf libxml-simple-perl all 2.25-2 [69.8 kB] Get: 137 http://deb.debian.org/debian trixie/main armhf libbio-eutilities-perl all 1.77-2 [124 kB] Get: 138 http://deb.debian.org/debian trixie/main armhf libfile-slurp-tiny-perl all 0.004-2 [7592 B] Get: 139 http://deb.debian.org/debian trixie/main armhf libtree-dagnode-perl all 1.32-1 [61.7 kB] Get: 140 http://deb.debian.org/debian trixie/main armhf libxml-perl all 0.08-4 [93.0 kB] Get: 141 http://deb.debian.org/debian trixie/main armhf libxml-regexp-perl all 0.04-1.1 [7500 B] Get: 142 http://deb.debian.org/debian trixie/main armhf libxml-dom-perl all 1.46-2 [152 kB] Get: 143 http://deb.debian.org/debian trixie/main armhf libxml-xpathengine-perl all 0.14-2 [33.5 kB] Get: 144 http://deb.debian.org/debian trixie/main armhf libxml-dom-xpath-perl all 0.14-4 [9352 B] Get: 145 http://deb.debian.org/debian trixie/main armhf libbio-featureio-perl all 1.6.905-2 [53.2 kB] Get: 146 http://deb.debian.org/debian trixie/main armhf libbio-tools-run-remoteblast-perl all 1.7.3-3 [17.5 kB] Get: 147 http://deb.debian.org/debian trixie/main armhf libmodule-pluggable-perl all 5.2-5 [23.0 kB] Get: 148 http://deb.debian.org/debian trixie/main armhf libconfig-any-perl all 0.33-1 [31.0 kB] Get: 149 http://deb.debian.org/debian trixie/main armhf libevent-core-2.1-7t64 armhf 2.1.12-stable-8.1+b3 [122 kB] Get: 150 http://deb.debian.org/debian trixie/main armhf libevent-pthreads-2.1-7t64 armhf 2.1.12-stable-8.1+b3 [53.8 kB] Get: 151 http://deb.debian.org/debian trixie/main armhf libnl-3-200 armhf 3.7.0-0.3 [51.7 kB] Get: 152 http://deb.debian.org/debian trixie/main armhf libnl-route-3-200 armhf 3.7.0-0.3 [153 kB] Get: 153 http://deb.debian.org/debian trixie/main armhf libibverbs1 armhf 50.0-2+b1 [55.0 kB] Get: 154 http://deb.debian.org/debian trixie/main armhf librdmacm1t64 armhf 50.0-2+b1 [62.1 kB] Get: 155 http://deb.debian.org/debian trixie/main armhf libfabric1 armhf 1.17.0-3+b1 [386 kB] Get: 156 http://deb.debian.org/debian trixie/main armhf libfile-sort-perl all 1.01-3 [21.3 kB] Get: 157 http://deb.debian.org/debian trixie/main armhf libpciaccess0 armhf 0.17-3+b1 [49.3 kB] Get: 158 http://deb.debian.org/debian trixie/main armhf libxau6 armhf 1:1.0.9-1+b1 [17.4 kB] Get: 159 http://deb.debian.org/debian trixie/main armhf libxdmcp6 armhf 1:1.1.2-3+b1 [23.0 kB] Get: 160 http://deb.debian.org/debian trixie/main armhf libxcb1 armhf 1.15-1 [140 kB] Get: 161 http://deb.debian.org/debian trixie/main armhf libx11-data all 2:1.8.7-1 [328 kB] Get: 162 http://deb.debian.org/debian trixie/main armhf libx11-6 armhf 2:1.8.7-1+b1 [739 kB] Get: 163 http://deb.debian.org/debian trixie/main armhf libxext6 armhf 2:1.3.4-1+b1 [47.8 kB] Get: 164 http://deb.debian.org/debian trixie/main armhf libxnvctrl0 armhf 535.171.04-1 [12.8 kB] Get: 165 http://deb.debian.org/debian trixie/main armhf ocl-icd-libopencl1 armhf 2.3.2-1+b1 [37.3 kB] Get: 166 http://deb.debian.org/debian trixie/main armhf libhwloc15 armhf 2.10.0-1+b1 [133 kB] Get: 167 http://deb.debian.org/debian trixie/main armhf libhwloc-plugins armhf 2.10.0-1+b1 [16.1 kB] Get: 168 http://deb.debian.org/debian trixie/main armhf libio-pty-perl armhf 1:1.20-1+b1 [33.9 kB] Get: 169 http://deb.debian.org/debian trixie/main armhf libipc-run-perl all 20231003.0-2 [101 kB] Get: 170 http://deb.debian.org/debian trixie/main armhf liblmdb0 armhf 0.9.31-1+b1 [37.6 kB] Get: 171 http://deb.debian.org/debian trixie/main armhf libmbedcrypto7t64 armhf 2.28.8-1 [251 kB] Get: 172 http://deb.debian.org/debian trixie/main armhf libmbedx509-1t64 armhf 2.28.8-1 [127 kB] Get: 173 http://deb.debian.org/debian trixie/main armhf libmbedtls14t64 armhf 2.28.8-1 [158 kB] Get: 174 http://deb.debian.org/debian trixie/main armhf libmodule-build-perl all 0.423400-2 [252 kB] Get: 175 http://deb.debian.org/debian trixie/main armhf libopenmpi3t64 armhf 4.1.6-13.2 [2198 kB] Get: 176 http://deb.debian.org/debian trixie/main armhf mafft armhf 7.505-1 [784 kB] Get: 177 http://deb.debian.org/debian trixie/main armhf muscle armhf 1:5.1.0-1 [248 kB] Get: 178 http://deb.debian.org/debian trixie/main armhf ncbi-data all 6.1.20170106+dfsg2-2 [3544 kB] Get: 179 http://deb.debian.org/debian trixie/main armhf ncbi-blast+ armhf 2.12.0+ds-4+b1 [10.9 MB] Get: 180 http://deb.debian.org/debian trixie/main armhf ncbi-blast+-legacy all 2.12.0+ds-4 [8956 B] Get: 181 http://deb.debian.org/debian trixie/main armhf ncoils armhf 2002-9 [21.4 kB] Get: 182 http://deb.debian.org/debian trixie/main armhf openmpi-common all 4.1.6-13.2 [169 kB] Get: 183 http://deb.debian.org/debian trixie/main armhf openmpi-bin armhf 4.1.6-13.2 [195 kB] Get: 184 http://deb.debian.org/debian trixie/main armhf pal2nal all 14.1-3 [17.8 kB] Get: 185 http://deb.debian.org/debian trixie/main armhf phyml armhf 3:3.3.20220408-3+b1 [987 kB] Get: 186 http://deb.debian.org/debian trixie/main armhf primer3 armhf 2.6.1-4 [182 kB] Get: 187 http://deb.debian.org/debian trixie/main armhf probcons armhf 1.12-14 [106 kB] Get: 188 http://deb.debian.org/debian trixie/main armhf raxml armhf 8.2.13+dfsg-1 [963 kB] Get: 189 http://deb.debian.org/debian trixie/main armhf sim4 armhf 0.0.20121010-8 [353 kB] Get: 190 http://deb.debian.org/debian trixie/main armhf wise-data all 2.4.1-24 [76.0 kB] Get: 191 http://deb.debian.org/debian trixie/main armhf wise armhf 2.4.1-24 [785 kB] Fetched 76.3 MB in 2s (34.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (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 ... 19445 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.9-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.6.2-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_armhf.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:armhf (3.11.9-1) ... Setting up libexpat1:armhf (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 ... 19761 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_armhf.deb ... 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Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:armhf (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:armhf. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_armhf.deb ... Unpacking libpython3.11-stdlib:armhf (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_armhf.deb ... Unpacking python3.11 (3.11.9-1) ... 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Selecting previously unselected package libtree-dagnode-perl. Preparing to unpack .../126-libtree-dagnode-perl_1.32-1_all.deb ... Unpacking libtree-dagnode-perl (1.32-1) ... Selecting previously unselected package libxml-perl. Preparing to unpack .../127-libxml-perl_0.08-4_all.deb ... Unpacking libxml-perl (0.08-4) ... Selecting previously unselected package libxml-regexp-perl. Preparing to unpack .../128-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 .../129-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 .../130-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 .../131-libxml-dom-xpath-perl_0.14-4_all.deb ... 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Selecting previously unselected package libfabric1:armhf. Preparing to unpack .../142-libfabric1_1.17.0-3+b1_armhf.deb ... Unpacking libfabric1:armhf (1.17.0-3+b1) ... Selecting previously unselected package libfile-sort-perl. Preparing to unpack .../143-libfile-sort-perl_1.01-3_all.deb ... Unpacking libfile-sort-perl (1.01-3) ... Selecting previously unselected package libpciaccess0:armhf. Preparing to unpack .../144-libpciaccess0_0.17-3+b1_armhf.deb ... Unpacking libpciaccess0:armhf (0.17-3+b1) ... Selecting previously unselected package libxau6:armhf. Preparing to unpack .../145-libxau6_1%3a1.0.9-1+b1_armhf.deb ... Unpacking libxau6:armhf (1:1.0.9-1+b1) ... Selecting previously unselected package libxdmcp6:armhf. Preparing to unpack .../146-libxdmcp6_1%3a1.1.2-3+b1_armhf.deb ... Unpacking libxdmcp6:armhf (1:1.1.2-3+b1) ... Selecting previously unselected package libxcb1:armhf. Preparing to unpack .../147-libxcb1_1.15-1_armhf.deb ... Unpacking libxcb1:armhf (1.15-1) ... 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Unpacking libhwloc15:armhf (2.10.0-1+b1) ... Selecting previously unselected package libhwloc-plugins:armhf. Preparing to unpack .../154-libhwloc-plugins_2.10.0-1+b1_armhf.deb ... Unpacking libhwloc-plugins:armhf (2.10.0-1+b1) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../155-libio-pty-perl_1%3a1.20-1+b1_armhf.deb ... Unpacking libio-pty-perl (1:1.20-1+b1) ... Selecting previously unselected package libipc-run-perl. Preparing to unpack .../156-libipc-run-perl_20231003.0-2_all.deb ... Unpacking libipc-run-perl (20231003.0-2) ... Selecting previously unselected package liblmdb0:armhf. Preparing to unpack .../157-liblmdb0_0.9.31-1+b1_armhf.deb ... Unpacking liblmdb0:armhf (0.9.31-1+b1) ... Selecting previously unselected package libmbedcrypto7t64:armhf. Preparing to unpack .../158-libmbedcrypto7t64_2.28.8-1_armhf.deb ... Unpacking libmbedcrypto7t64:armhf (2.28.8-1) ... Selecting previously unselected package libmbedx509-1t64:armhf. 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Unpacking mafft (7.505-1) ... Selecting previously unselected package muscle. Preparing to unpack .../164-muscle_1%3a5.1.0-1_armhf.deb ... Unpacking muscle (1:5.1.0-1) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../165-ncbi-data_6.1.20170106+dfsg2-2_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg2-2) ... Selecting previously unselected package ncbi-blast+. Preparing to unpack .../166-ncbi-blast+_2.12.0+ds-4+b1_armhf.deb ... Unpacking ncbi-blast+ (2.12.0+ds-4+b1) ... Selecting previously unselected package ncbi-blast+-legacy. Preparing to unpack .../167-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 .../168-ncoils_2002-9_armhf.deb ... Unpacking ncoils (2002-9) ... Selecting previously unselected package openmpi-common. Preparing to unpack .../169-openmpi-common_4.1.6-13.2_all.deb ... Unpacking openmpi-common (4.1.6-13.2) ... 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Unpacking sim4 (0.0.20121010-8) ... Selecting previously unselected package wise-data. Preparing to unpack .../177-wise-data_2.4.1-24_all.deb ... Unpacking wise-data (2.4.1-24) ... Selecting previously unselected package wise. Preparing to unpack .../178-wise_2.4.1-24_armhf.deb ... Unpacking wise (2.4.1-24) ... Setting up media-types (10.1.0) ... Setting up libmodule-pluggable-perl (5.2-5) ... Setting up libpipeline1:armhf (1.5.7-2) ... Setting up liblmdb0:armhf (0.9.31-1+b1) ... Setting up ncbi-data (6.1.20170106+dfsg2-2) ... Setting up libpciaccess0:armhf (0.17-3+b1) ... Setting up libxau6:armhf (1:1.0.9-1+b1) ... Setting up libkeyutils1:armhf (1.6.3-3) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up probcons (1.12-14) ... Setting up libmbedcrypto7t64:armhf (2.28.8-1) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libtest-deep-perl (1.204-1) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up libxml-regexp-perl (0.04-1.1) ... Setting up libio-pty-perl (1:1.20-1+b1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libcbor0.10:armhf (0.10.2-1.1) ... Setting up mafft (7.505-1) ... Setting up libclone-perl:armhf (0.46-1+b2) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:armhf (1.1.0-2+b3) ... Setting up libfile-slurp-tiny-perl (0.004-2) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libmagic1t64:armhf (1:5.45-3) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up libpsl5t64:armhf (0.21.2-1.1) ... Setting up libnghttp2-14:armhf (1.61.0-1+b1) ... Setting up perl-openssl-defaults:armhf (7+b2) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libencode-locale-perl (1.05-3) ... Setting up ncoils (2002-9) ... Setting up libcom-err2:armhf (1.47.1~rc2-1) ... Setting up hyphy-common (2.5.60+dfsg-1) ... Setting up file (1:5.45-3) ... Setting up muscle (1:5.1.0-1) ... Setting up libelf1t64:armhf (0.191-1+b1) ... Setting up libmodule-build-perl (0.423400-2) ... Setting up libkrb5support0:armhf (1.20.1-6+b1) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Thu May 9 17:43:22 UTC 2024. Universal Time is now: Thu May 9 17:43:22 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up primer3 (2.6.1-4) ... Setting up kalign (1:3.4.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:armhf (2.80.1-1) ... No schema files found: doing nothing. Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up lagan (2.0-10) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libtext-diff-perl (1.45-2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libxml-xpathengine-perl (0.14-2) ... Setting up sim4 (0.0.20121010-8) ... Setting up libxml-writer-perl (0.900-2) ... Setting up libhwloc15:armhf (2.10.0-1+b1) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.21-14) ... Setting up libb-hooks-op-check-perl:armhf (0.22-3+b1) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up wise-data (2.4.1-24) ... Setting up libk5crypto3:armhf (1.20.1-6+b1) ... Setting up amap-align (2.2+git20080214.600fc29+dfsg-2) ... Setting up autoconf (2.71-3) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libtree-dagnode-perl (1.32-1) ... Setting up dwz (0.15-1+b2) ... Setting up libdata-stag-perl (0.14-3) ... Setting up sensible-utils (0.0.22) ... Setting up ocl-icd-libopencl1:armhf (2.3.2-1+b1) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up pal2nal (14.1-3) ... Setting up libnl-3-200:armhf (3.7.0-0.3) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up openmpi-common (4.1.6-13.2) ... Setting up libconfig-any-perl (0.33-1) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up libsub-override-perl (0.10-1) ... Setting up fasttree (2.1.11-2) ... Setting up netbase (6.4) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b3) ... Setting up libkrb5-3:armhf (1.20.1-6+b1) ... Setting up libevent-core-2.1-7t64:armhf (2.1.12-stable-8.1+b3) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libssh2-1t64:armhf (1.11.0-4.1+b2) ... Setting up libexporter-tiny-perl (1.006002-1) ... Setting up libfido2-1:armhf (1.14.0-1+b2) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:armhf (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b3) ... Setting up exonerate (2.4.0-5+b1) ... Setting up liburi-perl (5.28-1) ... Setting up libfile-sort-perl (1.01-3) ... Setting up raxml (8.2.13+dfsg-1) ... Setting up libtext-csv-perl (2.04-1) ... Setting up libnet-ssleay-perl:armhf (1.94-1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libxdmcp6:armhf (1:1.1.2-3+b1) ... Setting up libxcb1:armhf (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libmbedx509-1t64:armhf (2.28.8-1) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libtool (2.4.7-7) ... Setting up libevent-pthreads-2.1-7t64:armhf (2.1.12-stable-8.1+b3) ... Setting up wise (2.4.1-24) ... Setting up libtest-warn-perl (0.37-2) ... Setting up libedit2:armhf (3.1-20230828-1+b1) ... Setting up libtype-tiny-perl (2.004000-1) ... Setting up libtest-differences-perl (0.71-1) ... Setting up libnet-http-perl (6.23-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:armhf (0.009-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnl-route-3-200:armhf (3.7.0-0.3) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libtest-exception-perl (0.43-3) ... Setting up libgssapi-krb5-2:armhf (1.20.1-6+b1) ... Setting up ucf (3.0043+nmu1) ... Setting up libreadline8t64:armhf (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libmbedtls14t64:armhf (2.28.8-1) ... Setting up groff-base (1.23.0-4) ... Setting up libhtml-parser-perl:armhf (3.82-1) ... Setting up libx11-6:armhf (2:1.8.7-1+b1) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libibverbs1:armhf (50.0-2+b1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libtest-most-perl (0.38-1) ... Setting up openssh-client (1:9.7p1-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:armhf (3.11.9-1) ... Setting up libparams-classify-perl:armhf (0.015-2+b3) ... Setting up libcurl3t64-gnutls:armhf (8.7.1-3) ... Setting up libxext6:armhf (2:1.3.4-1+b1) ... Setting up hyphy-pt (2.5.60+dfsg-1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxnvctrl0:armhf (535.171.04-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b4) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up librdmacm1t64:armhf (50.0-2+b1) ... Setting up libpython3-stdlib:armhf (3.11.8-1) ... Setting up bioperl (1.7.8-1) ... Setting up libfabric1:armhf (1.17.0-3+b1) ... Setting up python3.11 (3.11.9-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up libhwloc-plugins:armhf (2.10.0-1+b1) ... Setting up ncbi-blast+ (2.12.0+ds-4+b1) ... Setting up libarray-compare-perl (3.0.8-1) ... Setting up libxml-simple-perl (2.25-2) ... Setting up libopenmpi3t64:armhf (4.1.6-13.2) ... Setting up bedtools-test (2.31.1+dfsg-2) ... Setting up openmpi-bin (4.1.6-13.2) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up phyml (3:3.3.20220408-3+b1) ... Setting up ncbi-blast+-legacy (2.12.0+ds-4) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libwww-perl (6.77-1) ... Setting up libbio-tools-run-remoteblast-perl (1.7.3-3) ... Setting up libxml-parser-perl (2.47-1+b2) ... Setting up libxml-twig-perl (1:3.52-3) ... Setting up libbio-variation-perl (1.7.5-3) ... Setting up libxml-perl (0.08-4) ... Setting up libbio-cluster-perl (1.7.3-6) ... Setting up libxml-dom-perl (1.46-2) ... Setting up libbio-asn1-entrezgene-perl (1.730-3) ... Setting up libxml-dom-xpath-perl (0.14-4) ... Setting up libbio-eutilities-perl (1.77-2) ... Setting up libbio-featureio-perl (1.6.905-2) ... Processing triggers for libc-bin (2.38-7) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps 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 dpkg-buildpackage: info: source package bioperl-run dpkg-buildpackage: info: source version 1.7.3-11 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/bioperl-run-1.7.3' dh_auto_configure -- --install_scripts /usr/bin/perl Build.PL --installdirs vendor --config "optimize=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bioperl-run-1.7.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=arm-linux-gnueabihf-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bioperl-run-1.7.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro" --install_scripts Do you want to run tests that require connection to servers across the internet (likely to cause some failures)? y/n [n ]n Can't find dist packages without a MANIFEST file Run 'Build manifest' to generate one WARNING: Possible missing or corrupt 'MANIFEST' file. Nothing to enter for 'provides' field in metafile. - will not run internet-requiring tests Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'BioPerl-Run' version '1.007003' make[1]: Leaving directory '/build/reproducible-path/bioperl-run-1.7.3' dh_auto_build /usr/bin/perl Build Building BioPerl-Run debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/bioperl-run-1.7.3' mkdir t.skip for t in Blat Eponine Glimmer2 RepeatMasker Phyml Hyphy MCS ; do mv t/${t}.t t.skip ; done PATH=$PATH:/usr/lib/emboss:/usr/lib/phylip/bin/:/usr/lib/tigr-glimmer:debian/test_hack_bin \ PHYLIPDIR=/usr/lib/phylip/bin HOME_4_TCOFFEE=/tmp COILSDIR=/usr/share/ncoils/ \ dh_auto_test --no-parallel /usr/bin/perl Build test --verbose 1 AMAP version AMAP.2.2 - align multiple protein sequences and print to standard output PROBCONS Written by Chuong Do AMAP algorithm implemented by Ariel Schwartz Using parameter set: initDistrib[] = { 0.400000006 0.3000000119 0.3000000119 } gapOpen[] = { 0.01993141696 0.01993141696 } gapExtend[] = { 0.7943345308 0.7943345308 } Loading sequence file: t/data/cysprot.fa Computing posterior matrices Building DAG Starting the sequence annealing process Creating candidate edge list Adding edges to the DAG AMAP version AMAP.2.2 - align multiple protein sequences and print to standard output PROBCONS Written by Chuong Do AMAP algorithm implemented by Ariel Schwartz Using parameter set: initDistrib[] = { 0.400000006 0.3000000119 0.3000000119 } gapOpen[] = { 0.01993141696 0.01993141696 } gapExtend[] = { 0.7943345308 0.7943345308 } Loading sequence file: /tmp/EK_V14p9OF Computing posterior matrices Building DAG Starting the sequence annealing process Creating candidate edge list Adding edges to the DAG t/Amap.t ...................... 1..18 ok 1 - use Bio::Tools::Run::Alignment::Amap; ok 2 - use Bio::SeqIO; ok 3 - use File::Spec; ok 4 - Found input file ok 5 - An object of class 'Bio::Tools::Run::Alignment::Amap' isa 'Bio::Tools::Run::Alignment::Amap' ok 6 - program_dir returned correct default ok 7 - error_string returned correct default ok 8 - aformat returned correct default ok 9 - outfile_name returned correct default ok 10 - Correct exe default name ok 11 - Correct minimum program version ok 12 - No error occured ok 13 - outfile_name returned something ok 14 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 15 - Correct number of seqs returned ok 16 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 17 - Correct number of seqs returned ok 18 - Got the correct ave % identity ok # Required executable for Bio::Tools::Run::BEDTools is not present t/BEDTools.t .................. 1..423 ok 1 - make a default factory ok 2 - default to command 'bam_to_bed' ok 3 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 4 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 5 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 6 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 7 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 8 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 9 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 10 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 11 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 12 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 13 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 14 # 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skip Required executable for Bio::Tools::Run::BEDTools is not present ok 210 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 211 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 212 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 213 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 214 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 215 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 216 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 217 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 218 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 219 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 220 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 221 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 222 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 223 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 224 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 225 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 226 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 227 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 228 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 229 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 230 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 231 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 232 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 233 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 234 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 235 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 236 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 237 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 238 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 239 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 240 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 241 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 242 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 243 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 244 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 245 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 246 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 247 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 248 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 249 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 250 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 251 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 252 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 253 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 254 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 255 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 256 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 257 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 258 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 259 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 260 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 261 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 262 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 263 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 264 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 265 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 266 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 267 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 268 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 269 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 270 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 271 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 272 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 273 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 274 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 275 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 276 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 277 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 278 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 279 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 280 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 281 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 282 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 283 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 284 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 285 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 286 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 287 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 288 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 289 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 290 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 291 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 292 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 293 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 294 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 295 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 296 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 297 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 298 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 299 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 300 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 301 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 302 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 303 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 304 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 305 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 306 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 307 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 308 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 309 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 310 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 311 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 312 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 313 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 314 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 315 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 316 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 317 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 318 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 319 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 320 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 321 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 322 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 323 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 324 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 325 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 326 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 327 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 328 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 329 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 330 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 331 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 332 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 333 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 334 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 335 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 336 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 337 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 338 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 339 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 340 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 341 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 342 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 343 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 344 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 345 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 346 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 347 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 348 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 349 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 350 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 351 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 352 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 353 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 354 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 355 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 356 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 357 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 358 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 359 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 360 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 361 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 362 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 363 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 364 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 365 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 366 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 367 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 368 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 369 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 370 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 371 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 372 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 373 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 374 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 375 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 376 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 377 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 378 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 379 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 380 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 381 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 382 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 383 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 384 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 385 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 386 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 387 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 388 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 389 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 390 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 391 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 392 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 393 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 394 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 395 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 396 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 397 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 398 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 399 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 400 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 401 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 402 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 403 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 404 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 405 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 406 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 407 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 408 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 409 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 410 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 411 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 412 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 413 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 414 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 415 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 416 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 417 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 418 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 419 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 420 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 421 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 422 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 423 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok # You named your test '71'. You shouldn't use numbers for your test names. # Very confusing. # You named your test '91'. You shouldn't use numbers for your test names. # Very confusing. t/Coil.t ...................... 1..6 ok 1 - use Bio::Tools::Run::Coil; ok 2 - use Bio::SeqIO; ok 3 ok 4 ok 5 - 71 ok 6 - 91 ok # Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present t/Consense.t .................. 1..8 ok 1 - use Bio::Tools::Run::Phylo::Phylip::Consense; ok 2 - use Bio::AlignIO; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok Warning Error Strangely truncated line in fasta file Warning Error Strangely truncated line in fasta file Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 6%] 4000 Cells done [ 8%] 5000 Cells done [10%] 6000 Cells done [12%] 7000 Cells done [14%] 8000 Cells done [16%] 9000 Cells done [19%] 10000 Cells done [21%] 11000 Cells done [23%] 12000 Cells done [25%] 13000 Cells done [27%] 14000 Cells done [29%] 15000 Cells done [31%] 16000 Cells done [33%] 17000 Cells done [35%] 18000 Cells done [38%] 19000 Cells done [40%] 20000 Cells done [42%] 21000 Cells done [44%] 22000 Cells done [46%] 23000 Cells done [48%] 24000 Cells done [50%] 25000 Cells done [52%] 26000 Cells done [55%] 27000 Cells done [57%] 28000 Cells done [59%] 29000 Cells done [61%] 30000 Cells done [63%] 31000 Cells done [65%] 32000 Cells done [67%] 33000 Cells done [69%] 34000 Cells done [71%] 35000 Cells done [74%] 36000 Cells done [76%] 37000 Cells done [78%] 38000 Cells done [80%] 39000 Cells done [82%] 40000 Cells done [84%] 41000 Cells done [86%] 42000 Cells done [88%] 43000 Cells done [90%] 44000 Cells done [93%] 45000 Cells done [95%] 46000 Cells done [97%] 47000 Cells done [99%][0,0][0,0] Score 0 Recovering alignment: [0,0][0,0] Explicit read offWarning Error Major problem (!) - in DnaMatchBlock read off, position 0,0 state 0 no source found! Warning Error In DnaMatchBlock hidden read off, between 0:0,0:0 - at got bad read off. Problem! Warning Error In full dc, at 0:0,0:0 got a bad hidden explicit read off... Warning Error Major problem (!) - in DnaMatchBlock matrix to special read off, position 0,0 state 0 no source found! Warning Error Problem in reading off special state system, hit a non start state (or an internal error) in a single alignment mode Warning Error Strangely truncated line in fasta file Warning Error Strangely truncated line in fasta file Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 7%] 4000 Cells done [ 9%] 5000 Cells done [12%] 6000 Cells done [14%] 7000 Cells done [16%] 8000 Cells done [19%] 9000 Cells done [21%] 10000 Cells done [24%] 11000 Cells done [26%] 12000 Cells done [28%] 13000 Cells done [31%] 14000 Cells done [33%] 15000 Cells done [36%] 16000 Cells done [38%] 17000 Cells done [40%] 18000 Cells done [43%] 19000 Cells done [45%] 20000 Cells done [48%] 21000 Cells done [50%] 22000 Cells done [52%] 23000 Cells done [55%] 24000 Cells done [57%] 25000 Cells done [60%] 26000 Cells done [62%] 27000 Cells done [64%] 28000 Cells done [67%] 29000 Cells done [69%] 30000 Cells done [72%] 31000 Cells done [74%] 32000 Cells done [76%] 33000 Cells done [79%] 34000 Cells done [81%] 35000 Cells done [84%] 36000 Cells done [86%] 37000 Cells done [89%] 38000 Cells done [91%] 39000 Cells done [93%] 40000 Cells done [96%] 41000 Cells done [98%][0,0][0,0] Score 0 Recovering alignment: [0,0][0,0] Explicit read offWarning Error Major problem (!) - in DnaMatchBlock read off, position 0,0 state 0 no source found! Warning Error In DnaMatchBlock hidden read off, between 0:0,0:0 - at got bad read off. Problem! Warning Error In full dc, at 0:0,0:0 got a bad hidden explicit read off... Warning Error Major problem (!) - in DnaMatchBlock matrix to special read off, position 0,0 state 0 no source found! Warning Error Problem in reading off special state system, hit a non start state (or an internal error) in a single alignment mode Warning Error Strangely truncated line in fasta file Warning Error Strangely truncated line in fasta file Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 6%] 4000 Cells done [ 8%] 5000 Cells done [10%] 6000 Cells done [12%] 7000 Cells done [14%] 8000 Cells done [16%] 9000 Cells done [19%] 10000 Cells done [21%] 11000 Cells done [23%] 12000 Cells done [25%] 13000 Cells done [27%] 14000 Cells done [29%] 15000 Cells done [31%] 16000 Cells done [33%] 17000 Cells done [35%] 18000 Cells done [38%] 19000 Cells done [40%] 20000 Cells done [42%] 21000 Cells done [44%] 22000 Cells done [46%] 23000 Cells done [48%] 24000 Cells done [50%] 25000 Cells done [52%] 26000 Cells done [55%] 27000 Cells done [57%] 28000 Cells done [59%] 29000 Cells done [61%] 30000 Cells done [63%] 31000 Cells done [65%] 32000 Cells done [67%] 33000 Cells done [69%] 34000 Cells done [71%] 35000 Cells done [74%] 36000 Cells done [76%] 37000 Cells done [78%] 38000 Cells done [80%] 39000 Cells done [82%] 40000 Cells done [84%] 41000 Cells done [86%] 42000 Cells done [88%] 43000 Cells done [90%] 44000 Cells done [93%] 45000 Cells done [95%] 46000 Cells done [97%] 47000 Cells done [99%][0,0][0,0] Score 0 Recovering alignment: [0,0][0,0] Explicit read offWarning Error Major problem (!) - in DnaMatchBlock read off, position 0,0 state 0 no source found! Warning Error In DnaMatchBlock hidden read off, between 0:0,0:0 - at got bad read off. Problem! Warning Error In full dc, at 0:0,0:0 got a bad hidden explicit read off... Warning Error Major problem (!) - in DnaMatchBlock matrix to special read off, position 0,0 state 0 no source found! Warning Error Problem in reading off special state system, hit a non start state (or an internal error) in a single alignment mode t/DBA.t ....................... 1..5 ok 1 - use Bio::Tools::Run::Alignment::DBA; ok 2 - use Bio::SimpleAlign; ok 3 - use Bio::AlignIO; ok 4 - use Bio::SeqIO; ok 5 - An object of class 'Bio::Tools::Run::Alignment::DBA' isa 'Bio::Tools::Run::Alignment::DBA' ok # Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present t/DrawGram.t .................. 1..6 ok 1 - use Bio::Tools::Run::Phylo::Phylip::DrawGram; ok 2 - use Bio::TreeIO; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present ok # Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present t/DrawTree.t .................. 1..6 ok 1 - use Bio::Tools::Run::Phylo::Phylip::DrawTree; ok 2 - use Bio::TreeIO; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present ok t/EMBOSS.t .................... 1..31 ok 1 - use Bio::Root::IO; ok 2 - use Bio::SeqIO; ok 3 - use Bio::AlignIO; ok 4 - use Bio::Factory::EMBOSS; ok 5 ok 6 # skip EMBOSS not installed ok 7 # skip EMBOSS not installed ok 8 # skip EMBOSS not installed ok 9 # skip EMBOSS not installed ok 10 # skip EMBOSS not installed ok 11 # skip EMBOSS not installed ok 12 # skip EMBOSS not installed ok 13 # skip EMBOSS not installed ok 14 # skip EMBOSS not installed ok 15 # skip EMBOSS not installed ok 16 # skip EMBOSS not installed ok 17 # skip EMBOSS not installed ok 18 # skip EMBOSS not installed ok 19 # skip EMBOSS not installed ok 20 # skip EMBOSS not installed ok 21 # skip EMBOSS not installed ok 22 # skip EMBOSS not installed ok 23 # skip EMBOSS not installed ok 24 # skip EMBOSS not installed ok 25 # skip EMBOSS not installed ok 26 # skip EMBOSS not installed ok 27 # skip EMBOSS not installed ok 28 # skip EMBOSS not installed ok 29 # skip EMBOSS not installed ok 30 # skip EMBOSS not installed ok 31 # skip EMBOSS not installed ok t/Exonerate.t ................. 1..89 ok 1 - use Bio::Tools::Run::Alignment::Exonerate; ok 2 - An object of class 'Bio::Tools::Run::Alignment::Exonerate' isa 'Bio::Tools::Run::Alignment::Exonerate' ok 3 ok 4 - An object of class 'Bio::SearchIO::exonerate' isa 'Bio::SearchIO' ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 - An object of class 'Bio::SearchIO::exonerate' isa 'Bio::SearchIO' ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok t/FastTree.t .................. 1..9 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Phylo::FastTree; ok 3 - use Bio::AlignIO; ok 4 - Make the object ok 5 - Tree is defined ok 6 - Number of nodes is correct ok 7 - Tree is defined ok 8 - Tree is defined ok 9 - Tree is defined ok # Required executable for Bio::Tools::Run::FootPrinter is not present t/FootPrinter.t ............... 1..24 ok 1 - use Bio::Tools::Run::FootPrinter; ok 2 - use Bio::SeqIO; ok 3 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 4 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 5 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 6 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 7 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 8 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 9 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 10 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 11 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 12 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 13 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 14 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 15 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 16 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 17 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 18 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 19 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 20 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 21 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 22 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 23 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 24 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok # Required environment variable $GENEMARK_MODELS is not set t/Genemark.hmm.prokaryotic.t .. 1..99 ok 1 - use Bio::Tools::Run::Genemark; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 # skip Required environment variable $GENEMARK_MODELS is not set ok 5 # skip Required environment variable $GENEMARK_MODELS is not set ok 6 # skip Required environment variable $GENEMARK_MODELS is not set ok 7 # skip Required environment variable $GENEMARK_MODELS is not set ok 8 # skip Required environment variable $GENEMARK_MODELS is not set ok 9 # skip Required environment variable $GENEMARK_MODELS is not set ok 10 # skip Required environment variable $GENEMARK_MODELS is not set ok 11 # skip Required environment variable $GENEMARK_MODELS is not set ok 12 # skip Required environment variable $GENEMARK_MODELS is not set ok 13 # skip Required environment variable $GENEMARK_MODELS is not set ok 14 # skip Required environment variable $GENEMARK_MODELS is not set ok 15 # skip Required environment variable $GENEMARK_MODELS is not set ok 16 # skip Required environment variable $GENEMARK_MODELS is not set ok 17 # skip Required environment variable $GENEMARK_MODELS is not set ok 18 # skip Required environment variable $GENEMARK_MODELS is not set ok 19 # skip Required environment variable $GENEMARK_MODELS is not set ok 20 # skip Required environment variable $GENEMARK_MODELS is not set ok 21 # skip Required environment variable $GENEMARK_MODELS is not set ok 22 # skip Required environment variable $GENEMARK_MODELS is not set ok 23 # skip Required environment variable $GENEMARK_MODELS is not set ok 24 # skip Required environment variable $GENEMARK_MODELS is not set ok 25 # skip Required environment variable $GENEMARK_MODELS is not set ok 26 # skip Required environment variable $GENEMARK_MODELS is not set ok 27 # skip Required environment variable $GENEMARK_MODELS is not set ok 28 # skip Required environment variable $GENEMARK_MODELS is not set ok 29 # skip Required environment variable $GENEMARK_MODELS is not set ok 30 # skip Required environment variable $GENEMARK_MODELS is not set ok 31 # skip Required environment variable $GENEMARK_MODELS is not set ok 32 # skip Required environment variable $GENEMARK_MODELS is not set ok 33 # skip Required environment variable $GENEMARK_MODELS is not set ok 34 # skip Required environment variable $GENEMARK_MODELS is not set ok 35 # skip Required environment variable $GENEMARK_MODELS is not set ok 36 # skip Required environment variable $GENEMARK_MODELS is not set ok 37 # skip Required environment variable $GENEMARK_MODELS is not set ok 38 # skip Required environment variable $GENEMARK_MODELS is not set ok 39 # skip Required environment variable $GENEMARK_MODELS is not set ok 40 # skip Required environment variable $GENEMARK_MODELS is not set ok 41 # skip Required environment variable $GENEMARK_MODELS is not set ok 42 # skip Required environment variable $GENEMARK_MODELS is not set ok 43 # skip Required environment variable $GENEMARK_MODELS is not set ok 44 # skip Required environment variable $GENEMARK_MODELS is not set ok 45 # skip Required environment variable $GENEMARK_MODELS is not set ok 46 # skip Required environment variable $GENEMARK_MODELS is not set ok 47 # skip Required environment variable $GENEMARK_MODELS is not set ok 48 # skip Required environment variable $GENEMARK_MODELS is not set ok 49 # skip Required environment variable $GENEMARK_MODELS is not set ok 50 # skip Required environment variable $GENEMARK_MODELS is not set ok 51 # skip Required environment variable $GENEMARK_MODELS is not set ok 52 # skip Required environment variable $GENEMARK_MODELS is not set ok 53 # skip Required environment variable $GENEMARK_MODELS is not set ok 54 # skip Required environment variable $GENEMARK_MODELS is not set ok 55 # skip Required environment variable $GENEMARK_MODELS is not set ok 56 # skip Required environment variable $GENEMARK_MODELS is not set ok 57 # skip Required environment variable $GENEMARK_MODELS is not set ok 58 # skip Required environment variable $GENEMARK_MODELS is not set ok 59 # skip Required environment variable $GENEMARK_MODELS is not set ok 60 # skip Required environment variable $GENEMARK_MODELS is not set ok 61 # skip Required environment variable $GENEMARK_MODELS is not set ok 62 # skip Required environment variable $GENEMARK_MODELS is not set ok 63 # skip Required environment variable $GENEMARK_MODELS is not set ok 64 # skip Required environment variable $GENEMARK_MODELS is not set ok 65 # skip Required environment variable $GENEMARK_MODELS is not set ok 66 # skip Required environment variable $GENEMARK_MODELS is not set ok 67 # skip Required environment variable $GENEMARK_MODELS is not set ok 68 # skip Required environment variable $GENEMARK_MODELS is not set ok 69 # skip Required environment variable $GENEMARK_MODELS is not set ok 70 # skip Required environment variable $GENEMARK_MODELS is not set ok 71 # skip Required environment variable $GENEMARK_MODELS is not set ok 72 # skip Required environment variable $GENEMARK_MODELS is not set ok 73 # skip Required environment variable $GENEMARK_MODELS is not set ok 74 # skip Required environment variable $GENEMARK_MODELS is not set ok 75 # skip Required environment variable $GENEMARK_MODELS is not set ok 76 # skip Required environment variable $GENEMARK_MODELS is not set ok 77 # skip Required environment variable $GENEMARK_MODELS is not set ok 78 # skip Required environment variable $GENEMARK_MODELS is not set ok 79 # skip Required environment variable $GENEMARK_MODELS is not set ok 80 # skip Required environment variable $GENEMARK_MODELS is not set ok 81 # skip Required environment variable $GENEMARK_MODELS is not set ok 82 # skip Required environment variable $GENEMARK_MODELS is not set ok 83 # skip Required environment variable $GENEMARK_MODELS is not set ok 84 # skip Required environment variable $GENEMARK_MODELS is not set ok 85 # skip Required environment variable $GENEMARK_MODELS is not set ok 86 # skip Required environment variable $GENEMARK_MODELS is not set ok 87 # skip Required environment variable $GENEMARK_MODELS is not set ok 88 # skip Required environment variable $GENEMARK_MODELS is not set ok 89 # skip Required environment variable $GENEMARK_MODELS is not set ok 90 # skip Required environment variable $GENEMARK_MODELS is not set ok 91 # skip Required environment variable $GENEMARK_MODELS is not set ok 92 # skip Required environment variable $GENEMARK_MODELS is not set ok 93 # skip Required environment variable $GENEMARK_MODELS is not set ok 94 # skip Required environment variable $GENEMARK_MODELS is not set ok 95 # skip Required environment variable $GENEMARK_MODELS is not set ok 96 # skip Required environment variable $GENEMARK_MODELS is not set ok 97 # skip Required environment variable $GENEMARK_MODELS is not set ok 98 # skip Required environment variable $GENEMARK_MODELS is not set ok 99 # skip Required environment variable $GENEMARK_MODELS is not set ok These tests may fail because I'm not sure about your genewise version -- using wise 2.2.3-rc7 values t/Genewise.t .................. 1..17 ok 1 - use Bio::Tools::Run::Genewise; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Genewise' isa 'Bio::Tools::Run::Genewise' ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok # Required environment variable $GENSCANDIR is not set t/Genscan.t ................... 1..6 ok 1 - use Bio::Tools::Run::Genscan; ok 2 - use Bio::Root::IO; ok 3 # skip Required environment variable $GENSCANDIR is not set ok 4 # skip Required environment variable $GENSCANDIR is not set ok 5 # skip Required environment variable $GENSCANDIR is not set ok 6 # skip Required environment variable $GENSCANDIR is not set ok # Required executable for Bio::Tools::Run::Phylo::Gerp is not present t/Gerp.t ...................... 1..33 ok 1 - use Bio::Tools::Run::Phylo::Gerp; ok 2 - use Bio::AlignIO; ok 3 - use Bio::TreeIO; ok 4 - use Bio::Root::Utilities; ok 5 - Found input alignment file ok 6 - Found input tree file ok 7 - An object of class 'Bio::Tools::Run::Phylo::Gerp' isa 'Bio::Tools::Run::Phylo::Gerp' ok 8 - has a created method not in args supplied to new ok 9 - quiet was set ok 10 - program_dir returned correct default ok 11 - Correct exe default name ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 15 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 20 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 21 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 22 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 23 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 24 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 25 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 26 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 27 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 28 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 29 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 30 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 31 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 32 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 33 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok # Required executable for Bio::Tools::Run::Glimmer is not present t/Glimmer3.t .................. 1..111 ok 1 - use Bio::Tools::Run::Glimmer; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Glimmer' isa 'Bio::Tools::Run::Glimmer' ok 5 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 6 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 7 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 8 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 9 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 10 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 11 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 12 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 13 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 14 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 15 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 16 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 17 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 18 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 19 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 20 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 21 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 22 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 23 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 24 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 25 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 26 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 27 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 28 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 29 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 30 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 31 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 32 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 33 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 34 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 35 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 36 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 37 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 38 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 39 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 40 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 41 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 42 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 43 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 44 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 45 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 46 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 47 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 48 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 49 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 50 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 51 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 52 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 53 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 54 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 55 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 56 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 57 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 58 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 59 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 60 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 61 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 62 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 63 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 64 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 65 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 66 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 67 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 68 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 69 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 70 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 71 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 72 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 73 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 74 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 75 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 76 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 77 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 78 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 79 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 80 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 81 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 82 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 83 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 84 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 85 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 86 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 87 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 88 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 89 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 90 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 91 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 92 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 93 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 94 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 95 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 96 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 97 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 98 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 99 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 100 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 101 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 102 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 103 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 104 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 105 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 106 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 107 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 108 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 109 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 110 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok 111 # skip Required executable for Bio::Tools::Run::Glimmer is not present ok # Required executable for Bio::Tools::Run::Hmmer is not present t/Hmmer.t ..................... 1..27 ok 1 - use Bio::Tools::Run::Hmmer; ok 2 - use Bio::SeqIO; ok 3 - use Bio::AlignIO; ok 4 - An object of class 'Bio::Tools::Run::Hmmer' isa 'Bio::Tools::Run::Hmmer' ok 5 ok 6 ok 7 ok 8 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 9 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 10 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 11 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 12 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 13 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 14 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 15 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 16 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 17 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 18 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 19 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 20 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 21 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 22 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 23 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 24 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 25 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 26 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 27 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok t/Infernal.t .................. 1..3 ok 1 - use Bio::Tools::Run::Infernal; ok 2 - use Bio::SeqIO; ok 3 - use Bio::AlignIO; ok t/Kalign.t .................... 1..7 ok 1 - use Bio::Tools::Run::Alignment::Kalign; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - Code tested only on kalign versions >= 2 Kalign (3.4.0) Copyright (C) 2006,2019,2020,2021,2023 Timo Lassmann This program comes with ABSOLUTELY NO WARRANTY; for details type: `kalign -showw'. This is free software, and you are welcome to redistribute it under certain conditions; consult the COPYING file for details. Please cite: Lassmann, Timo. "Kalign 3: multiple sequence alignment of large data sets." Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795 [2024-05-09 05:47:25] : LOG : Detected protein sequences. [2024-05-09 05:47:25] : LOG : Read 7 sequences from standard input. [2024-05-09 05:47:25] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 [2024-05-09 05:47:25] : LOG : Calculating pairwise distances [2024-05-09 05:47:25] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 [2024-05-09 05:47:25] : LOG : Building guide tree. [2024-05-09 05:47:25] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 [2024-05-09 05:47:25] : LOG : Aligning [2024-05-09 05:47:25] : LOG : CPU Time: 0.12u 00:00:00.12 Elapsed: 00:00:00.00 ok 5 ok 6 Kalign (3.4.0) Copyright (C) 2006,2019,2020,2021,2023 Timo Lassmann This program comes with ABSOLUTELY NO WARRANTY; for details type: `kalign -showw'. This is free software, and you are welcome to redistribute it under certain conditions; consult the COPYING file for details. Please cite: Lassmann, Timo. "Kalign 3: multiple sequence alignment of large data sets." Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795 [2024-05-09 05:47:25] : LOG : Detected protein sequences. [2024-05-09 05:47:25] : LOG : Read 7 sequences from standard input. [2024-05-09 05:47:25] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2024-05-09 05:47:25] : LOG : Calculating pairwise distances [2024-05-09 05:47:25] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 [2024-05-09 05:47:25] : LOG : Building guide tree. [2024-05-09 05:47:25] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 [2024-05-09 05:47:25] : LOG : Aligning [2024-05-09 05:47:25] : LOG : CPU Time: 0.09u 00:00:00.09 Elapsed: 00:00:00.00 ok 7 ok # Required executable for Bio::Tools::Run::Phylo::LVB is not present t/LVB.t ....................... 1..19 ok 1 - use Bio::Tools::Run::Phylo::LVB; ok 2 - use Bio::AlignIO; ok 3 - An object of class 'Bio::Tools::Run::Phylo::LVB' isa 'Bio::Tools::Run::Phylo::LVB' ok 4 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 12 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 14 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 15 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 16 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 17 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 18 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 19 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok # Required executable for Bio::Tools::Run::Alignment::Lagan is not present t/Lagan.t ..................... 1..12 ok 1 - use Bio::AlignIO; ok 2 - use Bio::Tools::Run::Alignment::Lagan; ok 3 - use Bio::Root::IO; ok 4 - use Bio::SeqIO; ok 5 - use Bio::Seq; ok 6 - use Bio::Matrix::Mlagan; ok 7 - An object of class 'Bio::Tools::Run::Alignment::Lagan' isa 'Bio::Tools::Run::Alignment::Lagan' ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present ok 9 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present ok 10 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present ok 11 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present ok 12 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present ok t/MAFFT.t ..................... 1..23 ok 1 - use Bio::Tools::Run::Alignment::MAFFT; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - An object of class 'Bio::Tools::Run::Alignment::MAFFT' isa 'Bio::Tools::Run::Alignment::MAFFT' ok 5 ok 6 ok 7 ok 8 ok 9 - 42 or 43 expected ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 # skip Tests require version 6 of MAFFT ok 19 # skip Tests require version 6 of MAFFT ok 20 # skip Tests require version 6 of MAFFT ok 21 # skip Tests require version 6 of MAFFT ok 22 # skip Tests require version 6 of MAFFT ok 23 # skip Tests require version 6 of MAFFT ok # Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present t/MSAProbs.t .................. 1..19 ok 1 - use Bio::Tools::Run::Alignment::MSAProbs; ok 2 - use Bio::Tools::GuessSeqFormat; ok 3 - use Bio::AlignIO; ok 4 - use Bio::SeqIO; ok 5 - use Bio::Root::IO; ok 6 - use POSIX; ok 7 ok 8 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 9 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 10 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 11 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 12 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 13 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 14 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 15 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 16 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 17 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 18 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 19 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok # Required executable for Bio::Tools::Run::Match is not present t/Match.t ..................... 1..7 ok 1 - use Bio::Tools::Run::Match; ok 2 - An object of class 'Bio::Tools::Run::Match' isa 'Bio::Tools::Run::Match' ok 3 - mxlib parameter was set ok 4 - program_dir returned correct default ok 5 - Correct exe default name ok 6 # skip Required executable for Bio::Tools::Run::Match is not present ok 7 # skip Required executable for Bio::Tools::Run::Match is not present ok # Required executable for Bio::Tools::Run::Mdust is not present t/Mdust.t ..................... 1..5 ok 1 - use Bio::Tools::Run::Mdust; ok 2 - use Bio::SeqIO; ok 3 - An object of class 'Bio::Tools::Run::Mdust' isa 'Bio::Tools::Run::Mdust' ok 4 # skip Required executable for Bio::Tools::Run::Mdust is not present ok 5 # skip Required executable for Bio::Tools::Run::Mdust is not present ok # Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present t/Molphy.t .................... 1..10 ok 1 - use Bio::Tools::Phylo::Molphy; ok 2 - use Bio::Tools::Run::Phylo::Molphy::ProtML; ok 3 - use Bio::AlignIO; ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok t/Muscle.t .................... 1..16 ok 1 - use Bio::Tools::Run::Alignment::Muscle; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - use Bio::Root::IO; ok 5 - use POSIX; ok 6 ok 7 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests ok 8 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests ok 9 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests ok 10 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests ok 11 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests ok 12 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests ok 13 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests ok 14 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests ok 15 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests ok 16 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests ok # Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present t/Neighbor.t .................. 1..19 ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtDist; ok 2 - use Bio::Tools::Run::Phylo::Phylip::Neighbor; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 15 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok # Required executable for Bio::Tools::Run::Phylo::Njtree::Best is not present t/Njtree.t .................... 1..6 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Phylo::Njtree::Best; ok 3 - use Bio::AlignIO; ok 4 - use Bio::TreeIO; ok 5 ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Njtree::Best is not present ok --------------------- WARNING --------------------- MSG: In sequence pseudogene residue count gives end value 183. Overriding value [178] with value 183 for Bio::LocatableSeq::end(). ----LNCIVNDSQKMGIIRNGDLP*PQLKNKF2-FQRMTTPSSAEGKENLVFLIRKNWFSITEKNQPLKYIINLVVSRESKEPPQRPPFLD*SLGDALKRIEQLKLANKQDVFFTVGGSSVYKESMN*-DHFKLFVTWIMQDFQSDTFFS4EGDLEKYKLLPEYPQGVVSDVEEEKGIKYKFEVYEKND --------------------------------------------------- --------------------- WARNING --------------------- MSG: In sequence pseudogene residue count gives end value 183. Overriding value [178] with value 183 for Bio::LocatableSeq::end(). ----LNCIVNDSQKMGIIRNGDLP*PQLKNKF2-FQRMTTPSSAEGKENLVFLIRKNWFSITEKNQPLKYIINLVVSRESKEPPQRPPFLD*SLGDALKRIEQLKLANKQDVFFTVGGSSVYKESMN*-DHFKLFVTWIMQDFQSDTFFS4EGDLEKYKLLPEYPQGVVSDVEEEKGIKYKFEVYEKND --------------------------------------------------- t/Pal2Nal.t ................... 1..9 ok 1 - use Bio::Tools::Run::Alignment::Pal2Nal; ok 2 - An object of class 'Bio::Tools::Run::Alignment::Pal2Nal' isa 'Bio::Tools::Run::Alignment::Pal2Nal' ok 3 - program_dir returned correct default ok 4 - Correct exe default name ok 5 ok 6 - use Bio::AlignIO; ok 7 - use Bio::SeqIO; ok 8 ok 9 ok # Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present t/PhastCons.t ................. 1..181 ok 1 - use Bio::AlignIO; ok 2 - use Bio::TreeIO; ok 3 - use Bio::DB::Taxonomy; ok 4 - Found input alignment file ok 5 - Found input tree file ok 6 - use Bio::Tools::Run::Phylo::Phast::PhastCons; ok 7 - An object of class 'Bio::Tools::Run::Phylo::Phast::PhastCons' isa 'Bio::Tools::Run::Phylo::Phast::PhastCons' ok 8 - has a created method not in args ok 9 - dashed parameter with internal dash was set ok 10 - wrong-case method wasn't created ok 11 - dashless wrong-case parameter was set ok 12 - synonym installed and accessed primary value ok 13 - double-dashed parameter was set ok 14 - program_dir returned correct default ok 15 - Correct exe default name ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 20 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 21 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 22 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 23 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 24 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 25 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 26 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 27 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 28 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 29 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 30 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 31 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 32 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 33 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 34 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 35 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 36 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 37 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 38 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 39 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 40 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 41 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 42 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 43 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 44 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 45 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 46 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 47 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 48 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 49 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 50 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 51 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 52 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 53 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 54 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 55 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 56 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 57 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 58 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 59 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 60 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 61 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 62 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 63 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 64 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 65 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 66 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 67 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 68 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 69 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 70 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 71 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 72 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 73 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 74 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 75 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 76 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 77 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 78 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 79 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 80 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 81 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 82 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 83 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 84 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 85 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 86 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 87 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 88 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 89 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 90 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 91 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 92 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 93 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 94 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 95 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 96 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 97 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 98 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 99 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 100 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 101 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 102 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 103 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 104 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 105 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 106 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 107 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 108 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 109 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 110 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 111 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 112 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 113 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 114 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 115 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 116 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 117 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 118 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 119 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 120 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 121 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 122 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 123 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 124 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 125 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 126 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 127 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 128 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 129 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 130 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 131 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 132 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 133 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 134 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 135 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 136 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 137 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 138 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 139 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 140 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 141 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 142 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 143 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 144 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 145 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 146 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 147 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 148 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 149 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 150 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 151 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 152 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 153 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 154 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 155 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 156 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 157 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 158 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 159 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 160 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 161 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 162 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 163 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 164 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 165 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 166 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 167 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 168 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 169 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 170 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 171 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 172 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 173 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 174 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 175 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 176 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 177 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 178 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 179 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 180 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 181 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok # Required executable for Bio::Tools::Run::Primate is not present t/Primate.t ................... 1..8 ok 1 - use Bio::Tools::Run::Primate; ok 2 - use Bio::SeqIO; ok 3 # skip Required executable for Bio::Tools::Run::Primate is not present ok 4 # skip Required executable for Bio::Tools::Run::Primate is not present ok 5 # skip Required executable for Bio::Tools::Run::Primate is not present ok 6 # skip Required executable for Bio::Tools::Run::Primate is not present ok 7 # skip Required executable for Bio::Tools::Run::Primate is not present ok 8 # skip Required executable for Bio::Tools::Run::Primate is not present ok t/Primer3.t ................... 1..9 ok 1 - use Bio::Tools::Run::Primer3; ok 2 - use Bio::SeqIO; ok 3 ok 4 # skip Primer3 wrapper only supports Primer3 v1 ok 5 # skip Primer3 wrapper only supports Primer3 v1 ok 6 # skip Primer3 wrapper only supports Primer3 v1 ok 7 # skip Primer3 wrapper only supports Primer3 v1 ok 8 # skip Primer3 wrapper only supports Primer3 v1 ok 9 # skip Primer3 wrapper only supports Primer3 v1 ok # Required executable for Bio::Tools::Run::Prints is not present t/Prints.t .................... 1..7 ok 1 - use Bio::Tools::Run::Prints; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Prints' isa 'Bio::Tools::Run::Prints' ok 5 # skip Required executable for Bio::Tools::Run::Prints is not present ok 6 # skip Required executable for Bio::Tools::Run::Prints is not present ok 7 # skip Required executable for Bio::Tools::Run::Prints is not present ok # Required executable for Bio::Tools::Run::Alignment::Probalign is not present t/Probalign.t ................. 1..13 ok 1 - use Bio::Tools::Run::Alignment::Probalign; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - use Cwd; ok 5 - use POSIX; ok 6 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 7 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 9 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 10 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 11 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 12 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 13 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok PROBCONS version 1.12 - align multiple protein sequences and print to standard output Written by Chuong Do Using parameter set: initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } Loading sequence file: t/data/cysprot.fa Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) PROBCONS version 1.12 - align multiple protein sequences and print to standard output Written by Chuong Do Using parameter set: initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } Loading sequence file: /tmp/EPET6CEtdR Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) PROBCONS version 1.12 - align multiple protein sequences and print to standard output Written by Chuong Do Using parameter set: initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } Loading sequence file: /tmp/IPRD2pi1Zx 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. Computing posterior matrix: (1) CYS1_DICDI vs. (5) CATL_HUMAN -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (6) CATL_RAT -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (7) PAPA_CARPA -- done. Computing posterior matrix: (2) ALEU_HORVU vs. (3) CATH_HUMAN -- done. Computing posterior matrix: (2) ALEU_HORVU vs. (4) CATH_RAT -- done. Computing posterior matrix: (2) ALEU_HORVU vs. (5) CATL_HUMAN -- done. Computing posterior matrix: (2) ALEU_HORVU vs. (6) CATL_RAT -- done. Computing posterior matrix: (2) ALEU_HORVU vs. (7) PAPA_CARPA -- done. Computing posterior matrix: (3) CATH_HUMAN vs. (4) CATH_RAT -- done. Computing posterior matrix: (3) CATH_HUMAN vs. (5) CATL_HUMAN -- done. Computing posterior matrix: (3) CATH_HUMAN vs. (6) CATL_RAT -- done. Computing posterior matrix: (3) CATH_HUMAN vs. (7) PAPA_CARPA -- done. Computing posterior matrix: (4) CATH_RAT vs. (5) CATL_HUMAN -- done. Computing posterior matrix: (4) CATH_RAT vs. (6) CATL_RAT -- done. Computing posterior matrix: (4) CATH_RAT vs. (7) PAPA_CARPA -- done. Computing posterior matrix: (5) CATL_HUMAN vs. (6) CATL_RAT -- done. Computing posterior matrix: (5) CATL_HUMAN vs. (7) PAPA_CARPA -- done. Computing posterior matrix: (6) CATL_RAT vs. (7) PAPA_CARPA -- done. Trained parameter set: initDistrib[] = { 0.8318762183 5.24617426e-05 5.24617426e-05 0.08400939405 0.08400939405 } gapOpen[] = { 0.01386300847 0.01386300847 0.006556313485 0.006556313485 } gapExtend[] = { 0.360332042 0.360332042 0.7831901312 0.7831901312 } PROBCONS version 1.12 - align multiple protein sequences and print to standard output Written by Chuong Do Using parameter set: initDistrib[] = { 0.8318762183 5.246169894e-05 5.246169894e-05 0.08400939405 0.08400939405 } gapOpen[] = { 0.01386300847 0.01386300847 0.006556313485 0.006556313485 } gapExtend[] = { 0.360332042 0.360332042 0.7831901312 0.7831901312 } Loading sequence file: /tmp/6vJ3M9TvAc Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) t/Probcons.t .................. 1..11 ok 1 - use Bio::Tools::Run::Alignment::Probcons; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - Code tested only on probcons versions > 1.09 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok # Required executable for Bio::Tools::Run::Profile is not present t/Profile.t ................... 1..7 ok 1 - use Bio::Tools::Run::Profile; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Profile' isa 'Bio::Tools::Run::Profile' ok 5 # skip Required executable for Bio::Tools::Run::Profile is not present ok 6 # skip Required executable for Bio::Tools::Run::Profile is not present ok 7 # skip Required executable for Bio::Tools::Run::Profile is not present ok t/Promoterwise.t .............. 1..9 ok 1 - use Bio::Tools::Run::Promoterwise; ok 2 - use Bio::Seq; ok 3 - An object of class 'Bio::Tools::Run::Promoterwise' isa 'Bio::Tools::Run::Promoterwise' ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok t/ProtDist.t .................. 1..14 ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtDist; ok 2 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 3 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 4 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 5 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 6 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 7 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 8 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 9 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 10 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 11 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 12 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 13 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 14 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok t/ProtPars.t .................. 1..11 ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtPars; ok 2 - An object of class 'Bio::Tools::Run::Phylo::Phylip::ProtPars' isa 'Bio::Tools::Run::Phylo::Phylip::ProtPars' ok 3 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 4 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 5 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 6 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 7 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 8 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 9 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 10 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 11 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok # Required executable for Bio::Tools::Run::Pseudowise is not present t/Pseudowise.t ................ 1..18 ok 1 - use Bio::Tools::Run::Pseudowise; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 ok 5 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 6 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 7 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 8 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 9 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 10 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 11 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 12 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 13 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 14 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 15 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 16 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 17 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 18 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok # Required executable for Bio::Tools::Run::Phylo::QuickTree is not present t/QuickTree.t ................. 1..13 ok 1 - use Bio::Tools::Run::Phylo::QuickTree; ok 2 - use Bio::AlignIO; ok 3 - Found input file ok 4 - An object of class 'Bio::Tools::Run::Phylo::QuickTree' isa 'Bio::Tools::Run::Phylo::QuickTree' ok 5 - program_dir returned correct default ok 6 - Correct exe default name ok 7 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 12 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok t/Raxml.t ..................... 1..12 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Phylo::Raxml; ok 3 - use Bio::AlignIO; ok 4 - Make the object ok 5 - An object of class 'Bio::Tools::Run::Phylo::Raxml' isa 'Bio::Tools::Run::Phylo::Raxml' ok 6 - Tree is defined ok 7 - Tree is defined ok 8 - File containing best tree exists in tempdir ok 9 - Tree is defined ok 10 - Tree is defined ok 11 - Number of nodes is correct ok 12 - Tree is defined ok # DB and mask make tests # run BLAST methods t/SABlastPlus.t ............... 1..71 ok 1 - use Bio::Tools::Run::StandAloneBlastPlus; ok 2 - use Bio::Tools::Run::WrapperBase; ok 3 - use Bio::Tools::Run::WrapperBase::CommandExts; ok 4 - BlastPlus factory ok 5 - make factory ok 6 - test db made with fasta ok 7 - temp db ok 8 - right type ok 9 ok 10 - named db made ok 11 - check_db ok 12 - correct name ok 13 - dbinfo hash returned ok 14 - correct type ok 15 - windowmasker mask made ok 16 - dustmasker mask made ok 17 - check_db with arg ok 18 - db_info with arg ok 19 - protein db made ok 20 - correct type ok 21 - segmasker mask made ok 22 - segmasker mask made; blastdb as data ok 23 ok 24 - protein db made with pre-built mask ok 25 - db_info records mask info ok 26 ok 27 - mask built and db made on construction (windowmasker) ok 28 ok 29 - mask built and db made on construction (segmasker) ok 30 ok 31 - mask built and db made on construction (dustmasker) ok 32 ok 33 ok 34 ok 35 - make db from Bio::SeqIO ok 36 ok 37 - make db from Bio::AlignIO ok 38 ok 39 - make db from \@seqs ok 40 - dbdir : ./a/b; dbname : test; create ok 41 - make db ok 42 ok 43 ok 44 ok 45 ok 46 - run blastn ok 47 - default hit limit ok 48 - return more alignments (arg spec) ok 49 - got more hits ok 50 - run blastn with Bio::Seq query ok 51 - run tblastn ok 52 - tblastn hits ok 53 - run tblastx ok 54 - tblastx hits ok 55 ok 56 - run blastp ok 57 - blastp hits ok 58 - bl2seq (blastn) ok 59 - got hit ok 60 - bl2seq (tblastx) ok 61 - got hit ok 62 - bl2seq (blastx) ok 63 - got hit ok 64 - bl2seq (blastp) ok 65 - no hit ok 66 - bl2seq (blastp) ok 67 - got hit ok 68 - bl2seq (tblastx) - multiple outfmt options ok 69 - bl2seq (tblastx) - multiple outfmt options (use method arg) ok 70 - bl2seq (tblastx) - multiple outfmt options (no explict quotes should also work) ok 71 - bl2seq (tblastx) - multiple outfmt options (a single format number in quotes ok # Required executable for Bio::Tools::Run::Phylo::SLR is not present t/SLR.t ....................... 1..7 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Phylo::SLR; ok 3 - use Bio::AlignIO; ok 4 - use Bio::TreeIO; ok 5 ok 6 # skip Required executable for Bio::Tools::Run::Phylo::SLR is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::SLR is not present ok # Required executable for Bio::Tools::Run::Samtools is not present t/Samtools.t .................. 1..41 ok 1 - make a factory using command 'pileup' ok 2 - parameters changed on construction ok 3 - access parameter ok 4 - parameters_changed cleared on read ok 5 - set a param not set in constructor ok 6 - parameters_changed set ok 7 - parameter really set ok 8 - original parameter unchanged ok 9 - parameters_changed cleared on read ok 10 - change an original parameter ok 11 - parameter really changed ok 12 - reset parameters with arg ok 13 - original parameters undefined ok 14 - parameter really reset via arg ok 15 - parameters changed ok 16 - all available options ok 17 - available parameters ok 18 - available switches ok 19 - get_parameters correct ok 20 - command attribute set ok 21 - internal command array set ok 22 - internal prefix hash set ok 23 - commands filtered by prefix ok 24 - translate_params: command correct ok 25 - translate_params: options correct ok 26 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 27 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 28 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 29 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 30 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 31 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 32 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 33 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 34 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 35 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 36 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 37 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 38 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 39 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 40 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 41 # skip Required executable for Bio::Tools::Run::Samtools is not present ok # Required executable for Bio::Tools::Run::Seg is not present t/Seg.t ....................... 1..8 ok 1 - use Bio::Tools::Run::Seg; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Seg' isa 'Bio::Tools::Run::Seg' ok 5 # skip Required executable for Bio::Tools::Run::Seg is not present ok 6 # skip Required executable for Bio::Tools::Run::Seg is not present ok 7 # skip Required executable for Bio::Tools::Run::Seg is not present ok 8 # skip Required executable for Bio::Tools::Run::Seg is not present ok # Required executable for Bio::Tools::Run::Phylo::Semphy is not present t/Semphy.t .................... 1..19 ok 1 - use Bio::Tools::Run::Phylo::Semphy; ok 2 - An object of class 'Bio::Tools::Run::Phylo::Semphy' isa 'Bio::Tools::Run::Phylo::Semphy' ok 3 - has a created method not in args ok 4 - ratio param was set via -z ok 5 - jtt switch was set ok 6 - program_dir returned correct default ok 7 - Correct exe default name ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 15 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok # Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present t/SeqBoot.t ................... 1..9 ok 1 - use Bio::Tools::Run::Phylo::Phylip::SeqBoot; ok 2 - use Bio::AlignIO; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok # Required executable for Bio::Tools::Run::Signalp is not present t/Signalp.t ................... 1..7 ok 1 - use Bio::Tools::Run::Signalp; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Signalp' isa 'Bio::Tools::Run::Signalp' ok 5 # skip Required executable for Bio::Tools::Run::Signalp is not present ok 6 # skip Required executable for Bio::Tools::Run::Signalp is not present ok 7 # skip Required executable for Bio::Tools::Run::Signalp is not present ok t/Sim4.t ...................... 1..23 ok 1 - use Bio::Tools::Run::Alignment::Sim4; ok 2 - use Bio::SimpleAlign; ok 3 - use Bio::AlignIO; ok 4 - use Bio::SeqIO; ok 5 - An object of class 'Bio::Tools::Run::Alignment::Sim4' isa 'Bio::Tools::Run::Alignment::Sim4' ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok # Required executable for Bio::Tools::Run::Simprot is not present t/Simprot.t ................... 1..6 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Simprot; ok 3 - use Bio::AlignIO; ok 4 - use Bio::TreeIO; ok 5 ok 6 # skip Required executable for Bio::Tools::Run::Simprot is not present ok t/SoapEU-function.t ........... skipped: The optional module Bio::DB::ESoap (or dependencies thereof) was not installed t/SoapEU-unit.t ............... skipped: The optional module Bio::DB::ESoap (or dependencies thereof) was not installed # Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present t/StandAloneFasta.t ........... 1..15 ok 1 - use Bio::Tools::Run::Alignment::StandAloneFasta; ok 2 - use Bio::SeqIO; ok 3 ok 4 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 5 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 6 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 7 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 8 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 9 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 10 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 11 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 12 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 13 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 14 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 15 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok # Required executable for Bio::Tools::Run::Tmhmm is not present t/Tmhmm.t ..................... 1..9 ok 1 - use Bio::Tools::Run::Tmhmm; ok 2 - use Bio::SeqIO; ok 3 - An object of class 'Bio::Tools::Run::Tmhmm' isa 'Bio::Tools::Run::Tmhmm' ok 4 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 5 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 6 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 7 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 8 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 9 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok t/TribeMCL.t .................. 1..24 ok 1 - use Bio::Tools::Run::TribeMCL; ok 2 - use Bio::SearchIO; ok 3 - An object of class 'Bio::Tools::Run::TribeMCL' isa 'Bio::Tools::Run::TribeMCL' ok 4 # skip Tribe Matrix program not found. Skipping tests... ok 5 # skip Tribe Matrix program not found. Skipping tests... ok 6 # skip Tribe Matrix program not found. Skipping tests... ok 7 # skip Tribe Matrix program not found. Skipping tests... ok 8 # skip Tribe Matrix program not found. Skipping tests... ok 9 # skip Tribe Matrix program not found. Skipping tests... ok 10 # skip Tribe Matrix program not found. Skipping tests... ok 11 # skip Tribe Matrix program not found. Skipping tests... ok 12 # skip Tribe Matrix program not found. Skipping tests... ok 13 # skip Tribe Matrix program not found. Skipping tests... ok 14 # skip Tribe Matrix program not found. Skipping tests... ok 15 # skip Tribe Matrix program not found. Skipping tests... ok 16 # skip Tribe Matrix program not found. Skipping tests... ok 17 # skip Tribe Matrix program not found. Skipping tests... ok 18 # skip Tribe Matrix program not found. Skipping tests... ok 19 # skip Tribe Matrix program not found. Skipping tests... ok 20 # skip Tribe Matrix program not found. Skipping tests... ok 21 # skip Tribe Matrix program not found. Skipping tests... ok 22 # skip Tribe Matrix program not found. Skipping tests... ok 23 # skip Tribe Matrix program not found. Skipping tests... ok 24 # skip Tribe Matrix program not found. Skipping tests... ok t/Vista.t ..................... 1..7 ok 1 - use Bio::Tools::Run::Vista; ok 2 - use Bio::AlignIO; ok 3 # skip Skipping due to old java version ok 4 # skip Skipping due to old java version ok 5 # skip Skipping due to old java version ok 6 # skip Skipping due to old java version ok 7 # skip Skipping due to old java version ok # Required executable for Bio::Tools::Run::Alignment::Gmap is not present t/gmap-run.t .................. 1..8 ok 1 - use Bio::Tools::Run::Alignment::Gmap; ok 2 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 3 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 4 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 5 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 6 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 7 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok # Required executable for Bio::Tools::Run::tRNAscanSE is not present t/tRNAscanSE.t ................ 1..12 ok 1 - use Bio::Tools::Run::tRNAscanSE; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::tRNAscanSE' isa 'Bio::Tools::Run::tRNAscanSE' ok 5 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 6 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 7 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 8 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 9 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 10 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 11 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 12 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok All tests successful. Files=60, Tests=1652, 433 wallclock secs ( 1.82 usr 0.44 sys + 412.06 cusr 20.94 csys = 435.26 CPU) Result: PASS mv t.skip/* t rm -rf t.skip make[1]: Leaving directory '/build/reproducible-path/bioperl-run-1.7.3' create-stamp debian/debhelper-build-stamp dh_prep 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_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_run_protdist.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_multi_hmmsearch.pl.1p 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/Tools/Run/EMBOSSApplication.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/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/Eponine.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/EMBOSSacd.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/Infernal.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/Mdust.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/Simprot.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/Coil.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/RepeatMasker.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/Genscan.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/Prints.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/StandAloneBlast.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/Tmhmm.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/StandAloneBlastPlus.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/RNAMotif.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/Genewise.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/StandAloneWUBlast.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/tRNAscanSE.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/Pseudowise.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/AnalysisFactory/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/Alignment/Lagan.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/Probalign.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/Pal2Nal.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/Muscle.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/Probcons.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/StandAloneFasta.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/Blat.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/Kalign.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/BlastPlus/Config.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/Raxml.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/Semphy.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/Phyml.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/QuickTree.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/REL.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/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/SLAC.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/SeqBoot.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/Consense.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/DrawGram.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/Base.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/Njtree/Best.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/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/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/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/DocSumAdaptor.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/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/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::DB::SoapEUtilities::FetchAdaptor::species.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::BEDTools::Config.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::Lagan.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::Promoterwise.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::StandAloneBlastPlus.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::Alignment::StandAloneFasta.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::DB::SoapEUtilities.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::Phylo::Phylip::SeqBoot.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::DocSumAdaptor.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::Kalign.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::Signalp.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::Alignment::DBA.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::Genewise.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::Eponine.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::REL.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::BEDTools.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::Glimmer.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::Phylip::DrawGram.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::Genemark.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::DB::ESoap.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::Infernal.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::Hmmer.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::Prints.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::Semphy.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::Phylo::Hyphy::FEL.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::Tools::Run::Phylo::Gerp.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::DB::SoapEUtilities::FetchAdaptor.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::Genscan.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::DB::SoapEUtilities::GQueryAdaptor.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::Tools::Run::Alignment::Probcons.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::Phyml.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::Profile.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::Ensembl.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::Phylip::Consense.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::Primer3.3pm 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::Primate.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::Pseudowise.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::EMBOSSApplication.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::Samtools::Config.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::Alignment::Proda.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::Alignment::Amap.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::DB::SoapEUtilities::Result.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::Phylo::Molphy::ProtML.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::Alignment::MSAProbs.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::Probalign.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::Phylip::Base.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::Factory::EMBOSS.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::Alignment::Exonerate.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::Alignment::Gmap.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_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_run_protdist.pl dh_install dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package '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_armhf.buildinfo dpkg-genchanges --build=binary -O../bioperl-run_1.7.3-11_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2135 and its subdirectories I: Current time: Thu May 9 05:52:26 -12 2024 I: pbuilder-time-stamp: 1715277146 Thu May 9 17:52:35 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt32b-armhf-rb.debian.net. Thu May 9 17:52:35 UTC 2024 I: Preparing to do remote build '2' on virt32b-armhf-rb.debian.net. Thu May 9 17:58:12 UTC 2024 I: Deleting $TMPDIR on virt32b-armhf-rb.debian.net. Thu May 9 17:58:15 UTC 2024 I: bioperl-run_1.7.3-11_armhf.changes: Format: 1.8 Date: Sat, 27 Apr 2024 21:48:57 +0200 Source: bioperl-run Binary: bioperl-run libbio-perl-run-perl Architecture: all Version: 1.7.3-11 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: bioperl-run - BioPerl wrappers: scripts libbio-perl-run-perl - BioPerl wrappers: modules Changes: bioperl-run (1.7.3-11) unstable; urgency=medium . * d/control: restrict emboss build-dependency. emboss is not available anymore on 32-bit and big endian architectures. It is thus not possible anymore to test it in such context. * d/control: demote bioperl-run recommends to suggestions. emboss, hmmer and infernal are currently not available on some release architectures. Demoting them helps getting the autodep8 perl test back on tracks at least on s390x. * d/control: demote tigr-glimmer to suggestion. * d/control: also restrict tigr-glimmer build-deps architecture set. Checksums-Sha1: bae0d1cad0eeeeb17195ae113b1a93cd7f1e3ca1 36124 bioperl-run_1.7.3-11_all.deb 22e3492ada1e1d05da2fbb9e1ab770438fa4fb3c 10555 bioperl-run_1.7.3-11_armhf.buildinfo 47f8452ff5bd10d9dd71dacd503d6621bb3375cb 527556 libbio-perl-run-perl_1.7.3-11_all.deb Checksums-Sha256: c606dabe1c38cf4816434d26926518553d1fa0d7979c09178634a37603fe42db 36124 bioperl-run_1.7.3-11_all.deb aea835ecceb51eb034358dd6a064b9cc71f11fd8311a3d4b6b285d841c7c7a19 10555 bioperl-run_1.7.3-11_armhf.buildinfo e992367d0725c57df8d69df1946e79977c826525b70bc50b308af7674065e275 527556 libbio-perl-run-perl_1.7.3-11_all.deb Files: ea6f3378f66f851461f6aa8c5301c658 36124 science optional bioperl-run_1.7.3-11_all.deb 5727eae77d1be9e4821f082d2008a735 10555 science optional bioperl-run_1.7.3-11_armhf.buildinfo cc89ebd18b6e7a87d2f87f7dd3c26c29 527556 perl optional libbio-perl-run-perl_1.7.3-11_all.deb Thu May 9 17:58:16 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_13-2972.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.3wdGQBcw/bioperl-run_1.7.3-11.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.3wdGQBcw/bioperl-run_1.7.3-11.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.3wdGQBcw/bioperl-run_1.7.3-11.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.3wdGQBcw/b1/bioperl-run_1.7.3-11_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.3wdGQBcw/b2/bioperl-run_1.7.3-11_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.371s) 0.371s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.022s) 0.022s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 704ms CPU time consumed: 702ms Thu May 9 17:58:17 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Thu May 9 17:58:17 UTC 2024 I: bioperl-run from trixie built successfully and reproducibly on armhf. Thu May 9 17:58:19 UTC 2024 I: Submitting .buildinfo files to external archives: Thu May 9 17:58:19 UTC 2024 I: Submitting 12K b1/bioperl-run_1.7.3-11_armhf.buildinfo.asc Thu May 9 17:58:21 UTC 2024 I: Submitting 12K b2/bioperl-run_1.7.3-11_armhf.buildinfo.asc Thu May 9 17:58:22 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu May 9 17:58:22 UTC 2024 I: Done submitting .buildinfo files. Thu May 9 17:58:22 UTC 2024 I: Removing signed bioperl-run_1.7.3-11_armhf.buildinfo.asc files: removed './b1/bioperl-run_1.7.3-11_armhf.buildinfo.asc' removed './b2/bioperl-run_1.7.3-11_armhf.buildinfo.asc'