Tue Jul 27 06:06:17 UTC 2021 I: starting to build bioperl-run/bullseye/i386 on jenkins on '2021-07-27 06:06' Tue Jul 27 06:06:17 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_3/13766/console.log Tue Jul 27 06:06:17 UTC 2021 I: Downloading source for bullseye/bioperl-run=1.7.3-6 --2021-07-27 06:06:17-- http://cdn-fastly.deb.debian.org/debian/pool/main/b/bioperl-run/bioperl-run_1.7.3-6.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2850 (2.8K) Saving to: ‘bioperl-run_1.7.3-6.dsc’ 0K .. 100% 179M=0s 2021-07-27 06:06:17 (179 MB/s) - ‘bioperl-run_1.7.3-6.dsc’ saved [2850/2850] Tue Jul 27 06:06:17 UTC 2021 I: bioperl-run_1.7.3-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bioperl-run Binary: bioperl-run, libbio-perl-run-perl Architecture: all Version: 1.7.3-6 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: https://metacpan.org/release/BioPerl-Run Standards-Version: 4.5.1 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) Build-Depends-Indep: perl, libmodule-build-perl, bioperl (>= 1.7.4), libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, libfile-sort-perl, libtest-most-perl, libarray-compare-perl, libtree-dagnode-perl, libbio-cluster-perl, libbio-featureio-perl, libconfig-any-perl, libbio-tools-run-alignment-clustalw-perl, libbio-eutilities-perl, libbio-tools-run-remoteblast-perl, amap-align, bedtools, bedtools-test, ncbi-blast+-legacy, clustalw, emboss, exonerate, hmmer [any-amd64 any-i386 powerpc ppc64], hyphy-pt | hyphy-mpi, infernal [any-amd64 any-i386], kalign, mafft, muscle, ncoils, phyml, primer3, probcons, python3-pybedtools, raxml, samtools, sim4, tigr-glimmer, 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 8bfe04bef0d3b42aeed0d18e7316bad7e13df78d 17660 bioperl-run_1.7.3-6.debian.tar.xz Checksums-Sha256: 04f11b3a931f625bf80770c3aec1b57658b41cde54573132b58b6179adda7c65 4872163 bioperl-run_1.7.3.orig.tar.gz 8816c18ffbfe36ebd6dd6d905023e0ac21b2644e119b621636ac707637a4308e 17660 bioperl-run_1.7.3-6.debian.tar.xz Files: e582f2dc591b947348670ce1479da109 4872163 bioperl-run_1.7.3.orig.tar.gz 946069a02136b5ad3dc10db13221f0c6 17660 bioperl-run_1.7.3-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAl/2L8AACgkQeTz2fo8N EdpSbRAAuRpILkprnS3gi7ZTR91bVn7m8ZHCGqxYVRQHzTu+UyxJvMqk9WXrVJoc HTAGuACsa7QbjlrVKYHjv5pRXlpx4TsfLcta4UETvsBPAofKn3GEUN9IfMXXTN5f JXgs16Ru1TgwpGXuqLGVL9zHw4zGEYeIMNIpXOUDq1rCLXnHXm0Eq/qtrN7F9nR4 qGXOIvDyvAiWAFGWkzNIgV7n8aH/0qizx/S/qnZADh5WlrfKYV6OHHwGMg1IU9Da N9ibiZrQFJCQDVSt9WA/2Tw7AsS82q0TGa6b4kmy2QvOMmoVzxnMQ4uLg6BsjYpv /LOtpxuiutfR/4iwHmtS9S3C3rH0ugLPv44U+D3WtaqWipF1u/sdngMteNENif2s /HWWYX/1x3isBFtMBs8s96fBQmo7bM+Xf2Ccb79fMuvYpP89b1c+h1gZRp6m28gE x6UNDXwoGsU+wGpM7tFNPu2i8Ls2YbqJlZre3Z1BWFgNuEgFI1Ck0A3Sgrmbsuer GuxbaCqWQfdGa8H/4nPUmMd8jYcXVDT+MYihpzEycyrAqqTxaDDO+9ayXvwWIW21 EM1gI+yX2p+CVny6Gw3mkFgqblxHT/kuSbARyU2UbJlezBKxW7hBtDN4RXnq7ew+ pL6th9KTyl/F2j9uZUCiaXDpSvvxWLOb+sN8w6hVdx5f92MQGl8= =A/CX -----END PGP SIGNATURE----- Tue Jul 27 06:06:17 UTC 2021 I: Checking whether the package is not for us Tue Jul 27 06:06:17 UTC 2021 I: Starting 1st build on remote node ionos2-i386.debian.net. Tue Jul 27 06:06:17 UTC 2021 I: Preparing to do remote build '1' on ionos2-i386.debian.net. Tue Jul 27 06:48:07 UTC 2021 I: Deleting $TMPDIR on ionos2-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jul 26 18:06:22 -12 2021 I: pbuilder-time-stamp: 1627365982 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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: using eatmydata during job I: Copying source file I: copying [bioperl-run_1.7.3-6.dsc] I: copying [./bioperl-run_1.7.3.orig.tar.gz] I: copying [./bioperl-run_1.7.3-6.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.VN8g0ctO/trustedkeys.kbx': General error gpgv: Signature made Wed Jan 6 09:46:40 2021 -12 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bioperl-run_1.7.3-6.dsc 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_1.7.3-6.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_muscle.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4713/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='d7a1367b1aaa4c76b7b5dceb2ddbaa55' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='4713' 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/tmp.QD8aTJ1aHV/pbuilderrc_XQwt --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.QD8aTJ1aHV/b1 --logfile b1/build.log bioperl-run_1.7.3-6.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos2-i386 4.19.0-17-686-pae #1 SMP Debian 4.19.194-3 (2021-07-18) i686 GNU/Linux I: ls -l /bin total 5784 -rwxr-xr-x 1 root root 1367848 Jun 21 14:25 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 Feb 7 02:38 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 71928 Feb 7 02:38 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 100952 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Feb 7 02:38 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Feb 7 02:38 more -rwsr-xr-x 1 root root 50720 Feb 7 02:38 mount -rwxr-xr-x 1 root root 13856 Feb 7 02:38 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 14:25 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 25 21:26 sh -> dash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Feb 7 02:38 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 16 21:55 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 30236 Feb 7 02:38 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Feb 7 02:38 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/4713/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: i386 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), perl, libmodule-build-perl, bioperl (>= 1.7.4), libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, libfile-sort-perl, libtest-most-perl, libarray-compare-perl, libtree-dagnode-perl, libbio-cluster-perl, libbio-featureio-perl, libconfig-any-perl, libbio-tools-run-alignment-clustalw-perl, libbio-eutilities-perl, libbio-tools-run-remoteblast-perl, amap-align, bedtools, bedtools-test, ncbi-blast+-legacy, clustalw, emboss, exonerate, hmmer, hyphy-pt | hyphy-mpi, infernal, kalign, mafft, muscle, ncoils, phyml, primer3, probcons, python3-pybedtools, raxml, samtools, sim4, tigr-glimmer, wise, fasttree, lagan, pal2nal, 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 ... 19675 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-tools-run-alignment-clustalw-perl; however: Package libbio-tools-run-alignment-clustalw-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; however: Package bedtools 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 clustalw; however: Package clustalw is not installed. pbuilder-satisfydepends-dummy depends on emboss; however: Package emboss is not installed. pbuilder-satisfydepends-dummy depends on exonerate; however: Package exonerate is not installed. pbuilder-satisfydepends-dummy depends on hmmer; however: Package hmmer is not installed. pbuilder-satisfydepends-dummy depends on hyphy-pt | hyphy-mpi; however: Package hyphy-pt is not installed. Package hyphy-mpi is not installed. pbuilder-satisfydepends-dummy depends on infernal; however: Package infernal 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 python3-pybedtools; however: Package python3-pybedtools is not installed. pbuilder-satisfydepends-dummy depends on raxml; however: Package raxml is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on sim4; however: Package sim4 is not installed. pbuilder-satisfydepends-dummy depends on tigr-glimmer; however: Package tigr-glimmer 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{a} bedtools-test{a} bioperl{a} bsdextrautils{a} ca-certificates{a} clustalw{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} emboss{a} emboss-data{a} emboss-lib{a} exonerate{a} fasttree{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} hmmer{a} hyphy-common{a} hyphy-pt{a} ibverbs-providers{a} infernal{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-db-ncbihelper-perl{a} libbio-eutilities-perl{a} libbio-featureio-perl{a} libbio-perl-perl{a} libbio-perl-run-perl{a} libbio-tools-run-alignment-clustalw-perl{a} libbio-tools-run-remoteblast-perl{a} libbio-variation-perl{a} libbrotli1{a} libbsd0{a} libcache-cache-perl{a} libcapture-tiny-perl{a} libcbor0{a} libcgi-pm-perl{a} libclass-data-inheritable-perl{a} libclass-method-modifiers-perl{a} libconfig-any-perl{a} libcurl3-gnutls{a} libdata-stag-perl{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-stacktrace-perl{a} libdivsufsort3{a} libdynaloader-functions-perl{a} libedit2{a} libelf1{a} libencode-locale-perl{a} liberror-perl{a} libevent-core-2.1-7{a} libevent-pthreads-2.1-7{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} libfontconfig1{a} libfreetype6{a} libgd3{a} libglib2.0-0{a} libhpdf-2.3.0{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhts3{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhwloc-plugins{a} libhwloc15{a} libibverbs1{a} libicu67{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} libipc-sharelite-perl{a} libjbig0{a} libjpeg62-turbo{a} libldap-2.4-2{a} liblmdb0{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1{a} libmariadb3{a} libmbedcrypto3{a} libmbedtls12{a} libmbedx509-0{a} libmd0{a} libmodule-build-perl{a} libmodule-pluggable-perl{a} libmodule-runtime-perl{a} libmoo-perl{a} libmpdec3{a} libncurses6{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libnl-3-200{a} libnl-route-3-200{a} libopenmpi3{a} libparams-classify-perl{a} libpciaccess0{a} libpipeline1{a} libpmix2{a} libpng16-16{a} libpq5{a} libpsl5{a} libpsm-infinipath1{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} librdmacm1{a} libreadline8{a} librole-tiny-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libstrictures-perl{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} libtiff5{a} libtimedate-perl{a} libtool{a} libtree-dagnode-perl{a} libtry-tiny-perl{a} libtype-tiny-perl{a} libuchardet0{a} liburi-perl{a} libwebp6{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} libxpm4{a} m4{a} mafft{a} man-db{a} mariadb-common{a} media-types{a} muscle{a} mysql-common{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} ncoils{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} pal2nal{a} perl-openssl-defaults{a} phyml{a} po-debconf{a} primer3{a} probcons{a} python3{a} python3-minimal{a} python3-pybedtools{a} python3-pysam{a} python3-six{a} python3.9{a} python3.9-minimal{a} raxml{a} readline-common{a} samtools{a} sensible-utils{a} sim4{a} tigr-glimmer{a} ucf{a} wise{a} wise-data{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run curl dialign libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libcgi-fast-perl libclass-xsaccessor-perl libclone-perl libconfig-general-perl libconfig-tiny-perl libconvert-binary-c-perl libdata-dump-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libgd-perl libglib2.0-data libgpm2 libgraph-perl libgraphviz-perl libhtml-form-perl libhtml-format-perl libhtml-tableextract-perl libhttp-daemon-perl libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libmldbm-perl libmodule-signature-perl libnamespace-clean-perl libpod-readme-perl libpostscript-perl libref-util-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsoftware-license-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsub-name-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 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, 231 newly installed, 0 to remove and 0 not upgraded. Need to get 174 MB of archives. After unpacking 930 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-7 [148 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 libpython3.9-minimal i386 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2 [98.8 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 python3.9-minimal i386 3.9.2-1 [1956 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 python3-minimal i386 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libmpdec3 i386 2.5.1-1 [91.9 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 libreadline8 i386 8.1-1 [173 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 libpython3.9-stdlib i386 3.9.2-1 [1703 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 python3.9 i386 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 libpython3-stdlib i386 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 python3 i386 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 netbase all 6.3 [19.9 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 openssl i386 1.1.1k-1 [860 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 ca-certificates all 20210119 [158 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 libmd0 i386 1.0.3-3 [28.9 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 libbsd0 i386 0.11.3-1 [111 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 libedit2 i386 3.1-20191231-2+b1 [101 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 libcbor0 i386 0.5.0+dfsg-2 [26.2 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 libfido2-1 i386 1.6.0-2 [59.9 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 openssh-client i386 1:8.4p1-5 [991 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 ucf all 3.0043 [74.0 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 amap-align i386 2.2+git20080214.600fc29+dfsg-2 [115 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 bedtools i386 2.30.0+dfsg-1 [725 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 bedtools-test all 2.30.0+dfsg-1 [10.8 MB] Get: 42 http://deb.debian.org/debian bullseye/main i386 libio-string-perl all 1.08-3.1 [11.8 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 libdata-stag-perl all 0.14-2 [448 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 libbio-perl-perl all 1.7.7-2 [2607 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get: 46 http://deb.debian.org/debian bullseye/main i386 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 libexception-class-perl all 1.44-1 [32.3 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 libtest-deep-perl all 1.130-1 [49.3 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 libtext-diff-perl all 1.45-1 [27.7 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 libtest-differences-perl all 0.67-1 [18.7 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 libsub-uplevel-perl all 0.2800-1.1 [16.5 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 libtest-exception-perl all 0.43-1 [18.7 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 libtest-warn-perl all 0.36-1 [16.2 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 libtest-most-perl all 0.37-1 [24.9 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 bioperl all 1.7.7-2 [246 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 clustalw i386 2.1+lgpl-7 [302 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-7 [8775 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 71 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 72 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 74 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 75 http://deb.debian.org/debian bullseye/main i386 libpng16-16 i386 1.6.37-3 [303 kB] Get: 76 http://deb.debian.org/debian bullseye/main i386 libfreetype6 i386 2.10.4+dfsg-1 [429 kB] Get: 77 http://deb.debian.org/debian bullseye/main i386 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 78 http://deb.debian.org/debian bullseye/main i386 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 79 http://deb.debian.org/debian bullseye/main i386 libfontconfig1 i386 2.13.1-4.2 [358 kB] Get: 80 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo i386 1:2.0.6-4 [160 kB] Get: 81 http://deb.debian.org/debian bullseye/main i386 libdeflate0 i386 1.7-1 [48.4 kB] Get: 82 http://deb.debian.org/debian bullseye/main i386 libjbig0 i386 2.1-3.1+b2 [31.5 kB] Get: 83 http://deb.debian.org/debian bullseye/main i386 libwebp6 i386 0.6.1-2.1 [269 kB] Get: 84 http://deb.debian.org/debian bullseye/main i386 libtiff5 i386 4.2.0-1 [305 kB] Get: 85 http://deb.debian.org/debian bullseye/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 86 http://deb.debian.org/debian bullseye/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 87 http://deb.debian.org/debian bullseye/main i386 libxcb1 i386 1.14-3 [144 kB] Get: 88 http://deb.debian.org/debian bullseye/main i386 libx11-data all 2:1.7.1-1 [310 kB] Get: 89 http://deb.debian.org/debian bullseye/main i386 libx11-6 i386 2:1.7.1-1 [796 kB] Get: 90 http://deb.debian.org/debian bullseye/main i386 libxpm4 i386 1:3.5.12-1 [50.9 kB] Get: 91 http://deb.debian.org/debian bullseye/main i386 libgd3 i386 2.3.0-2 [142 kB] Get: 92 http://deb.debian.org/debian bullseye/main i386 libhpdf-2.3.0 i386 2.3.0+dfsg-1+b1 [348 kB] Get: 93 http://deb.debian.org/debian bullseye/main i386 mysql-common all 5.8+1.0.7 [7464 B] Get: 94 http://deb.debian.org/debian bullseye/main i386 mariadb-common all 1:10.5.10-2 [36.0 kB] Get: 95 http://deb.debian.org/debian bullseye/main i386 libmariadb3 i386 1:10.5.10-2 [173 kB] Get: 96 http://deb.debian.org/debian bullseye/main i386 libsasl2-modules-db i386 2.1.27+dfsg-2.1 [70.0 kB] Get: 97 http://deb.debian.org/debian bullseye/main i386 libsasl2-2 i386 2.1.27+dfsg-2.1 [110 kB] Get: 98 http://deb.debian.org/debian bullseye/main i386 libldap-2.4-2 i386 2.4.57+dfsg-3 [244 kB] Get: 99 http://deb.debian.org/debian bullseye/main i386 libpq5 i386 13.3-1 [186 kB] Get: 100 http://deb.debian.org/debian bullseye/main i386 emboss-lib i386 6.6.0+dfsg-9 [3043 kB] Get: 101 http://deb.debian.org/debian bullseye/main i386 emboss-data all 6.6.0+dfsg-9 [61.1 MB] Get: 102 http://deb.debian.org/debian bullseye/main i386 emboss i386 6.6.0+dfsg-9 [1060 kB] Get: 103 http://deb.debian.org/debian bullseye/main i386 libglib2.0-0 i386 2.66.8-1 [1437 kB] Get: 104 http://deb.debian.org/debian bullseye/main i386 exonerate i386 2.4.0-5 [1749 kB] Get: 105 http://deb.debian.org/debian bullseye/main i386 fasttree i386 2.1.11-2 [183 kB] Get: 106 http://deb.debian.org/debian bullseye/main i386 libdivsufsort3 i386 2.0.1-5 [49.5 kB] Get: 107 http://deb.debian.org/debian bullseye/main i386 hmmer i386 3.3.2+dfsg-1 [1172 kB] Get: 108 http://deb.debian.org/debian bullseye/main i386 hyphy-common all 2.5.28+dfsg-3 [566 kB] Get: 109 http://deb.debian.org/debian bullseye/main i386 libnghttp2-14 i386 1.43.0-1 [85.7 kB] Get: 110 http://deb.debian.org/debian bullseye/main i386 libpsl5 i386 0.21.0-1.2 [57.9 kB] Get: 111 http://deb.debian.org/debian bullseye/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 112 http://deb.debian.org/debian bullseye/main i386 libssh2-1 i386 1.9.0-2 [164 kB] Get: 113 http://deb.debian.org/debian bullseye/main i386 libcurl3-gnutls i386 7.74.0-1.3+b1 [368 kB] Get: 114 http://deb.debian.org/debian bullseye/main i386 hyphy-pt i386 2.5.28+dfsg-3 [971 kB] Get: 115 http://deb.debian.org/debian bullseye/main i386 libnl-3-200 i386 3.4.0-1+b1 [66.4 kB] Get: 116 http://deb.debian.org/debian bullseye/main i386 libnl-route-3-200 i386 3.4.0-1+b1 [168 kB] Get: 117 http://deb.debian.org/debian bullseye/main i386 libibverbs1 i386 33.2-1 [64.6 kB] Get: 118 http://deb.debian.org/debian bullseye/main i386 ibverbs-providers i386 33.2-1 [275 kB] Get: 119 http://deb.debian.org/debian bullseye/main i386 infernal i386 1.1.4-1 [5573 kB] Get: 120 http://deb.debian.org/debian bullseye/main i386 kalign i386 1:3.3-1+b3 [178 kB] Get: 121 http://deb.debian.org/debian bullseye/main i386 lagan i386 2.0-6 [188 kB] Get: 122 http://deb.debian.org/debian bullseye/main i386 libclass-method-modifiers-perl all 2.13-1 [19.2 kB] Get: 123 http://deb.debian.org/debian bullseye/main i386 libb-hooks-op-check-perl i386 0.22-1+b3 [11.4 kB] Get: 124 http://deb.debian.org/debian bullseye/main i386 libdynaloader-functions-perl all 0.003-1.1 [12.7 kB] Get: 125 http://deb.debian.org/debian bullseye/main i386 libdevel-callchecker-perl i386 0.008-1+b2 [15.9 kB] Get: 126 http://deb.debian.org/debian bullseye/main i386 libparams-classify-perl i386 0.015-1+b3 [26.4 kB] Get: 127 http://deb.debian.org/debian bullseye/main i386 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get: 128 http://deb.debian.org/debian bullseye/main i386 libimport-into-perl all 1.002005-1 [11.6 kB] Get: 129 http://deb.debian.org/debian bullseye/main i386 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 130 http://deb.debian.org/debian bullseye/main i386 libstrictures-perl all 2.000006-1 [18.6 kB] Get: 131 http://deb.debian.org/debian bullseye/main i386 libsub-quote-perl all 2.006006-1 [21.0 kB] Get: 132 http://deb.debian.org/debian bullseye/main i386 libmoo-perl all 2.004004-1 [59.9 kB] Get: 133 http://deb.debian.org/debian bullseye/main i386 libexporter-tiny-perl all 1.002002-1 [37.8 kB] Get: 134 http://deb.debian.org/debian bullseye/main i386 libtype-tiny-perl all 1.012001-2 [351 kB] Get: 135 http://deb.debian.org/debian bullseye/main i386 libarray-compare-perl all 3.0.8-1 [14.9 kB] Get: 136 http://deb.debian.org/debian bullseye/main i386 liberror-perl all 0.17029-1 [31.0 kB] Get: 137 http://deb.debian.org/debian bullseye/main i386 libipc-sharelite-perl i386 0.17-4+b5 [25.3 kB] Get: 138 http://deb.debian.org/debian bullseye/main i386 libcache-cache-perl all 1.08-2 [76.6 kB] Get: 139 http://deb.debian.org/debian bullseye/main i386 libhtml-tagset-perl all 3.20-4 [13.0 kB] Get: 140 http://deb.debian.org/debian bullseye/main i386 liburi-perl all 5.08-1 [90.6 kB] Get: 141 http://deb.debian.org/debian bullseye/main i386 libhtml-parser-perl i386 3.75-1+b1 [106 kB] Get: 142 http://deb.debian.org/debian bullseye/main i386 libcgi-pm-perl all 4.51-1 [224 kB] Get: 143 http://deb.debian.org/debian bullseye/main i386 libencode-locale-perl all 1.05-1.1 [13.2 kB] Get: 144 http://deb.debian.org/debian bullseye/main i386 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 145 http://deb.debian.org/debian bullseye/main i386 libhttp-date-perl all 6.05-1 [10.4 kB] Get: 146 http://deb.debian.org/debian bullseye/main i386 libio-html-perl all 1.004-2 [16.1 kB] Get: 147 http://deb.debian.org/debian bullseye/main i386 liblwp-mediatypes-perl all 6.04-1 [19.9 kB] Get: 148 http://deb.debian.org/debian bullseye/main i386 libhttp-message-perl all 6.28-1 [79.6 kB] Get: 149 http://deb.debian.org/debian bullseye/main i386 libfile-listing-perl all 6.14-1 [12.4 kB] Get: 150 http://deb.debian.org/debian bullseye/main i386 libhtml-tree-perl all 5.07-2 [213 kB] Get: 151 http://deb.debian.org/debian bullseye/main i386 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get: 152 http://deb.debian.org/debian bullseye/main i386 libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get: 153 http://deb.debian.org/debian bullseye/main i386 perl-openssl-defaults i386 5 [7360 B] Get: 154 http://deb.debian.org/debian bullseye/main i386 libnet-ssleay-perl i386 1.88-3+b1 [328 kB] Get: 155 http://deb.debian.org/debian bullseye/main i386 libio-socket-ssl-perl all 2.069-1 [215 kB] Get: 156 http://deb.debian.org/debian bullseye/main i386 libnet-http-perl all 6.20-1 [25.1 kB] Get: 157 http://deb.debian.org/debian bullseye/main i386 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get: 158 http://deb.debian.org/debian bullseye/main i386 libtry-tiny-perl all 0.30-1 [23.3 kB] Get: 159 http://deb.debian.org/debian bullseye/main i386 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 160 http://deb.debian.org/debian bullseye/main i386 libwww-perl all 6.52-1 [192 kB] Get: 161 http://deb.debian.org/debian bullseye/main i386 libxml-parser-perl i386 2.46-2 [209 kB] Get: 162 http://deb.debian.org/debian bullseye/main i386 libxml-twig-perl all 1:3.52-1 [181 kB] Get: 163 http://deb.debian.org/debian bullseye/main i386 libbio-db-ncbihelper-perl all 1.7.6-4 [58.1 kB] Get: 164 http://deb.debian.org/debian bullseye/main i386 libxml-writer-perl all 0.900-1 [29.9 kB] Get: 165 http://deb.debian.org/debian bullseye/main i386 libbio-variation-perl all 1.7.5-2 [72.5 kB] Get: 166 http://deb.debian.org/debian bullseye/main i386 libbio-cluster-perl all 1.7.3-5 [53.2 kB] Get: 167 http://deb.debian.org/debian bullseye/main i386 libbio-asn1-entrezgene-perl all 1.730-2 [48.6 kB] Get: 168 http://deb.debian.org/debian bullseye/main i386 libtext-csv-perl all 2.00-1 [105 kB] Get: 169 http://deb.debian.org/debian bullseye/main i386 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB] Get: 170 http://deb.debian.org/debian bullseye/main i386 libxml-sax-base-perl all 1.09-1.1 [20.7 kB] Get: 171 http://deb.debian.org/debian bullseye/main i386 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get: 172 http://deb.debian.org/debian bullseye/main i386 libxml-libxml-perl i386 2.0134+dfsg-2+b1 [353 kB] Get: 173 http://deb.debian.org/debian bullseye/main i386 libxml-simple-perl all 2.25-1 [72.0 kB] Get: 174 http://deb.debian.org/debian bullseye/main i386 libbio-eutilities-perl all 1.77-1 [124 kB] Get: 175 http://deb.debian.org/debian bullseye/main i386 libfile-slurp-tiny-perl all 0.004-1 [7288 B] Get: 176 http://deb.debian.org/debian bullseye/main i386 libtree-dagnode-perl all 1.32-1 [61.7 kB] Get: 177 http://deb.debian.org/debian bullseye/main i386 libxml-perl all 0.08-3.1 [93.9 kB] Get: 178 http://deb.debian.org/debian bullseye/main i386 libxml-regexp-perl all 0.04-1.1 [7500 B] Get: 179 http://deb.debian.org/debian bullseye/main i386 libxml-dom-perl all 1.46-1 [154 kB] Get: 180 http://deb.debian.org/debian bullseye/main i386 libxml-xpathengine-perl all 0.14-1 [33.3 kB] Get: 181 http://deb.debian.org/debian bullseye/main i386 libxml-dom-xpath-perl all 0.14-3 [9066 B] Get: 182 http://deb.debian.org/debian bullseye/main i386 libbio-featureio-perl all 1.6.905-2 [53.2 kB] Get: 183 http://deb.debian.org/debian bullseye/main i386 libio-pty-perl i386 1:1.15-2 [37.8 kB] Get: 184 http://deb.debian.org/debian bullseye/main i386 libipc-run-perl all 20200505.0-1 [102 kB] Get: 185 http://deb.debian.org/debian bullseye/main i386 libfile-sort-perl all 1.01-2 [21.2 kB] Get: 186 http://deb.debian.org/debian bullseye/main i386 libbio-perl-run-perl all 1.7.3-6 [606 kB] Get: 187 http://deb.debian.org/debian bullseye/main i386 libbio-tools-run-alignment-clustalw-perl all 1.7.4-2 [24.5 kB] Get: 188 http://deb.debian.org/debian bullseye/main i386 libbio-tools-run-remoteblast-perl all 1.7.3-3 [17.5 kB] Get: 189 http://deb.debian.org/debian bullseye/main i386 libmodule-pluggable-perl all 5.2-1 [25.7 kB] Get: 190 http://deb.debian.org/debian bullseye/main i386 libconfig-any-perl all 0.32-1 [32.2 kB] Get: 191 http://deb.debian.org/debian bullseye/main i386 libevent-core-2.1-7 i386 2.1.12-stable-1 [148 kB] Get: 192 http://deb.debian.org/debian bullseye/main i386 libevent-pthreads-2.1-7 i386 2.1.12-stable-1 [57.3 kB] Get: 193 http://deb.debian.org/debian bullseye/main i386 libpsm-infinipath1 i386 3.3+20.604758e7-6.1 [178 kB] Get: 194 http://deb.debian.org/debian bullseye/main i386 librdmacm1 i386 33.2-1 [75.2 kB] Get: 195 http://deb.debian.org/debian bullseye/main i386 libfabric1 i386 1.11.0-2 [518 kB] Get: 196 http://deb.debian.org/debian bullseye/main i386 libhts3 i386 1.11-4 [408 kB] Get: 197 http://deb.debian.org/debian bullseye/main i386 libpciaccess0 i386 0.16-1 [55.7 kB] Get: 198 http://deb.debian.org/debian bullseye/main i386 libxext6 i386 2:1.3.3-1.1 [55.2 kB] Get: 199 http://deb.debian.org/debian bullseye/main i386 libxnvctrl0 i386 460.73.01-1 [26.8 kB] Get: 200 http://deb.debian.org/debian bullseye/main i386 ocl-icd-libopencl1 i386 2.2.14-2 [45.0 kB] Get: 201 http://deb.debian.org/debian bullseye/main i386 libhwloc15 i386 2.4.1+dfsg-1 [164 kB] Get: 202 http://deb.debian.org/debian bullseye/main i386 libhwloc-plugins i386 2.4.1+dfsg-1 [22.0 kB] Get: 203 http://deb.debian.org/debian bullseye/main i386 liblmdb0 i386 0.9.24-1 [46.7 kB] Get: 204 http://deb.debian.org/debian bullseye/main i386 libmbedcrypto3 i386 2.16.9-0.1 [234 kB] Get: 205 http://deb.debian.org/debian bullseye/main i386 libmbedx509-0 i386 2.16.9-0.1 [110 kB] Get: 206 http://deb.debian.org/debian bullseye/main i386 libmbedtls12 i386 2.16.9-0.1 [143 kB] Get: 207 http://deb.debian.org/debian bullseye/main i386 libmodule-build-perl all 0.423100-1 [258 kB] Get: 208 http://deb.debian.org/debian bullseye/main i386 libncurses6 i386 6.2+20201114-2 [110 kB] Get: 209 http://deb.debian.org/debian bullseye/main i386 libpmix2 i386 4.0.0-4 [582 kB] Get: 210 http://deb.debian.org/debian bullseye/main i386 libopenmpi3 i386 4.1.0-10 [2144 kB] Get: 211 http://deb.debian.org/debian bullseye/main i386 mafft i386 7.475-1 [984 kB] Get: 212 http://deb.debian.org/debian bullseye/main i386 muscle i386 1:3.8.1551-2 [232 kB] Get: 213 http://deb.debian.org/debian bullseye/main i386 ncbi-data all 6.1.20170106+dfsg1-9 [3556 kB] Get: 214 http://deb.debian.org/debian bullseye/main i386 ncbi-blast+ i386 2.11.0+ds-1 [12.2 MB] Get: 215 http://deb.debian.org/debian bullseye/main i386 ncbi-blast+-legacy all 2.11.0+ds-1 [13.1 kB] Get: 216 http://deb.debian.org/debian bullseye/main i386 ncoils i386 2002-8 [22.0 kB] Get: 217 http://deb.debian.org/debian bullseye/main i386 openmpi-common all 4.1.0-10 [179 kB] Get: 218 http://deb.debian.org/debian bullseye/main i386 openmpi-bin i386 4.1.0-10 [209 kB] Get: 219 http://deb.debian.org/debian bullseye/main i386 pal2nal all 14.1-3 [17.8 kB] Get: 220 http://deb.debian.org/debian bullseye/main i386 phyml i386 3:3.3.20200621-1 [1677 kB] Get: 221 http://deb.debian.org/debian bullseye/main i386 primer3 i386 2.4.0-4 [184 kB] Get: 222 http://deb.debian.org/debian bullseye/main i386 probcons i386 1.12-13 [104 kB] Get: 223 http://deb.debian.org/debian bullseye/main i386 python3-pysam i386 0.15.4+ds-3+b2 [1571 kB] Get: 224 http://deb.debian.org/debian bullseye/main i386 python3-six all 1.16.0-1 [17.1 kB] Get: 225 http://deb.debian.org/debian bullseye/main i386 python3-pybedtools i386 0.8.0-5 [12.1 MB] Get: 226 http://deb.debian.org/debian bullseye/main i386 raxml i386 8.2.12+dfsg-6+b4 [973 kB] Get: 227 http://deb.debian.org/debian bullseye/main i386 samtools i386 1.11-1 [576 kB] Get: 228 http://deb.debian.org/debian bullseye/main i386 sim4 i386 0.0.20121010-8 [361 kB] Get: 229 http://deb.debian.org/debian bullseye/main i386 tigr-glimmer i386 3.02b-5 [293 kB] Get: 230 http://deb.debian.org/debian bullseye/main i386 wise-data all 2.4.1-23 [78.2 kB] Get: 231 http://deb.debian.org/debian bullseye/main i386 wise i386 2.4.1-23 [1078 kB] Fetched 174 MB in 15s (11.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19675 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-7_i386.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../1-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_i386.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../3-libpipeline1_1.5.3-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_i386.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:i386. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_i386.deb ... Unpacking libpython3.9-minimal:i386 (3.9.2-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../6-libexpat1_2.2.10-2_i386.deb ... Unpacking libexpat1:i386 (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_i386.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:i386 (3.9.2-1) ... Setting up libexpat1:i386 (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... 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 ... 20542 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_i386.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:i386. Preparing to unpack .../2-libmpdec3_2.5.1-1_i386.deb ... Unpacking libmpdec3:i386 (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:i386. Preparing to unpack .../4-libreadline8_8.1-1_i386.deb ... Unpacking libreadline8:i386 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:i386. Preparing to unpack .../5-libpython3.9-stdlib_3.9.2-1_i386.deb ... Unpacking libpython3.9-stdlib:i386 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../6-python3.9_3.9.2-1_i386.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../7-libpython3-stdlib_3.9.2-3_i386.deb ... Unpacking libpython3-stdlib:i386 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20963 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_i386.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package netbase. Preparing to unpack .../001-netbase_6.3_all.deb ... Unpacking netbase (6.3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_1.1.1k-1_i386.deb ... Unpacking openssl (1.1.1k-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.39-3_i386.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../006-libmagic1_1%3a5.39-3_i386.deb ... Unpacking libmagic1:i386 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.39-3_i386.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.21-4_i386.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libmd0:i386. Preparing to unpack .../009-libmd0_1.0.3-3_i386.deb ... Unpacking libmd0:i386 (1.0.3-3) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../010-libbsd0_0.11.3-1_i386.deb ... Unpacking libbsd0:i386 (0.11.3-1) ... Selecting previously unselected package libedit2:i386. Preparing to unpack .../011-libedit2_3.1-20191231-2+b1_i386.deb ... Unpacking libedit2:i386 (3.1-20191231-2+b1) ... Selecting previously unselected package libcbor0:i386. Preparing to unpack .../012-libcbor0_0.5.0+dfsg-2_i386.deb ... Unpacking libcbor0:i386 (0.5.0+dfsg-2) ... Selecting previously unselected package libfido2-1:i386. Preparing to unpack .../013-libfido2-1_1.6.0-2_i386.deb ... Unpacking libfido2-1:i386 (1.6.0-2) ... Selecting previously unselected package openssh-client. Preparing to unpack .../014-openssh-client_1%3a8.4p1-5_i386.deb ... Unpacking openssh-client (1:8.4p1-5) ... Selecting previously unselected package ucf. Preparing to unpack .../015-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package amap-align. Preparing to unpack .../016-amap-align_2.2+git20080214.600fc29+dfsg-2_i386.deb ... Unpacking amap-align (2.2+git20080214.600fc29+dfsg-2) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../017-libsigsegv2_2.13-1_i386.deb ... Unpacking libsigsegv2:i386 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../018-m4_1.4.18-5_i386.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../019-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../020-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../021-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../022-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package bedtools. Preparing to unpack .../023-bedtools_2.30.0+dfsg-1_i386.deb ... Unpacking bedtools (2.30.0+dfsg-1) ... Selecting previously unselected package bedtools-test. Preparing to unpack .../024-bedtools-test_2.30.0+dfsg-1_all.deb ... Unpacking bedtools-test (2.30.0+dfsg-1) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../025-libio-string-perl_1.08-3.1_all.deb ... Unpacking libio-string-perl (1.08-3.1) ... Selecting previously unselected package libdata-stag-perl. Preparing to unpack .../026-libdata-stag-perl_0.14-2_all.deb ... Unpacking libdata-stag-perl (0.14-2) ... Selecting previously unselected package libbio-perl-perl. Preparing to unpack .../027-libbio-perl-perl_1.7.7-2_all.deb ... Unpacking libbio-perl-perl (1.7.7-2) ... Selecting previously unselected package libclass-data-inheritable-perl. Preparing to unpack .../028-libclass-data-inheritable-perl_0.08-3_all.deb ... Unpacking libclass-data-inheritable-perl (0.08-3) ... Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../029-libdevel-stacktrace-perl_2.0400-1_all.deb ... Unpacking libdevel-stacktrace-perl (2.0400-1) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../030-libexception-class-perl_1.44-1_all.deb ... Unpacking libexception-class-perl (1.44-1) ... Selecting previously unselected package libtest-deep-perl. Preparing to unpack .../031-libtest-deep-perl_1.130-1_all.deb ... Unpacking libtest-deep-perl (1.130-1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../032-libcapture-tiny-perl_0.48-1_all.deb ... Unpacking libcapture-tiny-perl (0.48-1) ... Selecting previously unselected package libalgorithm-diff-perl. 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Selecting previously unselected package libio-pty-perl. Preparing to unpack .../166-libio-pty-perl_1%3a1.15-2_i386.deb ... Unpacking libio-pty-perl (1:1.15-2) ... Selecting previously unselected package libipc-run-perl. Preparing to unpack .../167-libipc-run-perl_20200505.0-1_all.deb ... Unpacking libipc-run-perl (20200505.0-1) ... Selecting previously unselected package libfile-sort-perl. Preparing to unpack .../168-libfile-sort-perl_1.01-2_all.deb ... Unpacking libfile-sort-perl (1.01-2) ... Selecting previously unselected package libbio-perl-run-perl. Preparing to unpack .../169-libbio-perl-run-perl_1.7.3-6_all.deb ... Unpacking libbio-perl-run-perl (1.7.3-6) ... Selecting previously unselected package libbio-tools-run-alignment-clustalw-perl. Preparing to unpack .../170-libbio-tools-run-alignment-clustalw-perl_1.7.4-2_all.deb ... Unpacking libbio-tools-run-alignment-clustalw-perl (1.7.4-2) ... Selecting previously unselected package libbio-tools-run-remoteblast-perl. 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Preparing to unpack .../182-libxnvctrl0_460.73.01-1_i386.deb ... Unpacking libxnvctrl0:i386 (460.73.01-1) ... Selecting previously unselected package ocl-icd-libopencl1:i386. Preparing to unpack .../183-ocl-icd-libopencl1_2.2.14-2_i386.deb ... Unpacking ocl-icd-libopencl1:i386 (2.2.14-2) ... Selecting previously unselected package libhwloc15:i386. Preparing to unpack .../184-libhwloc15_2.4.1+dfsg-1_i386.deb ... Unpacking libhwloc15:i386 (2.4.1+dfsg-1) ... Selecting previously unselected package libhwloc-plugins:i386. Preparing to unpack .../185-libhwloc-plugins_2.4.1+dfsg-1_i386.deb ... Unpacking libhwloc-plugins:i386 (2.4.1+dfsg-1) ... Selecting previously unselected package liblmdb0:i386. Preparing to unpack .../186-liblmdb0_0.9.24-1_i386.deb ... Unpacking liblmdb0:i386 (0.9.24-1) ... Selecting previously unselected package libmbedcrypto3:i386. Preparing to unpack .../187-libmbedcrypto3_2.16.9-0.1_i386.deb ... Unpacking libmbedcrypto3:i386 (2.16.9-0.1) ... Selecting previously unselected package libmbedx509-0:i386. Preparing to unpack .../188-libmbedx509-0_2.16.9-0.1_i386.deb ... Unpacking libmbedx509-0:i386 (2.16.9-0.1) ... Selecting previously unselected package libmbedtls12:i386. Preparing to unpack .../189-libmbedtls12_2.16.9-0.1_i386.deb ... Unpacking libmbedtls12:i386 (2.16.9-0.1) ... Selecting previously unselected package libmodule-build-perl. Preparing to unpack .../190-libmodule-build-perl_0.423100-1_all.deb ... Adding 'diversion of /usr/bin/config_data to /usr/bin/config_data.diverted by libmodule-build-perl' Adding 'diversion of /usr/share/man/man1/config_data.1.gz to /usr/share/man/man1/config_data.diverted.1.gz by libmodule-build-perl' Unpacking libmodule-build-perl (0.423100-1) ... Selecting previously unselected package libncurses6:i386. Preparing to unpack .../191-libncurses6_6.2+20201114-2_i386.deb ... Unpacking libncurses6:i386 (6.2+20201114-2) ... Selecting previously unselected package libpmix2:i386. 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Unpacking ncbi-blast+-legacy (2.11.0+ds-1) ... Selecting previously unselected package ncoils. Preparing to unpack .../199-ncoils_2002-8_i386.deb ... Unpacking ncoils (2002-8) ... Selecting previously unselected package openmpi-common. Preparing to unpack .../200-openmpi-common_4.1.0-10_all.deb ... Unpacking openmpi-common (4.1.0-10) ... Selecting previously unselected package openmpi-bin. Preparing to unpack .../201-openmpi-bin_4.1.0-10_i386.deb ... Unpacking openmpi-bin (4.1.0-10) ... Selecting previously unselected package pal2nal. Preparing to unpack .../202-pal2nal_14.1-3_all.deb ... Unpacking pal2nal (14.1-3) ... Selecting previously unselected package phyml. Preparing to unpack .../203-phyml_3%3a3.3.20200621-1_i386.deb ... Unpacking phyml (3:3.3.20200621-1) ... Selecting previously unselected package primer3. Preparing to unpack .../204-primer3_2.4.0-4_i386.deb ... Unpacking primer3 (2.4.0-4) ... Selecting previously unselected package probcons. 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Unpacking sim4 (0.0.20121010-8) ... Selecting previously unselected package tigr-glimmer. Preparing to unpack .../212-tigr-glimmer_3.02b-5_i386.deb ... Unpacking tigr-glimmer (3.02b-5) ... Selecting previously unselected package wise-data. Preparing to unpack .../213-wise-data_2.4.1-23_all.deb ... Unpacking wise-data (2.4.1-23) ... Selecting previously unselected package wise. Preparing to unpack .../214-wise_2.4.1-23_i386.deb ... Unpacking wise (2.4.1-23) ... Setting up media-types (4.0.0) ... Setting up libmodule-pluggable-perl (5.2-1) ... Setting up libpipeline1:i386 (1.5.3-1) ... Setting up liblmdb0:i386 (0.9.24-1) ... Setting up ncbi-data (6.1.20170106+dfsg1-9) ... Setting up libpciaccess0:i386 (0.16-1) ... Setting up mysql-common (5.8+1.0.7) ... update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libxau6:i386 (1:1.0.9-1) ... Setting up libpsl5:i386 (0.21.0-1.2) ... Setting up bsdextrautils (2.36.1-7) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up probcons (1.12-13) ... Setting up libicu67:i386 (67.1-7) ... Setting up libdynaloader-functions-perl (0.003-1.1) ... Setting up libtest-deep-perl (1.130-1) ... Setting up libclass-method-modifiers-perl (2.13-1) ... Setting up libxml-regexp-perl (0.04-1.1) ... Setting up libio-pty-perl (1:1.15-2) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up mafft (7.475-1) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:i386 (2.66.8-1) ... No schema files found: doing nothing. Setting up libhtml-tagset-perl (3.20-4) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:i386 (1.0.9-2+b2) ... Setting up libfile-slurp-tiny-perl (0.004-1) ... Setting up libipc-sharelite-perl (0.17-4+b5) ... Setting up libcbor0:i386 (0.5.0+dfsg-2) ... Setting up liblwp-mediatypes-perl (6.04-1) ... Setting up libtry-tiny-perl (0.30-1) ... Setting up libnghttp2-14:i386 (1.43.0-1) ... Setting up libmagic1:i386 (1:5.39-3) ... Setting up libdeflate0:i386 (1.7-1) ... Setting up perl-openssl-defaults:i386 (5) ... Setting up libxml-namespacesupport-perl (1.12-1.1) ... Setting up gettext-base (0.21-4) ... Setting up libencode-locale-perl (1.05-1.1) ... Setting up ncoils (2002-8) ... Setting up hyphy-common (2.5.28+dfsg-3) ... Setting up file (1:5.39-3) ... Setting up muscle (1:3.8.1551-2) ... Setting up emboss-data (6.6.0+dfsg-9) ... Setting up libjbig0:i386 (2.1-3.1+b2) ... Setting up libmodule-build-perl (0.423100-1) ... Setting up libsasl2-modules-db:i386 (2.1.27+dfsg-2.1) ... Setting up liberror-perl (0.17029-1) ... Setting up mariadb-common (1:10.5.10-2) ... update-alternatives: using /etc/mysql/mariadb.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up infernal (1.1.4-1) ... Setting up libxml-sax-base-perl (1.09-1.1) ... Setting up libio-string-perl (1.08-3.1) ... Setting up primer3 (2.4.0-4) ... Setting up kalign (1:3.3-1+b3) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up lagan (2.0-6) ... Setting up libjpeg62-turbo:i386 (1:2.0.6-4) ... Setting up libx11-data (2:1.7.1-1) ... Setting up libtext-diff-perl (1.45-1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libxml-xpathengine-perl (0.14-1) ... Setting up sim4 (0.0.20121010-8) ... Setting up libxml-writer-perl (0.900-1) ... Setting up libncurses6:i386 (6.2+20201114-2) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up libpng16-16:i386 (1.6.37-3) ... Setting up libhwloc15:i386 (2.4.1+dfsg-1) ... Setting up libevent-core-2.1-7:i386 (2.1.12-stable-1) ... Setting up libio-html-perl (1.004-2) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:i386 (0.6.1-2.1) ... Setting up libb-hooks-op-check-perl (0.22-1+b3) ... Setting up libmariadb3:i386 (1:10.5.10-2) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up libipc-run-perl (20200505.0-1) ... Setting up wise-data (2.4.1-23) ... Setting up amap-align (2.2+git20080214.600fc29+dfsg-2) ... Setting up libsasl2-2:i386 (2.1.27+dfsg-2.1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libtree-dagnode-perl (1.32-1) ... Setting up libmd0:i386 (1.0.3-3) ... Setting up libdata-stag-perl (0.14-2) ... Setting up sensible-utils (0.0.14) ... Setting up ocl-icd-libopencl1:i386 (2.2.14-2) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up pal2nal (14.1-3) ... Setting up libnl-3-200:i386 (3.4.0-1+b1) ... Setting up libmpdec3:i386 (2.5.1-1) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up openmpi-common (4.1.0-10) ... Setting up libconfig-any-perl (0.32-1) ... Setting up clustalw (2.1+lgpl-7) ... Setting up libmbedcrypto3:i386 (2.16.9-0.1) ... Setting up libsub-uplevel-perl (0.2800-1.1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:i386 (1.9.0-2) ... Setting up fasttree (2.1.11-2) ... Setting up netbase (6.3) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006006-1) ... Setting up libdevel-stacktrace-perl (2.0400-1) ... Setting up libtiff5:i386 (4.2.0-1) ... Setting up libbio-perl-perl (1.7.7-2) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.1) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/i386-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up bedtools-test (2.30.0+dfsg-1) ... Setting up libexporter-tiny-perl (1.002002-1) ... Setting up libfido2-1:i386 (1.6.0-2) ... Setting up libdivsufsort3:i386 (2.0.1-5) ... Setting up openssl (1.1.1k-1) ... Setting up libbsd0:i386 (0.11.3-1) ... Setting up tigr-glimmer (3.02b-5) ... Setting up libelf1:i386 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:i386 (2.9.10+dfsg-6.7) ... Setting up exonerate (2.4.0-5) ... Setting up bedtools (2.30.0+dfsg-1) ... Setting up liburi-perl (5.08-1) ... Setting up libfile-sort-perl (1.01-2) ... Setting up libevent-pthreads-2.1-7:i386 (2.1.12-stable-1) ... Setting up raxml (8.2.12+dfsg-6+b4) ... Setting up libtext-csv-perl (2.00-1) ... Setting up libnet-ssleay-perl (1.88-3+b1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libbio-perl-run-perl (1.7.3-6) ... Setting up libhttp-date-perl (6.05-1) ... Setting up libhpdf-2.3.0:i386 (2.3.0+dfsg-1+b1) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up libxcb1:i386 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libfile-listing-perl (6.14-1) ... Setting up libcache-cache-perl (1.08-2) ... Setting up libtool (2.4.6-15) ... Setting up libmbedx509-0:i386 (2.16.9-0.1) ... Setting up wise (2.4.1-23) ... Setting up libtest-warn-perl (0.36-1) ... Setting up libedit2:i386 (3.1-20191231-2+b1) ... Setting up libreadline8:i386 (8.1-1) ... Setting up libmbedtls12:i386 (2.16.9-0.1) ... Setting up libtype-tiny-perl (1.012001-2) ... Setting up libtest-differences-perl (0.67-1) ... Setting up libldap-2.4-2:i386 (2.4.57+dfsg-3) ... Setting up libnet-http-perl (6.20-1) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:i386 (7.74.0-1.3+b1) ... Setting up libexception-class-perl (1.44-1) ... Setting up hyphy-pt (2.5.28+dfsg-3) ... Setting up libdevel-callchecker-perl (0.008-1+b2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libnl-route-3-200:i386 (3.4.0-1+b1) ... Setting up libbio-tools-run-alignment-clustalw-perl (1.7.4-2) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libtest-exception-perl (0.43-1) ... Setting up libfreetype6:i386 (2.10.4+dfsg-1) ... Setting up ucf (3.0043) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libhtml-parser-perl (3.75-1+b1) ... Setting up hmmer (3.3.2+dfsg-1) ... Setting up libx11-6:i386 (2:1.7.1-1) ... Setting up libio-socket-ssl-perl (2.069-1) ... Setting up libpython3.9-stdlib:i386 (3.9.2-1) ... Setting up libpython3-stdlib:i386 (3.9.2-3) ... Setting up libhttp-message-perl (6.28-1) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhttp-negotiate-perl (6.01-1) ... Setting up libibverbs1:i386 (33.2-1) ... Setting up libhts3:i386 (1.11-4) ... Setting up libxpm4:i386 (1:3.5.12-1) ... Setting up ibverbs-providers:i386 (33.2-1) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libtest-most-perl (0.37-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up openssh-client (1:8.4p1-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-2) ... Setting up libparams-classify-perl (0.015-1+b3) ... Setting up libcgi-pm-perl (4.51-1) ... Setting up libpq5:i386 (13.3-1) ... Setting up libxext6:i386 (2:1.3.3-1.1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-1) ... 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 samtools (1.11-1) ... Setting up libxnvctrl0:i386 (460.73.01-1) ... Setting up dh-autoreconf (20) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libxml-libxml-perl (2.0134+dfsg-2+b1) ... 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 libfontconfig1:i386 (2.13.1-4.2) ... Setting up python3.9 (3.9.2-1) ... Setting up bioperl (1.7.7-2) ... Setting up librdmacm1:i386 (33.2-1) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libmoo-perl (2.004004-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up libhwloc-plugins:i386 (2.4.1+dfsg-1) ... Setting up ncbi-blast+ (2.11.0+ds-1) ... Setting up python3-six (1.16.0-1) ... Setting up libarray-compare-perl (3.0.8-1) ... Setting up libgd3:i386 (2.3.0-2) ... Setting up libxml-simple-perl (2.25-1) ... Setting up emboss-lib (6.6.0+dfsg-9) ... Setting up ncbi-blast+-legacy (2.11.0+ds-1) ... Setting up libfabric1 (1.11.0-2) ... Setting up python3-pysam (0.15.4+ds-3+b2) ... Setting up emboss (6.6.0+dfsg-9) ... Setting up libpmix2:i386 (4.0.0-4) ... Setting up libopenmpi3:i386 (4.1.0-10) ... Setting up openmpi-bin (4.1.0-10) ... 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 (3:3.3.20200621-1) ... Setting up python3-pybedtools (0.8.0-5) ... Setting up libbio-asn1-entrezgene-perl (1.730-2) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up libwww-perl (6.52-1) ... Setting up libbio-eutilities-perl (1.77-1) ... Setting up libbio-tools-run-remoteblast-perl (1.7.3-3) ... Setting up libxml-parser-perl:i386 (2.46-2) ... Setting up libxml-twig-perl (1:3.52-1) ... Setting up libbio-db-ncbihelper-perl (1.7.6-4) ... Setting up libxml-perl (0.08-3.1) ... Setting up libxml-dom-perl (1.46-1) ... Setting up libxml-dom-xpath-perl (0.14-3) ... Setting up libbio-variation-perl (1.7.5-2) ... Setting up libbio-featureio-perl (1.6.905-2) ... Setting up libbio-cluster-perl (1.7.3-5) ... Processing triggers for libc-bin (2.31-13) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/bioperl-run-1.7.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package bioperl-run dpkg-buildpackage: info: source version 1.7.3-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 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/bioperl-run-1.7.3' dh_auto_configure -- --install_scripts perl Build.PL --installdirs vendor --config "optimize=-g -O2 -fdebug-prefix-map=/build/bioperl-run-1.7.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=i686-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/build/bioperl-run-1.7.3=. -fstack-protector-strong -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/bioperl-run-1.7.3' dh_auto_build perl Build Building BioPerl-Run debian/rules override_dh_auto_test make[1]: Entering directory '/build/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 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/XQRd2s3G6t 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 t/BEDTools.t .................. 1..423 ok 1 - make a default factory ok 2 - default to command 'bam_to_bed' ok 3 - make a factory using command 'annotate' ok 4 - factory command for 'annotate' is correct ok 5 - all available options for 'annotate' ok 6 - available parameters for 'annotate' ok 7 - available switches for 'annotate' ok 8 - get version for 'annotate' ok 9 - can run command 'annotate' ok 10 - result files exists for command 'annotate' ok 11 - can return output format for command 'annotate' ok 12 - result claims to be in correct format for command 'annotate' ok 13 - can return output file for command 'annotate' ok 14 - file format of '/tmp/PIzDyYSqwd/DWyuJYBsDO.bed' consistent with claim for 'annotate' ok 15 - can set want to IO object for command 'annotate' ok 16 - can get the basic object result for command 'annotate' ok 17 - 'returned object is correct for command 'annotate'' isa 'Bio::Root::IO' ok 18 - can get the specific object result for command 'annotate' ok 19 - 'returned object is correct for command 'annotate'' isa 'Bio::SeqFeature::Collection' ok 20 - correct number of features for command 'annotate' # TODO maybe adapt reference results to Debian specific dataset ok 21 - make a factory using command 'fasta_from_bed' ok 22 - factory command for 'fasta_from_bed' is correct ok 23 - all available options for 'fasta_from_bed' ok 24 - available parameters for 'fasta_from_bed' ok 25 - available switches for 'fasta_from_bed' ok 26 - get version for 'fasta_from_bed' ok 27 - can run command 'fasta_from_bed' ok 28 - result files exists for command 'fasta_from_bed' ok 29 - can return output format for command 'fasta_from_bed' ok 30 - result claims to be in correct format for command 'fasta_from_bed' ok 31 - can return output file for command 'fasta_from_bed' ok 32 - file format consistent with claim for 'fasta_from_bed' ok 33 - can set want to IO object for command 'fasta_from_bed' ok 34 - can get the basic object result for command 'fasta_from_bed' ok 35 - 'returned object is correct for command 'fasta_from_bed'' isa 'Bio::Root::IO' ok 36 - can get the specific object result for command 'fasta_from_bed' ok 37 - 'returned object is correct for command 'fasta_from_bed'' isa 'Bio::SeqIO' ok 38 - correct number of sequences for command 'fasta_from_bed' ok 39 - make a factory using command 'overlap' ok 40 - factory command for 'overlap' is correct ok 41 - all available options for 'overlap' ok 42 - available parameters for 'overlap' ok 43 - available switches for 'overlap' ok 44 - get version for 'overlap' ok 45 - can set parameter -columns => '2,3,5,6' ok 46 - can run command 'overlap' ok 47 - result files exists for command 'overlap' ok 48 - can return output format for command 'overlap' ok 49 - result claims to be in correct format for command 'overlap' ok 50 - can return output file for command 'overlap' ok 51 - file format of '/tmp/TjzaWIalNw/ivIUAMpzfo.bed' consistent with claim for 'overlap' ok 52 - can set want to IO object for command 'overlap' ok 53 - can get the basic object result for command 'overlap' ok 54 - 'returned object is correct for command 'overlap'' isa 'Bio::Root::IO' ok 55 - can get the specific object result for command 'overlap' ok 56 - 'returned object is correct for command 'overlap'' isa 'Bio::SeqFeature::Collection' ok 57 - correct number of features for command 'overlap' # TODO maybe adapt reference results to Debian specific dataset ok 58 - make a factory using command 'bam_to_bed' ok 59 - factory command for 'bam_to_bed' is correct ok 60 - all available options for 'bam_to_bed' ok 61 - available parameters for 'bam_to_bed' ok 62 - available switches for 'bam_to_bed' ok 63 - get version for 'bam_to_bed' ok 64 - can run command 'bam_to_bed' ok 65 - result files exists for command 'bam_to_bed' ok 66 - can return output format for command 'bam_to_bed' ok 67 - result claims to be in correct format for command 'bam_to_bed' ok 68 - can return output file for command 'bam_to_bed' ok 69 - file format of '/tmp/m7JIXYY5OQ/Ry6hTAz4pK.bed' consistent with claim for 'bam_to_bed' ok 70 - can set want to IO object for command 'bam_to_bed' ok 71 - can get the basic object result for command 'bam_to_bed' ok 72 - 'returned object is correct for command 'bam_to_bed'' isa 'Bio::Root::IO' ok 73 - can get the specific object result for command 'bam_to_bed' ok 74 - 'returned object is correct for command 'bam_to_bed'' isa 'Bio::SeqFeature::Collection' ok 75 - correct number of features for command 'bam_to_bed' # TODO maybe adapt reference results to Debian specific dataset ok 76 - make a factory using command 'genome_coverage' ok 77 - factory command for 'genome_coverage' is correct ok 78 - all available options for 'genome_coverage' ok 79 - available parameters for 'genome_coverage' ok 80 - available switches for 'genome_coverage' ok 81 - get version for 'genome_coverage' ok 82 - can run command 'genome_coverage' ok 83 - result files exists for command 'genome_coverage' ok 84 - can return output format for command 'genome_coverage' ok 85 - result claims to be in correct format for command 'genome_coverage' ok 86 - can return output file for command 'genome_coverage' ok 87 - make readable output not ok 88 - - number of lines # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test ' - number of lines' # at t/BEDTools.t line 331. # got: '87' # expected: '38' ok 89 - can set want to IO object for command 'genome_coverage' ok 90 - can get the basic object result for command 'genome_coverage' ok 91 - 'returned object is correct for command 'genome_coverage'' isa 'Bio::Root::IO' ok 92 - make a factory using command 'pair_to_pair' ok 93 - factory command for 'pair_to_pair' is correct ok 94 - all available options for 'pair_to_pair' ok 95 - available parameters for 'pair_to_pair' ok 96 - available switches for 'pair_to_pair' ok 97 - get version for 'pair_to_pair' ok 98 - can set parameter -type => 'neither' ok 99 - can run command 'pair_to_pair' ok 100 - result files exists for command 'pair_to_pair' ok 101 - can return output format for command 'pair_to_pair' ok 102 - result claims to be in correct format for command 'pair_to_pair' ok 103 - can return output file for command 'pair_to_pair' ok 104 - file format of '/tmp/MuHKI6EriE/K3fIcUMyBp.bedpe' consistent with claim for 'pair_to_pair' ok 105 - can set want to IO object for command 'pair_to_pair' ok 106 - can get the basic object result for command 'pair_to_pair' ok 107 - 'returned object is correct for command 'pair_to_pair'' isa 'Bio::Root::IO' ok 108 - can get the specific object result for command 'pair_to_pair' ok 109 - 'returned object is correct for command 'pair_to_pair'' isa 'Bio::SeqFeature::Collection' ok 110 - correct number of features for command 'pair_to_pair' # TODO maybe adapt reference results to Debian specific dataset ok 111 - make a factory using command 'bed_to_bam' ok 112 - factory command for 'bed_to_bam' is correct ok 113 - all available options for 'bed_to_bam' ok 114 - available parameters for 'bed_to_bam' ok 115 - available switches for 'bed_to_bam' ok 116 - get version for 'bed_to_bam' ok 117 - can run command 'bed_to_bam' ok 118 - result files exists for command 'bed_to_bam' ok 119 - can return output format for command 'bed_to_bam' ok 120 - result claims to be in correct format for command 'bed_to_bam' ok 121 - can return output file for command 'bed_to_bam' ok 122 - can set want to IO object for command 'bed_to_bam' ok 123 - can get the basic object result for command 'bed_to_bam' ok 124 - 'returned object is correct for command 'bed_to_bam'' isa 'Bio::Root::IO' ok 125 - make a factory using command 'graph_union' ok 126 - factory command for 'graph_union' is correct ok 127 - all available options for 'graph_union' ok 128 - available parameters for 'graph_union' ok 129 - available switches for 'graph_union' ok 130 - get version for 'graph_union' ok 131 - can run command 'graph_union' ok 132 - result files exists for command 'graph_union' ok 133 - can return output format for command 'graph_union' ok 134 - result claims to be in correct format for command 'graph_union' ok 135 - can return output file for command 'graph_union' ok 136 - can set want to IO object for command 'graph_union' ok 137 - can get the basic object result for command 'graph_union' ok 138 - 'returned object is correct for command 'graph_union'' isa 'Bio::Root::IO' ok 139 - make a factory using command 'pair_to_bed' ok 140 - factory command for 'pair_to_bed' is correct ok 141 - all available options for 'pair_to_bed' ok 142 - available parameters for 'pair_to_bed' ok 143 - available switches for 'pair_to_bed' ok 144 - get version for 'pair_to_bed' ok 145 - can run command 'pair_to_bed' ok 146 - result files exists for command 'pair_to_bed' ok 147 - can return output format for command 'pair_to_bed' ok 148 - result claims to be in correct format for command 'pair_to_bed' ok 149 - can return output file for command 'pair_to_bed' ok 150 - can set want to IO object for command 'pair_to_bed' ok 151 - can get the basic object result for command 'pair_to_bed' ok 152 - 'returned object is correct for command 'pair_to_bed'' isa 'Bio::Root::IO' ok 153 - can get the specific object result for command 'pair_to_bed' ok 154 - 'returned object is correct for command 'pair_to_bed'' isa 'Bio::SeqFeature::Collection' ok 155 - correct number of features for command 'pair_to_bed' # TODO maybe adapt reference results to Debian specific dataset ok 156 - make a factory using command 'bed_to_IGV' ok 157 - factory command for 'bed_to_IGV' is correct ok 158 - all available options for 'bed_to_IGV' ok 159 - available parameters for 'bed_to_IGV' ok 160 - available switches for 'bed_to_IGV' ok 161 - get version for 'bed_to_IGV' ok 162 - can run command 'bed_to_IGV' ok 163 - result files exists for command 'bed_to_IGV' ok 164 - can return output format for command 'bed_to_IGV' ok 165 - result claims to be in correct format for command 'bed_to_IGV' ok 166 - can return output file for command 'bed_to_IGV' ok 167 - can set want to IO object for command 'bed_to_IGV' ok 168 - can get the basic object result for command 'bed_to_IGV' ok 169 - 'returned object is correct for command 'bed_to_IGV'' isa 'Bio::Root::IO' ok 170 - make a factory using command 'group_by' ok 171 - factory command for 'group_by' is correct ok 172 - all available options for 'group_by' ok 173 - available parameters for 'group_by' ok 174 - available switches for 'group_by' ok 175 - get version for 'group_by' ok 176 - can set parameter -group => 1 ok 177 - can set parameter -columns => '2,2,3,3' ok 178 - can set parameter -operations => 'min,max,min,max' ok 179 - can run command 'group_by' ok 180 - result files exists for command 'group_by' ok 181 - can return output format for command 'group_by' ok 182 - result claims to be in correct format for command 'group_by' ok 183 - can return output file for command 'group_by' ok 184 - file format of '/tmp/IpVZ68WadB/60thiQ6zpC.bed' consistent with claim for 'group_by' ok 185 - can set want to IO object for command 'group_by' ok 186 - can get the basic object result for command 'group_by' ok 187 - 'returned object is correct for command 'group_by'' isa 'Bio::Root::IO' ok 188 - can get the specific object result for command 'group_by' ok 189 - 'returned object is correct for command 'group_by'' isa 'Bio::SeqFeature::Collection' ok 190 - correct number of features for command 'group_by' # TODO maybe adapt reference results to Debian specific dataset ok 191 - make a factory using command 'shuffle' ok 192 - factory command for 'shuffle' is correct ok 193 - all available options for 'shuffle' ok 194 - available parameters for 'shuffle' ok 195 - available switches for 'shuffle' ok 196 - get version for 'shuffle' ok 197 - can run command 'shuffle' ok 198 - result files exists for command 'shuffle' ok 199 - can return output format for command 'shuffle' ok 200 - result claims to be in correct format for command 'shuffle' ok 201 - can return output file for command 'shuffle' ok 202 - file format of '/tmp/1K9DjO2pbT/YHobIrcU5U.bed' consistent with claim for 'shuffle' ok 203 - can set want to IO object for command 'shuffle' ok 204 - can get the basic object result for command 'shuffle' ok 205 - 'returned object is correct for command 'shuffle'' isa 'Bio::Root::IO' ok 206 - can get the specific object result for command 'shuffle' ok 207 - 'returned object is correct for command 'shuffle'' isa 'Bio::SeqFeature::Collection' ok 208 - correct number of features for command 'shuffle' # TODO maybe adapt reference results to Debian specific dataset ok 209 - make a factory using command 'b12_to_b6' ok 210 - factory command for 'b12_to_b6' is correct ok 211 - all available options for 'b12_to_b6' ok 212 - available parameters for 'b12_to_b6' ok 213 - available switches for 'b12_to_b6' ok 214 - get version for 'b12_to_b6' ok 215 - can run command 'b12_to_b6' ok 216 - result files exists for command 'b12_to_b6' ok 217 - can return output format for command 'b12_to_b6' ok 218 - result claims to be in correct format for command 'b12_to_b6' ok 219 - can return output file for command 'b12_to_b6' ok 220 - file format of '/tmp/FUvD2FErbc/w2a07_glyl.bed' consistent with claim for 'b12_to_b6' ok 221 - can set want to IO object for command 'b12_to_b6' ok 222 - can get the basic object result for command 'b12_to_b6' ok 223 - 'returned object is correct for command 'b12_to_b6'' isa 'Bio::Root::IO' ok 224 - can get the specific object result for command 'b12_to_b6' ok 225 - 'returned object is correct for command 'b12_to_b6'' isa 'Bio::SeqFeature::Collection' ok 226 - correct number of features for command 'b12_to_b6' # TODO maybe adapt reference results to Debian specific dataset ok 227 - make a factory using command 'intersect' ok 228 - factory command for 'intersect' is correct ok 229 - all available options for 'intersect' ok 230 - available parameters for 'intersect' ok 231 - available switches for 'intersect' ok 232 - get version for 'intersect' ok 233 - can run command 'intersect' ok 234 - result files exists for command 'intersect' ok 235 - can return output format for command 'intersect' ok 236 - result claims to be in correct format for command 'intersect' ok 237 - can return output file for command 'intersect' ok 238 - can set want to IO object for command 'intersect' ok 239 - can get the basic object result for command 'intersect' ok 240 - 'returned object is correct for command 'intersect'' isa 'Bio::Root::IO' ok 241 - can get the specific object result for command 'intersect' ok 242 - 'returned object is correct for command 'intersect'' isa 'Bio::SeqFeature::Collection' not ok 243 - correct number of features for command 'intersect' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'intersect'' # at t/BEDTools.t line 364. # got: '1305' # expected: '72534' ok 244 - make a factory using command 'slop' ok 245 - factory command for 'slop' is correct ok 246 - all available options for 'slop' ok 247 - available parameters for 'slop' ok 248 - available switches for 'slop' ok 249 - get version for 'slop' ok 250 - can set parameter -add_bidirectional => 100 ok 251 - can run command 'slop' ok 252 - result files exists for command 'slop' ok 253 - can return output format for command 'slop' ok 254 - result claims to be in correct format for command 'slop' ok 255 - can return output file for command 'slop' ok 256 - file format of '/tmp/2t2CZ4SCI_/af3H86Ouo_.bed' consistent with claim for 'slop' ok 257 - can set want to IO object for command 'slop' ok 258 - can get the basic object result for command 'slop' ok 259 - 'returned object is correct for command 'slop'' isa 'Bio::Root::IO' ok 260 - can get the specific object result for command 'slop' ok 261 - 'returned object is correct for command 'slop'' isa 'Bio::SeqFeature::Collection' ok 262 - correct number of features for command 'slop' # TODO maybe adapt reference results to Debian specific dataset ok 263 - make a factory using command 'closest' ok 264 - factory command for 'closest' is correct ok 265 - all available options for 'closest' ok 266 - available parameters for 'closest' ok 267 - available switches for 'closest' ok 268 - get version for 'closest' ok 269 - can run command 'closest' ok 270 - result files exists for command 'closest' ok 271 - can return output format for command 'closest' ok 272 - result claims to be in correct format for command 'closest' ok 273 - can return output file for command 'closest' ok 274 - file format of '/tmp/kCOWAuNlps/mjRM0Zqx1L.bedpe' consistent with claim for 'closest' ok 275 - can set want to IO object for command 'closest' ok 276 - can get the basic object result for command 'closest' ok 277 - 'returned object is correct for command 'closest'' isa 'Bio::Root::IO' ok 278 - can get the specific object result for command 'closest' ok 279 - 'returned object is correct for command 'closest'' isa 'Bio::SeqFeature::Collection' not ok 280 - correct number of features for command 'closest' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'closest'' # at t/BEDTools.t line 364. # got: '2121' # expected: '845' ok 281 - make a factory using command 'links' ok 282 - factory command for 'links' is correct ok 283 - all available options for 'links' ok 284 - available parameters for 'links' ok 285 - available switches for 'links' ok 286 - get version for 'links' ok 287 - can run command 'links' ok 288 - result files exists for command 'links' ok 289 - can return output format for command 'links' ok 290 - result claims to be in correct format for command 'links' ok 291 - can return output file for command 'links' ok 292 - make readable output ok 293 - - html tag line ok 294 - - number of lines ok 295 - can set want to IO object for command 'links' ok 296 - can get the basic object result for command 'links' ok 297 - 'returned object is correct for command 'links'' isa 'Bio::Root::IO' ok 298 - make a factory using command 'sort' ok 299 - factory command for 'sort' is correct ok 300 - all available options for 'sort' ok 301 - available parameters for 'sort' ok 302 - available switches for 'sort' ok 303 - get version for 'sort' ok 304 - can run command 'sort' ok 305 - result files exists for command 'sort' ok 306 - can return output format for command 'sort' ok 307 - result claims to be in correct format for command 'sort' ok 308 - can return output file for command 'sort' ok 309 - file format of '/tmp/oTFnkvjCEO/6c2VHfVrac.bed' consistent with claim for 'sort' ok 310 - can set want to IO object for command 'sort' ok 311 - can get the basic object result for command 'sort' ok 312 - 'returned object is correct for command 'sort'' isa 'Bio::Root::IO' ok 313 - can get the specific object result for command 'sort' ok 314 - 'returned object is correct for command 'sort'' isa 'Bio::SeqFeature::Collection' ok 315 - correct number of features for command 'sort' # TODO maybe adapt reference results to Debian specific dataset ok 316 - make a factory using command 'complement' ok 317 - factory command for 'complement' is correct ok 318 - all available options for 'complement' ok 319 - available parameters for 'complement' ok 320 - available switches for 'complement' ok 321 - get version for 'complement' ok 322 - can run command 'complement' ok 323 - result files exists for command 'complement' ok 324 - can return output format for command 'complement' ok 325 - result claims to be in correct format for command 'complement' ok 326 - can return output file for command 'complement' ok 327 - file format of '/tmp/33N4sM_pOI/SCjU8HLFHs.bed' consistent with claim for 'complement' ok 328 - can set want to IO object for command 'complement' ok 329 - can get the basic object result for command 'complement' ok 330 - 'returned object is correct for command 'complement'' isa 'Bio::Root::IO' ok 331 - can get the specific object result for command 'complement' ok 332 - 'returned object is correct for command 'complement'' isa 'Bio::SeqFeature::Collection' not ok 333 - correct number of features for command 'complement' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'complement'' # at t/BEDTools.t line 364. # got: '292' # expected: '291' ok 334 - make a factory using command 'mask_fasta_from_bed' ok 335 - factory command for 'mask_fasta_from_bed' is correct ok 336 - all available options for 'mask_fasta_from_bed' ok 337 - available parameters for 'mask_fasta_from_bed' ok 338 - available switches for 'mask_fasta_from_bed' ok 339 - get version for 'mask_fasta_from_bed' ok 340 - can run command 'mask_fasta_from_bed' ok 341 - result files exists for command 'mask_fasta_from_bed' ok 342 - can return output format for command 'mask_fasta_from_bed' ok 343 - result claims to be in correct format for command 'mask_fasta_from_bed' ok 344 - can return output file for command 'mask_fasta_from_bed' ok 345 - file format consistent with claim for 'mask_fasta_from_bed' ok 346 - can set want to IO object for command 'mask_fasta_from_bed' ok 347 - can get the basic object result for command 'mask_fasta_from_bed' ok 348 - 'returned object is correct for command 'mask_fasta_from_bed'' isa 'Bio::Root::IO' ok 349 - can get the specific object result for command 'mask_fasta_from_bed' ok 350 - 'returned object is correct for command 'mask_fasta_from_bed'' isa 'Bio::SeqIO' ok 351 - correct number of sequences for command 'mask_fasta_from_bed' ok 352 - make a factory using command 'subtract' ok 353 - factory command for 'subtract' is correct ok 354 - all available options for 'subtract' ok 355 - available parameters for 'subtract' ok 356 - available switches for 'subtract' ok 357 - get version for 'subtract' ok 358 - can run command 'subtract' ok 359 - result files exists for command 'subtract' ok 360 - can return output format for command 'subtract' ok 361 - result claims to be in correct format for command 'subtract' ok 362 - can return output file for command 'subtract' ok 363 - file format of '/tmp/Htp64C_X9A/im3vjckZ81.bed' consistent with claim for 'subtract' ok 364 - can set want to IO object for command 'subtract' ok 365 - can get the basic object result for command 'subtract' ok 366 - 'returned object is correct for command 'subtract'' isa 'Bio::Root::IO' ok 367 - can get the specific object result for command 'subtract' ok 368 - 'returned object is correct for command 'subtract'' isa 'Bio::SeqFeature::Collection' not ok 369 - correct number of features for command 'subtract' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'subtract'' # at t/BEDTools.t line 364. # got: '1802' # expected: '57959' ok 370 - make a factory using command 'coverage' ok 371 - factory command for 'coverage' is correct ok 372 - all available options for 'coverage' ok 373 - available parameters for 'coverage' ok 374 - available switches for 'coverage' ok 375 - get version for 'coverage' ok 376 - can run command 'coverage' ok 377 - result files exists for command 'coverage' ok 378 - can return output format for command 'coverage' ok 379 - result claims to be in correct format for command 'coverage' ok 380 - can return output file for command 'coverage' ok 381 - file format of '/tmp/eqQfw4cMRc/95FRlnTI7F.bed' consistent with claim for 'coverage' ok 382 - can set want to IO object for command 'coverage' ok 383 - can get the basic object result for command 'coverage' ok 384 - 'returned object is correct for command 'coverage'' isa 'Bio::Root::IO' ok 385 - can get the specific object result for command 'coverage' ok 386 - 'returned object is correct for command 'coverage'' isa 'Bio::SeqFeature::Collection' not ok 387 - correct number of features for command 'coverage' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'coverage'' # at t/BEDTools.t line 364. # got: '828' # expected: '57261' ok 388 - make a factory using command 'merge' ok 389 - factory command for 'merge' is correct ok 390 - all available options for 'merge' ok 391 - available parameters for 'merge' ok 392 - available switches for 'merge' ok 393 - get version for 'merge' ok 394 - can run command 'merge' ok 395 - result files exists for command 'merge' ok 396 - can return output format for command 'merge' ok 397 - result claims to be in correct format for command 'merge' ok 398 - can return output file for command 'merge' ok 399 - file format of '/tmp/IAqVI4l2zV/yTfjdSPVOc.bed' consistent with claim for 'merge' ok 400 - can set want to IO object for command 'merge' ok 401 - can get the basic object result for command 'merge' ok 402 - 'returned object is correct for command 'merge'' isa 'Bio::Root::IO' ok 403 - can get the specific object result for command 'merge' ok 404 - 'returned object is correct for command 'merge'' isa 'Bio::SeqFeature::Collection' ok 405 - correct number of features for command 'merge' # TODO maybe adapt reference results to Debian specific dataset ok 406 - make a factory using command 'window' ok 407 - factory command for 'window' is correct ok 408 - all available options for 'window' ok 409 - available parameters for 'window' ok 410 - available switches for 'window' ok 411 - get version for 'window' ok 412 - can run command 'window' ok 413 - result files exists for command 'window' ok 414 - can return output format for command 'window' ok 415 - result claims to be in correct format for command 'window' ok 416 - can return output file for command 'window' ok 417 - file format of '/tmp/1fyXQN6E4d/xrLrj8c0Jx.bedpe' consistent with claim for 'window' ok 418 - can set want to IO object for command 'window' ok 419 - can get the basic object result for command 'window' ok 420 - 'returned object is correct for command 'window'' isa 'Bio::Root::IO' ok 421 - can get the specific object result for command 'window' ok 422 - 'returned object is correct for command 'window'' isa 'Bio::SeqFeature::Collection' not ok 423 - correct number of features for command 'window' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'window'' # at t/BEDTools.t line 364. # got: '1331' # expected: '74998' 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 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 [17%] 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 [32%] 16000 Cells done [34%] 17000 Cells done [36%] 18000 Cells done [38%] 19000 Cells done [40%] 20000 Cells done [42%] 21000 Cells done [44%] 22000 Cells done [46%] 23000 Cells done [49%] 24000 Cells done [51%] 25000 Cells done [53%] 26000 Cells done [55%] 27000 Cells done [57%] 28000 Cells done [59%] 29000 Cells done [61%] 30000 Cells done [64%] 31000 Cells done [66%] 32000 Cells done [68%] 33000 Cells done [70%] 34000 Cells done [72%] 35000 Cells done [74%] 36000 Cells done [76%] 37000 Cells done [79%] 38000 Cells done [81%] 39000 Cells done [83%] 40000 Cells done [85%] 41000 Cells done [87%] 42000 Cells done [89%] 43000 Cells done [91%] 44000 Cells done [93%] 45000 Cells done [96%] 46000 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 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 [17%] 8000 Cells done [19%] 9000 Cells done [21%] 10000 Cells done [24%] 11000 Cells done [26%] 12000 Cells done [29%] 13000 Cells done [31%] 14000 Cells done [34%] 15000 Cells done [36%] 16000 Cells done [38%] 17000 Cells done [41%] 18000 Cells done [43%] 19000 Cells done [46%] 20000 Cells done [48%] 21000 Cells done [51%] 22000 Cells done [53%] 23000 Cells done [55%] 24000 Cells done [58%] 25000 Cells done [60%] 26000 Cells done [63%] 27000 Cells done [65%] 28000 Cells done [68%] 29000 Cells done [70%] 30000 Cells done [72%] 31000 Cells done [75%] 32000 Cells done [77%] 33000 Cells done [80%] 34000 Cells done [82%] 35000 Cells done [85%] 36000 Cells done [87%] 37000 Cells done [89%] 38000 Cells done [92%] 39000 Cells done [94%] 40000 Cells done [97%] 41000 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 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 [17%] 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 [32%] 16000 Cells done [34%] 17000 Cells done [36%] 18000 Cells done [38%] 19000 Cells done [40%] 20000 Cells done [42%] 21000 Cells done [44%] 22000 Cells done [46%] 23000 Cells done [49%] 24000 Cells done [51%] 25000 Cells done [53%] 26000 Cells done [55%] 27000 Cells done [57%] 28000 Cells done [59%] 29000 Cells done [61%] 30000 Cells done [64%] 31000 Cells done [66%] 32000 Cells done [68%] 33000 Cells done [70%] 34000 Cells done [72%] 35000 Cells done [74%] 36000 Cells done [76%] 37000 Cells done [79%] 38000 Cells done [81%] 39000 Cells done [83%] 40000 Cells done [85%] 41000 Cells done [87%] 42000 Cells done [89%] 43000 Cells done [91%] 44000 Cells done [93%] 45000 Cells done [96%] 46000 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 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 -- namet is "-sequence" associated seqall qualifiers -- namet is "-outfile" associated outfile qualifiers 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 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE 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 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 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 - An object of class 'Bio::Tools::Glimmer' isa 'Bio::Tools::Glimmer' ok 6 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 7 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 8 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 9 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 10 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 11 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 12 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 13 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 14 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 15 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 16 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 17 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 18 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 19 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 20 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 21 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 22 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 23 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 24 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 25 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 26 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 27 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 28 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 29 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 30 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 31 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 32 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 33 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 34 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 35 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 36 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 37 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 38 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 39 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 40 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 41 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 42 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 43 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 44 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 45 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 46 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 47 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 48 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 49 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 50 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 51 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 52 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 53 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 54 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 55 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 56 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 57 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 58 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 59 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 60 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 61 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 62 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 63 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 64 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 65 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 66 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 67 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 68 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 69 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 70 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 71 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 72 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 73 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 74 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 75 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 76 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 77 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 78 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 79 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 80 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 81 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 82 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 83 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 84 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 85 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 86 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 87 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 88 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 89 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 90 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 91 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 92 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 93 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 94 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 95 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 96 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 97 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 98 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 99 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 100 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 101 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 102 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 103 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 104 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 105 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 106 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 107 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 108 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 109 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 110 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 111 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' 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 (3.3) Copyright (C) 2006,2019,2020 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 WARNING: AVX2 instruction set not found! Kalign will not run optimally. [2021-07-26 18:46:32] : LOG : Detected protein sequences. [2021-07-26 18:46:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2021-07-26 18:46:32] : LOG : Detected: 7 sequences. [2021-07-26 18:46:32] : LOG : Calculating pairwise distances [2021-07-26 18:46:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2021-07-26 18:46:32] : LOG : 7 anchors [2021-07-26 18:46:32] : LOG : Building guide tree. [2021-07-26 18:46:32] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 [2021-07-26 18:46:32] : LOG : Aligning [2021-07-26 18:46:32] : LOG : CPU Time: 0.09u 00:00:00.09 Elapsed: 00:00:00.00 ok 5 ok 6 Kalign (3.3) Copyright (C) 2006,2019,2020 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 WARNING: AVX2 instruction set not found! Kalign will not run optimally. [2021-07-26 18:46:32] : LOG : Detected protein sequences. [2021-07-26 18:46:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2021-07-26 18:46:32] : LOG : Detected: 7 sequences. [2021-07-26 18:46:32] : LOG : Calculating pairwise distances [2021-07-26 18:46:32] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 [2021-07-26 18:46:32] : LOG : 7 anchors [2021-07-26 18:46:32] : LOG : Building guide tree. [2021-07-26 18:46:32] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 [2021-07-26 18:46:32] : LOG : Aligning [2021-07-26 18:46:32] : LOG : CPU Time: 0.10u 00:00:00.10 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..8 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 - Code tested only on muscle versions > 3.6 ok 8 - log file 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 t/PhastCons.t ................. skipped: The optional module Clone (or dependencies thereof) was not installed # 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 ................... skipped: The optional module Clone (or dependencies thereof) was not installed # 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/rszOMFp4xo 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/aY0bcrVtzP 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[] = { 0.8318780065 5.246741057e-05 5.246741057e-05 0.08400853723 0.08400853723 } gapOpen[] = { 0.01386913192 0.01386913192 0.006558840629 0.006558840629 } gapExtend[] = { 0.3603840172 0.3603840172 0.7831536531 0.7831536531 } PROBCONS version 1.12 - align multiple protein sequences and print to standard output Written by Chuong Do Using parameter set: initDistrib[] = { 0.8318780065 5.246739966e-05 5.246739966e-05 0.08400853723 0.08400853723 } gapOpen[] = { 0.01386913192 0.01386913192 0.006558840629 0.006558840629 } gapExtend[] = { 0.3603840172 0.3603840172 0.7831536531 0.7831536531 } Loading sequence file: /tmp/ShiqoyRlzF 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 # Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present t/ProtDist.t .................. 1..14 ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtDist; ok 2 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok # Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present 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 Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present 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 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 - merge bam factory instantiated ok 27 - merged bam file created ok 28 - fasta index factory ok 29 - make fasta index ok 30 - fai file present ok 31 - bam -> sam cvt factory ok 32 - convert bam -> sam ok 33 - sam file present and text ok 34 - sam -> bam cvt factory ok 35 - convert sam -> bam ok 36 - bam file present and binary ok 37 - bam sort factory ok 38 - sort bam file ok 39 - bam index factory ok 40 - make bam index ok 41 - bai file present and binary 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. Test Summary Report ------------------- t/BEDTools.t (Wstat: 0 Tests: 423 Failed: 0) TODO passed: 20, 57, 75, 110, 155, 190, 208, 226, 262 315, 405 Files=60, Tests=1454, 511 wallclock secs ( 0.46 usr 0.32 sys + 410.89 cusr 20.83 csys = 432.50 CPU) Result: PASS mv t.skip/* t rm -rf t.skip make[1]: Leaving directory '/build/bioperl-run-1.7.3' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install perl Build install --destdir /build/bioperl-run-1.7.3/debian/tmp --create_packlist 0 Building BioPerl-Run Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_multi_hmmsearch.pl.1p Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_papplmaker.pl.1p Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_panalysis.pl.1p Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_protdist.pl.1p Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_neighbor.pl.1p Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/ESoap.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/GQueryAdaptor.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/DocSumAdaptor.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/Result.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/LinkAdaptor.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/ESoap/WSDL.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Glimmer.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Promoterwise.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Eponine.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Signalp.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Pseudowise.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Prints.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genemark.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Ensembl.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/tRNAscanSE.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primate.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Coil.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Tmhmm.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primer3.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/MCS.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Seg.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/ERPIN.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Mdust.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/TribeMCL.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Hmmer.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Match.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneWUBlast.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genewise.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RepeatMasker.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Vista.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RNAMotif.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Simprot.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSacd.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genscan.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneNCBIBlast.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSApplication.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Profile.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/FootPrinter.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Infernal.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus/Config.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phyml.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/SLR.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Raxml.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/LVB.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Semphy.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/QuickTree.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/FastTree.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Gerp.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhastCons.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Consense.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Base.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/REL.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Base.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/FEL.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Njtree/Best.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Molphy/ProtML.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools/Config.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Proda.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MSAProbs.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Lagan.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Amap.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Sim4.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/StandAloneFasta.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probalign.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Gmap.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Exonerate.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Kalign.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Blat.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/DBA.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probcons.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Muscle.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Pal2Nal.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MAFFT.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools/Config.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Analysis/soap.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/AnalysisFactory/soap.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Factory/EMBOSS.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genewise.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Tmhmm.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Prints.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneWUBlast.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::SLR.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Primate.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawGram.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Promoterwise.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Primer3.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phyml.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Consense.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::ESoap.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::Base.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Kalign.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Pal2Nal.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::PhylipConf.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BEDTools.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::RepeatMasker.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Amap.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genscan.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::TribeMCL.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Molphy::ProtML.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::QuickTree.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Match.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneNCBIBlast.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Probcons.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Glimmer.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::GQueryAdaptor.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Samtools.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::SLAC.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Semphy.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtPars.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::DBA.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Base.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Factory::EMBOSS.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::EMBOSSacd.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::Modeltest.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Mdust.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Eponine.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Probalign.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawTree.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Signalp.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::MCS.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::SeqBoot.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor::seq.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::FastTree.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phast::PhastCons.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::ESoap::WSDL.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::FootPrinter.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlast.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor::species.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::StandAloneFasta.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::FEL.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Sim4.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Coil.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Proda.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Samtools::Config.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Hmmer.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::RNAMotif.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phast::PhyloFit.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::DocSumAdaptor.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::MSAProbs.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Blat.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Pseudowise.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::Result.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Infernal.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genemark.3pm Installing 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/build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::ERPIN.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Exonerate.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Muscle.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Seg.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Njtree::Best.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus::BlastMethods.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Neighbor.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::AnalysisFactory::soap.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Vista.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::EMBOSSApplication.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::REL.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::LinkAdaptor.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BEDTools::Config.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Analysis::soap.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::LVB.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Ensembl.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::tRNAscanSE.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Simprot.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_multi_hmmsearch.pl Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_protdist.pl Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_papplmaker.pl Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_panalysis.pl Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_neighbor.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_1.7.3-6_all.deb'. dpkg-deb: building package 'libbio-perl-run-perl' in '../libbio-perl-run-perl_1.7.3-6_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bioperl-run_1.7.3-6_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/4713 and its subdirectories I: Current time: Mon Jul 26 18:48:06 -12 2021 I: pbuilder-time-stamp: 1627368486 Tue Jul 27 06:48:07 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos16-i386.debian.net. Tue Jul 27 06:48:07 UTC 2021 I: Preparing to do remote build '2' on ionos16-i386.debian.net. Tue Jul 27 06:52:33 UTC 2021 I: Deleting $TMPDIR on ionos16-i386.debian.net. Tue Jul 27 06:52:34 UTC 2021 I: bioperl-run_1.7.3-6_i386.changes: Format: 1.8 Date: Wed, 06 Jan 2021 22:38:23 +0100 Source: bioperl-run Binary: bioperl-run libbio-perl-run-perl Architecture: all Version: 1.7.3-6 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 (1.7.3-6) unstable; urgency=medium . * Team upload. * d/control: restrict build-dependencies to their supported architectures. * added skip-test-for-kalign.patch Checksums-Sha1: 99d109f83278635b98dda301c1b0dcc434f4a360 42176 bioperl-run_1.7.3-6_all.deb f3335fb23ed40e12f0892639f6a4085dd98341a8 11503 bioperl-run_1.7.3-6_i386.buildinfo 757daf5c0a5d4517a2208e442feb4b2236ec564c 606844 libbio-perl-run-perl_1.7.3-6_all.deb Checksums-Sha256: 96539756f48b8dfeeb51070cef9b0a1bb37e3ef6b46b3c4e7ed5f187a7011cc8 42176 bioperl-run_1.7.3-6_all.deb f673f7c6a8e392cbfabc6a171121ca72056eeca51981f92786bf63ab77398890 11503 bioperl-run_1.7.3-6_i386.buildinfo 657ff72c856ff81268d90502df4d4fff107de08995fb856bb1a670ca0a27ee4c 606844 libbio-perl-run-perl_1.7.3-6_all.deb Files: f3fc8572e09a0026869345f1484bce9f 42176 science optional bioperl-run_1.7.3-6_all.deb 9ee8e655e35aa5fc25ef013019b6b2ed 11503 science optional bioperl-run_1.7.3-6_i386.buildinfo 6de08d7bc14fe9a4b5a71024b607bdc6 606844 perl optional libbio-perl-run-perl_1.7.3-6_all.deb Tue Jul 27 06:52:35 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.QD8aTJ1aHV/bioperl-run_1.7.3-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.QD8aTJ1aHV/bioperl-run_1.7.3-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.QD8aTJ1aHV/bioperl-run_1.7.3-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.QD8aTJ1aHV/b1/bioperl-run_1.7.3-6_i386.changes /srv/reproducible-results/rbuild-debian/tmp.QD8aTJ1aHV/b2/bioperl-run_1.7.3-6_i386.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: 0.284s) 0.284s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.026s) 0.025s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Tue Jul 27 06:52:38 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Tue Jul 27 06:52:38 UTC 2021 I: bioperl-run from bullseye built successfully and reproducibly on i386. Tue Jul 27 06:52:40 UTC 2021 I: Submitting .buildinfo files to external archives: Tue Jul 27 06:52:40 UTC 2021 I: Submitting 16K b1/bioperl-run_1.7.3-6_i386.buildinfo.asc Tue Jul 27 06:52:42 UTC 2021 I: Submitting 16K b2/bioperl-run_1.7.3-6_i386.buildinfo.asc Tue Jul 27 06:52:43 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Jul 27 06:52:43 UTC 2021 I: Done submitting .buildinfo files. Tue Jul 27 06:52:43 UTC 2021 I: Removing signed bioperl-run_1.7.3-6_i386.buildinfo.asc files: removed './b1/bioperl-run_1.7.3-6_i386.buildinfo.asc' removed './b2/bioperl-run_1.7.3-6_i386.buildinfo.asc'