sbuild (Debian sbuild) 0.85.9 (29 May 2024) on carme.larted.org.uk

+==============================================================================+
| bioperl-run 1.7.3-11 (amd64)                 Sun, 02 Jun 2024 23:59:39 +0000 |
+==============================================================================+

Package: bioperl-run
Version: 1.7.3-11
Source Version: 1.7.3-11
Distribution: perl-5.40-throwaway
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
Build Type: full

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-50d3ded9-1036-4fe1-ba23-75bd170b246c' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Chroot Setup Commands                                                        |
+------------------------------------------------------------------------------+


/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bioperl-run_1.7.3-11 perl-5.40-throwaway amd64
---------------------------------------------------------------------------------------------------------------------


I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bioperl-run_1.7.3-11 perl-5.40-throwaway amd64'.

Finished processing commands.
--------------------------------------------------------------------------------
I: NOTICE: Log filtering will replace 'build/bioperl-run-3zEIsh/resolver-8XgrWB' with '<<RESOLVERDIR>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B]
Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B]
Get:2 file:/srv/reprepro perl-5.40/main amd64 Packages [598 kB]
Hit:3 http://localhost:3142/debian unstable InRelease
Hit:4 http://localhost:3142/debian sid InRelease
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Local sources
-------------

/srv/debomatic/incoming/bioperl-run_1.7.3-11.dsc exists in /srv/debomatic/incoming; copying to chroot
I: NOTICE: Log filtering will replace 'build/bioperl-run-3zEIsh/bioperl-run-1.7.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/bioperl-run-3zEIsh' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), libmodule-build-perl, build-essential, fakeroot, perl, bioperl (>= 1.7.4), libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, libfile-sort-perl, libtest-most-perl, libarray-compare-perl, libtree-dagnode-perl, libbio-cluster-perl, libbio-featureio-perl, libconfig-any-perl, libbio-tools-run-alignment-clustalw-perl, libbio-eutilities-perl, libbio-tools-run-remoteblast-perl, amap-align, bedtools, bedtools-test, ncbi-blast+-legacy, clustalw, emboss, exonerate, hmmer, hyphy-pt | hyphy-mpi, infernal, kalign, mafft, muscle, ncoils, phyml, primer3, probcons, python3-pybedtools, raxml, samtools, sim4, tigr-glimmer, wise, fasttree, lagan, pal2nal, pftools, libwww-perl
Filtered Build-Depends: debhelper-compat (= 13), libmodule-build-perl, build-essential, fakeroot, 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, infernal, kalign, mafft, muscle, ncoils, phyml, primer3, probcons, python3-pybedtools, raxml, samtools, sim4, tigr-glimmer, wise, fasttree, lagan, pal2nal, pftools, libwww-perl
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [615 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [1533 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [1305 B]
Fetched 3453 B in 0s (0 B/s)
Reading package lists...
Reading package lists...

Install main build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  amap-align autoconf automake autopoint autotools-dev bedtools bedtools-test
  bioperl bsdextrautils ca-certificates clustalw debhelper dh-autoreconf
  dh-strip-nondeterminism dwz emboss emboss-data emboss-lib exonerate fakeroot
  fasttree file fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext
  gettext-base groff-base hmmer hyphy-common hyphy-pt ibverbs-providers
  infernal intltool-debian kalign lagan libabsl20230802 libalgorithm-diff-perl
  libamd-comgr2 libamdhip64-5 libaom3 libarchive-zip-perl
  libarray-compare-perl libavif16 libb-hooks-op-check-perl
  libbio-asn1-entrezgene-perl libbio-cluster-perl libbio-eutilities-perl
  libbio-featureio-perl libbio-perl-perl libbio-perl-run-perl
  libbio-tools-run-alignment-clustalw-perl libbio-tools-run-remoteblast-perl
  libbio-variation-perl libblas3 libbrotli1 libbsd0 libcapture-tiny-perl
  libcbor0.10 libclass-data-inheritable-perl libclass-method-modifiers-perl
  libclass-xsaccessor-perl libclone-perl libcom-err2 libconfig-any-perl
  libcurl3t64-gnutls libdata-stag-perl libdav1d7 libde265-0 libdebhelper-perl
  libdeflate0 libdevel-callchecker-perl libdevel-stacktrace-perl
  libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm2
  libdynaloader-functions-perl libedit2 libelf1t64 libencode-locale-perl
  libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libexception-class-perl
  libexpat1 libexporter-tiny-perl libfabric1 libfakeroot libfido2-1
  libfile-listing-perl libfile-slurp-perl libfile-slurp-tiny-perl
  libfile-sort-perl libfile-stripnondeterminism-perl libfontconfig1
  libfreetype6 libgav1-1 libgd3 libgfortran5 libglib2.0-0t64 libgssapi-krb5-2
  libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhpdf-2.3.0
  libhsa-runtime64-1 libhsakmt1 libhtml-parser-perl libhtml-tagset-perl
  libhtml-tree-perl libhts3t64 libhtscodecs2 libhttp-cookies-perl
  libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl
  libhwloc-plugins libhwloc15 libibverbs1 libicu72 libimport-into-perl
  libio-html-perl libio-pty-perl libio-socket-ssl-perl libio-string-perl
  libipc-run-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3
  libkrb5support0 liblapack3 liblerc4 libllvm17t64 liblmdb0
  liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1t64
  libmariadb3 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64
  libmodule-build-perl libmodule-pluggable-perl libmodule-runtime-perl
  libmoo-perl libmunge2 libncurses6 libnet-http-perl libnet-ssleay-perl
  libnghttp2-14 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3t64
  libparams-classify-perl libpciaccess0 libpipeline1 libpmix2t64
  libpng16-16t64 libpq5 libpsl5t64 libpsm-infinipath1 libpsm2-2
  libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librav1e0
  librdmacm1t64 librole-tiny-perl librtmp1 libsharpyuv0 libssh2-1t64
  libsub-quote-perl libsub-uplevel-perl libsvtav1enc1d1 libtest-deep-perl
  libtest-differences-perl libtest-exception-perl libtest-most-perl
  libtest-warn-perl libtext-csv-perl libtext-diff-perl libtiff6
  libtimedate-perl libtool libtree-dagnode-perl libtry-tiny-perl
  libtype-tiny-perl libuchardet0 libucx0 liburi-perl libwebp7 libwww-perl
  libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6
  libxext6 libxml-dom-perl libxml-dom-xpath-perl libxml-libxml-perl
  libxml-namespacesupport-perl libxml-parser-perl libxml-perl
  libxml-regexp-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl
  libxml-twig-perl libxml-writer-perl libxml-xpathengine-perl libxml2
  libxnvctrl0 libxpm4 libyuv0 libz3-4 m4 mafft man-db mariadb-common
  media-types muscle mysql-common ncbi-blast+ ncbi-blast+-legacy ncbi-data
  ncoils netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client
  openssl pal2nal perl-openssl-defaults pftools phyml po-debconf primer3
  probcons python3 python3-minimal python3-numpy python3-pkg-resources
  python3-pybedtools python3-pysam python3.11 python3.11-minimal raxml
  samtools sensible-utils sim4 tigr-glimmer tzdata ucf wise wise-data
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc clustalx seaview dh-make
  emboss-doc emboss-test embassy gettext-doc libasprintf-dev libgettextpo-dev
  groff hmmer-doc libxml-sax-expatxs-perl libgd-tools low-memory-monitor
  krb5-doc krb5-user libheif-plugin-ffmpegdec libheif-plugin-jpegdec
  libheif-plugin-jpegenc libheif-plugin-j2kdec libheif-plugin-j2kenc
  libheif-plugin-rav1e libheif-plugin-svtenc libdata-dump-perl
  libhwloc-contrib-plugins libcrypt-ssleay-perl libscalar-number-perl pciutils
  libtool-doc gfortran | fortran95-compiler gcj-jdk libsub-name-perl
  libdevel-lexalias-perl libbusiness-isbn-perl libregexp-ipv6-perl
  libauthen-ntlm-perl libunicode-map8-perl libunicode-string-perl
  xml-twig-tools m4-doc apparmor less www-browser gnuplot opencl-icd gfortran
  | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass
  libmail-box-perl ncbi-epcr probcons-extra python3-doc python3-tk
  python3-venv gfortran python-numpy-doc python3-dev python3-pytest
  python3-setuptools python-pybedtools-doc python3.11-venv python3.11-doc
  binfmt-support cwltool wise-doc
Recommended packages:
  bioperl-run perl-doc libcache-cache-perl libdbi-perl libgd-gd2-perl
  libapache-dbi-perl libyaml-perl libace-perl liblist-moreutils-perl
  libset-scalar-perl dialign curl | wget | lynx libalgorithm-diff-xs-perl
  libalgorithm-munkres-perl libconvert-binary-c-perl libdbd-sqlite3-perl
  libdbd-mysql-perl libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl
  libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl
  libsort-naturally-perl libspreadsheet-parseexcel-perl
  libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl
  libxml-sax-writer-perl libconfig-general-perl libconfig-tiny-perl
  libyaml-libyaml-perl | libyaml-syck-perl | libyaml-perl perl-tk
  libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl
  libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs
  libheif-plugin-aomenc libheif-plugin-x265 libhtml-format-perl
  libio-compress-brotli-perl krb5-locales libmodule-signature-perl
  libpod-readme-perl libsoftware-license-perl libnamespace-clean-perl libgpm2
  publicsuffix libxstring-perl libtext-csv-xs-perl libltdl-dev
  libref-util-perl libtype-tiny-xs-perl libdata-dump-perl libhtml-form-perl
  libhttp-daemon-perl libmailtools-perl libxml-sax-expat-perl
  libtext-iconv-perl libtie-ixhash-perl blast2 lynx ruby xauth paml
  libmail-sendmail-perl
The following NEW packages will be installed:
  amap-align autoconf automake autopoint autotools-dev bedtools bedtools-test
  bioperl bsdextrautils ca-certificates clustalw debhelper dh-autoreconf
  dh-strip-nondeterminism dwz emboss emboss-data emboss-lib exonerate fakeroot
  fasttree file fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext
  gettext-base groff-base hmmer hyphy-common hyphy-pt ibverbs-providers
  infernal intltool-debian kalign lagan libabsl20230802 libalgorithm-diff-perl
  libamd-comgr2 libamdhip64-5 libaom3 libarchive-zip-perl
  libarray-compare-perl libavif16 libb-hooks-op-check-perl
  libbio-asn1-entrezgene-perl libbio-cluster-perl libbio-eutilities-perl
  libbio-featureio-perl libbio-perl-perl libbio-perl-run-perl
  libbio-tools-run-alignment-clustalw-perl libbio-tools-run-remoteblast-perl
  libbio-variation-perl libblas3 libbrotli1 libbsd0 libcapture-tiny-perl
  libcbor0.10 libclass-data-inheritable-perl libclass-method-modifiers-perl
  libclass-xsaccessor-perl libclone-perl libcom-err2 libconfig-any-perl
  libcurl3t64-gnutls libdata-stag-perl libdav1d7 libde265-0 libdebhelper-perl
  libdeflate0 libdevel-callchecker-perl libdevel-stacktrace-perl
  libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm2
  libdynaloader-functions-perl libedit2 libelf1t64 libencode-locale-perl
  libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libexception-class-perl
  libexpat1 libexporter-tiny-perl libfabric1 libfakeroot libfido2-1
  libfile-listing-perl libfile-slurp-perl libfile-slurp-tiny-perl
  libfile-sort-perl libfile-stripnondeterminism-perl libfontconfig1
  libfreetype6 libgav1-1 libgd3 libgfortran5 libglib2.0-0t64 libgssapi-krb5-2
  libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhpdf-2.3.0
  libhsa-runtime64-1 libhsakmt1 libhtml-parser-perl libhtml-tagset-perl
  libhtml-tree-perl libhts3t64 libhtscodecs2 libhttp-cookies-perl
  libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl
  libhwloc-plugins libhwloc15 libibverbs1 libicu72 libimport-into-perl
  libio-html-perl libio-pty-perl libio-socket-ssl-perl libio-string-perl
  libipc-run-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3
  libkrb5support0 liblapack3 liblerc4 libllvm17t64 liblmdb0
  liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1t64
  libmariadb3 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64
  libmodule-build-perl libmodule-pluggable-perl libmodule-runtime-perl
  libmoo-perl libmunge2 libncurses6 libnet-http-perl libnet-ssleay-perl
  libnghttp2-14 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3t64
  libparams-classify-perl libpciaccess0 libpipeline1 libpmix2t64
  libpng16-16t64 libpq5 libpsl5t64 libpsm-infinipath1 libpsm2-2
  libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librav1e0
  librdmacm1t64 librole-tiny-perl librtmp1 libsharpyuv0 libssh2-1t64
  libsub-quote-perl libsub-uplevel-perl libsvtav1enc1d1 libtest-deep-perl
  libtest-differences-perl libtest-exception-perl libtest-most-perl
  libtest-warn-perl libtext-csv-perl libtext-diff-perl libtiff6
  libtimedate-perl libtool libtree-dagnode-perl libtry-tiny-perl
  libtype-tiny-perl libuchardet0 libucx0 liburi-perl libwebp7 libwww-perl
  libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6
  libxext6 libxml-dom-perl libxml-dom-xpath-perl libxml-libxml-perl
  libxml-namespacesupport-perl libxml-parser-perl libxml-perl
  libxml-regexp-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl
  libxml-twig-perl libxml-writer-perl libxml-xpathengine-perl libxml2
  libxnvctrl0 libxpm4 libyuv0 libz3-4 m4 mafft man-db mariadb-common
  media-types muscle mysql-common ncbi-blast+ ncbi-blast+-legacy ncbi-data
  ncoils netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client
  openssl pal2nal perl-openssl-defaults pftools phyml po-debconf primer3
  probcons python3 python3-minimal python3-numpy python3-pkg-resources
  python3-pybedtools python3-pysam python3.11 python3.11-minimal raxml
  samtools sbuild-build-depends-main-dummy sensible-utils sim4 tigr-glimmer
  tzdata ucf wise wise-data
0 upgraded, 263 newly installed, 0 to remove and 0 not upgraded.
Need to get 275 MB/276 MB of archives.
After this operation, 1364 MB of additional disk space will be used.
Get:1 file:/srv/reprepro perl-5.40/main amd64 libpq5 amd64 16.3-1+b1 [219 kB]
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1188 B]
Get:3 file:/srv/reprepro perl-5.40/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b4 [36.3 kB]
Get:4 file:/srv/reprepro perl-5.40/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB]
Get:5 file:/srv/reprepro perl-5.40/main amd64 libdevel-callchecker-perl amd64 0.009-1+b1 [16.1 kB]
Get:6 file:/srv/reprepro perl-5.40/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.4 kB]
Get:7 file:/srv/reprepro perl-5.40/main amd64 libhtml-parser-perl amd64 3.82-1+b1 [99.2 kB]
Get:8 file:/srv/reprepro perl-5.40/main amd64 libclone-perl amd64 0.46-1+b3 [13.7 kB]
Get:9 file:/srv/reprepro perl-5.40/main amd64 libnet-ssleay-perl amd64 1.94-1+b2 [339 kB]
Get:10 file:/srv/reprepro perl-5.40/main amd64 libxml-parser-perl amd64 2.47-1+b3 [199 kB]
Get:11 file:/srv/reprepro perl-5.40/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-3+b1 [313 kB]
Get:12 file:/srv/reprepro perl-5.40/main amd64 libio-pty-perl amd64 1:1.20-1+b2 [34.3 kB]
Get:13 http://localhost:3142/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB]
Get:14 http://localhost:3142/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB]
Get:15 http://localhost:3142/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB]
Get:16 http://localhost:3142/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB]
Get:17 http://localhost:3142/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB]
Get:18 http://localhost:3142/debian unstable/main amd64 netbase all 6.4 [12.8 kB]
Get:19 http://localhost:3142/debian unstable/main amd64 tzdata all 2024a-4 [255 kB]
Get:20 http://localhost:3142/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB]
Get:21 http://localhost:3142/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB]
Get:22 http://localhost:3142/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B]
Get:23 http://localhost:3142/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB]
Get:24 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB]
Get:25 http://localhost:3142/debian unstable/main amd64 openssl amd64 3.2.1-3 [1360 kB]
Get:26 http://localhost:3142/debian unstable/main amd64 ca-certificates all 20240203 [158 kB]
Get:27 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB]
Get:28 http://localhost:3142/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB]
Get:29 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB]
Get:30 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB]
Get:31 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB]
Get:32 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB]
Get:33 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.40.1-7 [95.9 kB]
Get:34 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB]
Get:35 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB]
Get:36 http://localhost:3142/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB]
Get:37 http://localhost:3142/debian unstable/main amd64 libedit2 amd64 3.1-20240517-1 [93.3 kB]
Get:38 http://localhost:3142/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-1.2 [28.2 kB]
Get:39 http://localhost:3142/debian unstable/main amd64 libfido2-1 amd64 1.14.0-1+b2 [77.7 kB]
Get:40 http://localhost:3142/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB]
Get:41 http://localhost:3142/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB]
Get:42 http://localhost:3142/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB]
Get:43 http://localhost:3142/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B]
Get:44 http://localhost:3142/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB]
Get:45 http://localhost:3142/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB]
Get:46 http://localhost:3142/debian unstable/main amd64 openssh-client amd64 1:9.7p1-5 [964 kB]
Get:47 http://localhost:3142/debian unstable/main amd64 ucf all 3.0043+nmu1 [55.2 kB]
Get:48 http://localhost:3142/debian unstable/main amd64 amap-align amd64 2.2+git20080214.600fc29+dfsg-2 [132 kB]
Get:49 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB]
Get:50 http://localhost:3142/debian unstable/main amd64 autoconf all 2.71-3 [332 kB]
Get:51 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get:52 http://localhost:3142/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get:53 http://localhost:3142/debian unstable/main amd64 autopoint all 0.21-14 [496 kB]
Get:54 http://localhost:3142/debian unstable/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB]
Get:55 http://localhost:3142/debian unstable/main amd64 bedtools-test all 2.31.1+dfsg-2 [10.9 MB]
Get:56 http://localhost:3142/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB]
Get:57 http://localhost:3142/debian unstable/main amd64 libdata-stag-perl all 0.14-3 [448 kB]
Get:58 http://localhost:3142/debian unstable/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB]
Get:59 http://localhost:3142/debian unstable/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B]
Get:60 http://localhost:3142/debian unstable/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB]
Get:61 http://localhost:3142/debian unstable/main amd64 libexception-class-perl all 1.45-1 [34.6 kB]
Get:62 http://localhost:3142/debian unstable/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB]
Get:63 http://localhost:3142/debian unstable/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB]
Get:64 http://localhost:3142/debian unstable/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB]
Get:65 http://localhost:3142/debian unstable/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB]
Get:66 http://localhost:3142/debian unstable/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB]
Get:67 http://localhost:3142/debian unstable/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB]
Get:68 http://localhost:3142/debian unstable/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB]
Get:69 http://localhost:3142/debian unstable/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB]
Get:70 http://localhost:3142/debian unstable/main amd64 libtest-most-perl all 0.38-1 [25.1 kB]
Get:71 http://localhost:3142/debian unstable/main amd64 bioperl all 1.7.8-1 [246 kB]
Get:72 http://localhost:3142/debian unstable/main amd64 clustalw amd64 2.1+lgpl-7 [282 kB]
Get:73 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB]
Get:74 http://localhost:3142/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB]
Get:75 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get:76 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:77 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get:78 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get:79 http://localhost:3142/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB]
Get:80 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get:81 http://localhost:3142/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB]
Get:82 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-2 [670 kB]
Get:83 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB]
Get:84 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:85 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:86 http://localhost:3142/debian unstable/main amd64 debhelper all 13.15.3 [901 kB]
Get:87 http://localhost:3142/debian unstable/main amd64 libaom3 amd64 3.8.2-2 [1869 kB]
Get:88 http://localhost:3142/debian unstable/main amd64 libdav1d7 amd64 1.4.2-1 [551 kB]
Get:89 http://localhost:3142/debian unstable/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB]
Get:90 http://localhost:3142/debian unstable/main amd64 libgav1-1 amd64 0.19.0-2+b1 [351 kB]
Get:91 http://localhost:3142/debian unstable/main amd64 librav1e0 amd64 0.7.1-2 [900 kB]
Get:92 http://localhost:3142/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB]
Get:93 http://localhost:3142/debian unstable/main amd64 libsvtav1enc1d1 amd64 1.7.0+dfsg-2+b1 [2169 kB]
Get:94 http://localhost:3142/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB]
Get:95 http://localhost:3142/debian unstable/main amd64 libyuv0 amd64 0.0.1888.20240509-4 [170 kB]
Get:96 http://localhost:3142/debian unstable/main amd64 libavif16 amd64 1.0.4-3 [106 kB]
Get:97 http://localhost:3142/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB]
Get:98 http://localhost:3142/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB]
Get:99 http://localhost:3142/debian unstable/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB]
Get:100 http://localhost:3142/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get:101 http://localhost:3142/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB]
Get:102 http://localhost:3142/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB]
Get:103 http://localhost:3142/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB]
Get:104 http://localhost:3142/debian unstable/main amd64 libheif-plugin-dav1d amd64 1.17.6-1+b2 [9856 B]
Get:105 http://localhost:3142/debian unstable/main amd64 libde265-0 amd64 1.0.15-1+b1 [187 kB]
Get:106 http://localhost:3142/debian unstable/main amd64 libheif-plugin-libde265 amd64 1.17.6-1+b2 [13.1 kB]
Get:107 http://localhost:3142/debian unstable/main amd64 libheif1 amd64 1.17.6-1+b2 [284 kB]
Get:108 http://localhost:3142/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB]
Get:109 http://localhost:3142/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB]
Get:110 http://localhost:3142/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB]
Get:111 http://localhost:3142/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB]
Get:112 http://localhost:3142/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB]
Get:113 http://localhost:3142/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB]
Get:114 http://localhost:3142/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB]
Get:115 http://localhost:3142/debian unstable/main amd64 libxcb1 amd64 1.17.0-2 [144 kB]
Get:116 http://localhost:3142/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB]
Get:117 http://localhost:3142/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB]
Get:118 http://localhost:3142/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b1 [56.1 kB]
Get:119 http://localhost:3142/debian unstable/main amd64 libgd3 amd64 2.3.3-9+b3 [125 kB]
Get:120 http://localhost:3142/debian unstable/main amd64 libhpdf-2.3.0 amd64 2.3.0+dfsg-1+b2 [346 kB]
Get:121 http://localhost:3142/debian unstable/main amd64 mysql-common all 5.8+1.1.0 [6636 B]
Get:122 http://localhost:3142/debian unstable/main amd64 mariadb-common all 1:10.11.8-1 [26.4 kB]
Get:123 http://localhost:3142/debian unstable/main amd64 libmariadb3 amd64 1:10.11.8-1 [176 kB]
Get:124 http://localhost:3142/debian unstable/main amd64 emboss-lib amd64 6.6.0+dfsg-15 [2874 kB]
Get:125 http://localhost:3142/debian unstable/main amd64 emboss-data all 6.6.0+dfsg-15 [61.1 MB]
Get:126 http://localhost:3142/debian unstable/main amd64 emboss amd64 6.6.0+dfsg-15 [1072 kB]
Get:127 http://localhost:3142/debian unstable/main amd64 libglib2.0-0t64 amd64 2.80.2-2 [1485 kB]
Get:128 http://localhost:3142/debian unstable/main amd64 exonerate amd64 2.4.0-5+b1 [1963 kB]
Get:129 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.34-1 [28.9 kB]
Get:130 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.34-1 [74.0 kB]
Get:131 http://localhost:3142/debian unstable/main amd64 fasttree amd64 2.1.11-2 [181 kB]
Get:132 http://localhost:3142/debian unstable/main amd64 libdivsufsort3 amd64 2.0.1-6 [45.6 kB]
Get:133 http://localhost:3142/debian unstable/main amd64 hmmer amd64 3.4+dfsg-2 [1062 kB]
Get:134 http://localhost:3142/debian unstable/main amd64 hyphy-common all 2.5.62+dfsg-1 [607 kB]
Get:135 http://localhost:3142/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB]
Get:136 http://localhost:3142/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB]
Get:137 http://localhost:3142/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB]
Get:138 http://localhost:3142/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-5 [215 kB]
Get:139 http://localhost:3142/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.8.0-1 [434 kB]
Get:140 http://localhost:3142/debian unstable/main amd64 hyphy-pt amd64 2.5.62+dfsg-1 [1485 kB]
Get:141 http://localhost:3142/debian unstable/main amd64 libnl-3-200 amd64 3.7.0-0.3 [59.0 kB]
Get:142 http://localhost:3142/debian unstable/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [181 kB]
Get:143 http://localhost:3142/debian unstable/main amd64 libibverbs1 amd64 50.0-2+b1 [61.7 kB]
Get:144 http://localhost:3142/debian unstable/main amd64 ibverbs-providers amd64 50.0-2+b1 [342 kB]
Get:145 http://localhost:3142/debian unstable/main amd64 infernal amd64 1.1.5-2 [5914 kB]
Get:146 http://localhost:3142/debian unstable/main amd64 kalign amd64 1:3.4.0-1 [138 kB]
Get:147 http://localhost:3142/debian unstable/main amd64 lagan amd64 2.0-10 [184 kB]
Get:148 http://localhost:3142/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB]
Get:149 http://localhost:3142/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-12 [23.7 MB]
Get:150 http://localhost:3142/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b1 [13.0 MB]
Get:151 http://localhost:3142/debian unstable/main amd64 libdrm-common all 2.4.120-2 [7688 B]
Get:152 http://localhost:3142/debian unstable/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB]
Get:153 http://localhost:3142/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB]
Get:154 http://localhost:3142/debian unstable/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB]
Get:155 http://localhost:3142/debian unstable/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB]
Get:156 http://localhost:3142/debian unstable/main amd64 libhsa-runtime64-1 amd64 5.7.1-2 [504 kB]
Get:157 http://localhost:3142/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-3 [8760 kB]
Get:158 http://localhost:3142/debian unstable/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB]
Get:159 http://localhost:3142/debian unstable/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB]
Get:160 http://localhost:3142/debian unstable/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB]
Get:161 http://localhost:3142/debian unstable/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB]
Get:162 http://localhost:3142/debian unstable/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB]
Get:163 http://localhost:3142/debian unstable/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB]
Get:164 http://localhost:3142/debian unstable/main amd64 libmoo-perl all 2.005005-1 [58.0 kB]
Get:165 http://localhost:3142/debian unstable/main amd64 libexporter-tiny-perl all 1.006002-1 [38.7 kB]
Get:166 http://localhost:3142/debian unstable/main amd64 libtype-tiny-perl all 2.004000-1 [357 kB]
Get:167 http://localhost:3142/debian unstable/main amd64 libarray-compare-perl all 3.0.8-1 [14.9 kB]
Get:168 http://localhost:3142/debian unstable/main amd64 liburi-perl all 5.28-1 [98.6 kB]
Get:169 http://localhost:3142/debian unstable/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB]
Get:170 http://localhost:3142/debian unstable/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB]
Get:171 http://localhost:3142/debian unstable/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB]
Get:172 http://localhost:3142/debian unstable/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB]
Get:173 http://localhost:3142/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB]
Get:174 http://localhost:3142/debian unstable/main amd64 libhtml-tree-perl all 5.07-3 [211 kB]
Get:175 http://localhost:3142/debian unstable/main amd64 libio-html-perl all 1.004-3 [16.2 kB]
Get:176 http://localhost:3142/debian unstable/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB]
Get:177 http://localhost:3142/debian unstable/main amd64 libhttp-message-perl all 6.46-1 [79.7 kB]
Get:178 http://localhost:3142/debian unstable/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB]
Get:179 http://localhost:3142/debian unstable/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB]
Get:180 http://localhost:3142/debian unstable/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B]
Get:181 http://localhost:3142/debian unstable/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB]
Get:182 http://localhost:3142/debian unstable/main amd64 libnet-http-perl all 6.23-1 [23.9 kB]
Get:183 http://localhost:3142/debian unstable/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB]
Get:184 http://localhost:3142/debian unstable/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB]
Get:185 http://localhost:3142/debian unstable/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB]
Get:186 http://localhost:3142/debian unstable/main amd64 libwww-perl all 6.77-1 [183 kB]
Get:187 http://localhost:3142/debian unstable/main amd64 libxml-twig-perl all 1:3.52-3 [177 kB]
Get:188 http://localhost:3142/debian unstable/main amd64 libxml-writer-perl all 0.900-2 [26.8 kB]
Get:189 http://localhost:3142/debian unstable/main amd64 libbio-variation-perl all 1.7.5-3 [72.6 kB]
Get:190 http://localhost:3142/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB]
Get:191 http://localhost:3142/debian unstable/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB]
Get:192 http://localhost:3142/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB]
Get:193 http://localhost:3142/debian unstable/main amd64 libbio-cluster-perl all 1.7.3-6 [53.3 kB]
Get:194 http://localhost:3142/debian unstable/main amd64 libbio-asn1-entrezgene-perl all 1.730-3 [46.3 kB]
Get:195 http://localhost:3142/debian unstable/main amd64 libtext-csv-perl all 2.04-1 [112 kB]
Get:196 http://localhost:3142/debian unstable/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB]
Get:197 http://localhost:3142/debian unstable/main amd64 libbio-eutilities-perl all 1.77-2 [124 kB]
Get:198 http://localhost:3142/debian unstable/main amd64 libfile-slurp-tiny-perl all 0.004-2 [7592 B]
Get:199 http://localhost:3142/debian unstable/main amd64 libtree-dagnode-perl all 1.32-1 [61.7 kB]
Get:200 http://localhost:3142/debian unstable/main amd64 libxml-perl all 0.08-4 [93.0 kB]
Get:201 http://localhost:3142/debian unstable/main amd64 libxml-regexp-perl all 0.04-1.1 [7500 B]
Get:202 http://localhost:3142/debian unstable/main amd64 libxml-dom-perl all 1.46-2 [152 kB]
Get:203 http://localhost:3142/debian unstable/main amd64 libxml-xpathengine-perl all 0.14-2 [33.5 kB]
Get:204 http://localhost:3142/debian unstable/main amd64 libxml-dom-xpath-perl all 0.14-4 [9352 B]
Get:205 http://localhost:3142/debian unstable/main amd64 libbio-featureio-perl all 1.6.905-2 [53.2 kB]
Get:206 http://localhost:3142/debian unstable/main amd64 libipc-run-perl all 20231003.0-2 [101 kB]
Get:207 http://localhost:3142/debian unstable/main amd64 libfile-sort-perl all 1.01-3 [21.3 kB]
Get:208 http://localhost:3142/debian unstable/main amd64 libbio-perl-run-perl all 1.7.3-11 [528 kB]
Get:209 http://localhost:3142/debian unstable/main amd64 libbio-tools-run-alignment-clustalw-perl all 1.7.4-4 [24.5 kB]
Get:210 http://localhost:3142/debian unstable/main amd64 libbio-tools-run-remoteblast-perl all 1.7.3-3 [17.5 kB]
Get:211 http://localhost:3142/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB]
Get:212 http://localhost:3142/debian unstable/main amd64 libmodule-pluggable-perl all 5.2-5 [23.0 kB]
Get:213 http://localhost:3142/debian unstable/main amd64 libconfig-any-perl all 0.33-1 [31.0 kB]
Get:214 http://localhost:3142/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10 [131 kB]
Get:215 http://localhost:3142/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [53.9 kB]
Get:216 http://localhost:3142/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB]
Get:217 http://localhost:3142/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB]
Get:218 http://localhost:3142/debian unstable/main amd64 librdmacm1t64 amd64 50.0-2+b1 [70.2 kB]
Get:219 http://localhost:3142/debian unstable/main amd64 libfabric1 amd64 1.17.0-3+b1 [628 kB]
Get:220 http://localhost:3142/debian unstable/main amd64 libfile-slurp-perl all 9999.32-2 [26.7 kB]
Get:221 http://localhost:3142/debian unstable/main amd64 libgfortran5 amd64 14.1.0-1 [836 kB]
Get:222 http://localhost:3142/debian unstable/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB]
Get:223 http://localhost:3142/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB]
Get:224 http://localhost:3142/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB]
Get:225 http://localhost:3142/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB]
Get:226 http://localhost:3142/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1 [13.8 kB]
Get:227 http://localhost:3142/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b1 [40.3 kB]
Get:228 http://localhost:3142/debian unstable/main amd64 libhwloc15 amd64 2.10.0-1+b1 [161 kB]
Get:229 http://localhost:3142/debian unstable/main amd64 libhwloc-plugins amd64 2.10.0-1+b1 [18.0 kB]
Get:230 http://localhost:3142/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB]
Get:231 http://localhost:3142/debian unstable/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB]
Get:232 http://localhost:3142/debian unstable/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB]
Get:233 http://localhost:3142/debian unstable/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB]
Get:234 http://localhost:3142/debian unstable/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB]
Get:235 http://localhost:3142/debian unstable/main amd64 libmodule-build-perl all 0.423400-2 [252 kB]
Get:236 http://localhost:3142/debian unstable/main amd64 libmunge2 amd64 0.5.15-4 [19.8 kB]
Get:237 http://localhost:3142/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB]
Get:238 http://localhost:3142/debian unstable/main amd64 libpmix2t64 amd64 5.0.2-3 [652 kB]
Get:239 http://localhost:3142/debian unstable/main amd64 libucx0 amd64 1.16.0+ds-5 [1109 kB]
Get:240 http://localhost:3142/debian unstable/main amd64 libopenmpi3t64 amd64 4.1.6-13.3 [2426 kB]
Get:241 http://localhost:3142/debian unstable/main amd64 mafft amd64 7.505-1 [1078 kB]
Get:242 http://localhost:3142/debian unstable/main amd64 muscle amd64 1:5.1.0-1 [297 kB]
Get:243 http://localhost:3142/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-2 [3544 kB]
Get:244 http://localhost:3142/debian unstable/main amd64 ncbi-blast+ amd64 2.12.0+ds-4+b1 [12.5 MB]
Get:245 http://localhost:3142/debian unstable/main amd64 ncbi-blast+-legacy all 2.12.0+ds-4 [8956 B]
Get:246 http://localhost:3142/debian unstable/main amd64 ncoils amd64 2002-9 [22.2 kB]
Get:247 http://localhost:3142/debian unstable/main amd64 openmpi-common all 4.1.6-13.3 [169 kB]
Get:248 http://localhost:3142/debian unstable/main amd64 openmpi-bin amd64 4.1.6-13.3 [226 kB]
Get:249 http://localhost:3142/debian unstable/main amd64 pal2nal all 14.1-3 [17.8 kB]
Get:250 http://localhost:3142/debian unstable/main amd64 pftools amd64 3.2.12-1 [24.8 MB]
Get:251 http://localhost:3142/debian unstable/main amd64 phyml amd64 3:3.3.20220408-3+b1 [1105 kB]
Get:252 http://localhost:3142/debian unstable/main amd64 primer3 amd64 2.6.1-4 [202 kB]
Get:253 http://localhost:3142/debian unstable/main amd64 probcons amd64 1.12-14 [119 kB]
Get:254 http://localhost:3142/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB]
Get:255 http://localhost:3142/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [5465 kB]
Get:256 http://localhost:3142/debian unstable/main amd64 python3-pysam amd64 0.22.1+ds-2 [4652 kB]
Get:257 http://localhost:3142/debian unstable/main amd64 python3-pybedtools amd64 0.10.0-1 [12.3 MB]
Get:258 http://localhost:3142/debian unstable/main amd64 raxml amd64 8.2.13+dfsg-1 [1480 kB]
Get:259 http://localhost:3142/debian unstable/main amd64 samtools amd64 1.20-3 [653 kB]
Get:260 http://localhost:3142/debian unstable/main amd64 sim4 amd64 0.0.20121010-8 [359 kB]
Get:261 http://localhost:3142/debian unstable/main amd64 tigr-glimmer amd64 3.02b-6+b1 [283 kB]
Get:262 http://localhost:3142/debian unstable/main amd64 wise-data all 2.4.1-24 [76.0 kB]
Get:263 http://localhost:3142/debian unstable/main amd64 wise amd64 2.4.1-24 [1041 kB]
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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'
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Setting up libhtscodecs2:amd64 (1.6.0-1+b1) ...
Setting up media-types (10.1.0) ...
Setting up libmodule-pluggable-perl (5.2-5) ...
Setting up libpipeline1:amd64 (1.5.7-2) ...
Setting up liblmdb0:amd64 (0.9.31-1+b1) ...
Setting up ncbi-data (6.1.20170106+dfsg2-2) ...
Setting up libsharpyuv0:amd64 (1.4.0-0.1) ...
Setting up libaom3:amd64 (3.8.2-2) ...
Setting up libpciaccess0:amd64 (0.17-3+b1) ...
Setting up mysql-common (5.8+1.1.0) ...
update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode
Setting up libxau6:amd64 (1:1.0.9-1+b1) ...
Setting up libkeyutils1:amd64 (1.6.3-3) ...
Setting up libfile-slurp-perl (9999.32-2) ...
Setting up libicu72:amd64 (72.1-4+b1) ...
Setting up liblerc4:amd64 (4.0.0+ds-4+b1) ...
Setting up bsdextrautils (2.40.1-7) ...
Setting up probcons (1.12-14) ...
Setting up libmbedcrypto7t64:amd64 (2.28.8-1) ...
Setting up libdynaloader-functions-perl (0.003-3) ...
Setting up libtest-deep-perl (1.204-1) ...
Setting up libclass-method-modifiers-perl (2.15-1) ...
Setting up libxml-regexp-perl (0.04-1.1) ...
Setting up libio-pty-perl (1:1.20-1+b2) ...
Setting up libmagic-mgc (1:5.45-3) ...
Setting up libcbor0.10:amd64 (0.10.2-1.2) ...
Setting up mafft (7.505-1) ...
Setting up libclone-perl:amd64 (0.46-1+b3) ...
Setting up libalgorithm-diff-perl (1.201-1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libhtml-tagset-perl (3.24-1) ...
Setting up libdebhelper-perl (13.15.3) ...
Setting up libbrotli1:amd64 (1.1.0-2+b3) ...
Setting up libfile-slurp-tiny-perl (0.004-2) ...
Setting up liblwp-mediatypes-perl (6.04-2) ...
Setting up libmagic1t64:amd64 (1:5.45-3) ...
Setting up libtry-tiny-perl (0.31-2) ...
Setting up libpsl5t64:amd64 (0.21.2-1.1) ...
Setting up libnghttp2-14:amd64 (1.61.0-1+b1) ...
Setting up libdeflate0:amd64 (1.20-1) ...
Setting up perl-openssl-defaults:amd64 (7+b2) ...
Setting up libxml-namespacesupport-perl (1.12-2) ...
Setting up gettext-base (0.21-14+b1) ...
Setting up m4 (1.4.19-4) ...
Setting up libencode-locale-perl (1.05-3) ...
Setting up ncoils (2002-9) ...
Setting up libsvtav1enc1d1:amd64 (1.7.0+dfsg-2+b1) ...
Setting up libcom-err2:amd64 (1.47.1-1) ...
Setting up hyphy-common (2.5.62+dfsg-1) ...
Setting up file (1:5.45-3) ...
Setting up muscle (1:5.1.0-1) ...
Setting up emboss-data (6.6.0+dfsg-15) ...
Setting up libjbig0:amd64 (2.1-6.1+b1) ...
Setting up librav1e0:amd64 (0.7.1-2) ...
Setting up libfakeroot:amd64 (1.34-1) ...
Setting up libelf1t64:amd64 (0.191-1+b1) ...
Setting up libmodule-build-perl (0.423400-2) ...
Setting up libkrb5support0:amd64 (1.20.1-6+b1) ...
Setting up tzdata (2024a-4) ...

Current default time zone: 'Etc/UTC'
Local time is now:      Mon Jun  3 00:00:19 UTC 2024.
Universal Time is now:  Mon Jun  3 00:00:19 UTC 2024.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

Setting up fakeroot (1.34-1) ...
update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode
Setting up mariadb-common (1:10.11.8-1) ...
update-alternatives: using /etc/mysql/mariadb.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode
Setting up infernal (1.1.5-2) ...
Setting up libxml-sax-base-perl (1.09-3) ...
Setting up libio-string-perl (1.08-4) ...
Setting up primer3 (2.6.1-4) ...
Setting up kalign (1:3.4.0-1) ...
Setting up autotools-dev (20220109.1) ...
Setting up libz3-4:amd64 (4.8.12-3.1+b2) ...
Setting up libglib2.0-0t64:amd64 (2.80.2-2) ...
No schema files found: doing nothing.
Setting up libblas3:amd64 (3.12.0-3) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
Setting up libclass-data-inheritable-perl (0.08-3) ...
Setting up libmunge2:amd64 (0.5.15-4) ...
Setting up lagan (2.0-10) ...
Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ...
Setting up libx11-data (2:1.8.7-1) ...
Setting up libtext-diff-perl (1.45-2) ...
Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ...
Setting up libxml-xpathengine-perl (0.14-2) ...
Setting up sim4 (0.0.20121010-8) ...
Setting up libxml-writer-perl (0.900-2) ...
Setting up libncurses6:amd64 (6.5-2) ...
Setting up fonts-dejavu-mono (2.37-8) ...
Setting up libpng16-16t64:amd64 (1.6.43-5) ...
Setting up libhwloc15:amd64 (2.10.0-1+b1) ...
Setting up libio-html-perl (1.004-3) ...
Setting up autopoint (0.21-14) ...
Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b2) ...
Setting up libmariadb3:amd64 (1:10.11.8-1) ...
Setting up fonts-dejavu-core (2.37-8) ...
Setting up libipc-run-perl (20231003.0-2) ...
Setting up wise-data (2.4.1-24) ...
Setting up libk5crypto3:amd64 (1.20.1-6+b1) ...
Setting up amap-align (2.2+git20080214.600fc29+dfsg-2) ...
Setting up libgfortran5:amd64 (14.1.0-1) ...
Setting up autoconf (2.71-3) ...
Setting up libwebp7:amd64 (1.4.0-0.1) ...
Setting up libcapture-tiny-perl (0.48-2) ...
Setting up libtimedate-perl (2.3300-2) ...
Setting up libnuma1:amd64 (2.0.18-1) ...
Setting up libtree-dagnode-perl (1.32-1) ...
Setting up dwz (0.15-1+b1) ...
Setting up libdata-stag-perl (0.14-3) ...
Setting up libdav1d7:amd64 (1.4.2-1) ...
Setting up sensible-utils (0.0.22) ...
Setting up ocl-icd-libopencl1:amd64 (2.3.2-1+b1) ...
Setting up pftools (3.2.12-1) ...
Setting up libtiff6:amd64 (4.5.1+git230720-4) ...
Setting up libuchardet0:amd64 (0.0.8-1+b1) ...
Setting up pal2nal (14.1-3) ...
Setting up libnl-3-200:amd64 (3.7.0-0.3) ...
Setting up librole-tiny-perl (2.002004-1) ...
Setting up libpsm2-2 (11.2.185-2) ...
Setting up openmpi-common (4.1.6-13.3) ...
Setting up libconfig-any-perl (0.33-1) ...
Setting up clustalw (2.1+lgpl-7) ...

Configuration file '/etc/protocols'
 ==> File on system created by you or by a script.
 ==> File also in package provided by package maintainer.
 ==> Using current old file as you requested.

Configuration file '/etc/services'
 ==> File on system created by you or by a script.
 ==> File also in package provided by package maintainer.
 ==> Using current old file as you requested.
Setting up libsub-uplevel-perl (0.2800-3) ...
Setting up fasttree (2.1.11-2) ...
Setting up netbase (6.4) ...
Setting up libabsl20230802:amd64 (20230802.1-4) ...
Setting up libsub-quote-perl (2.006008-1) ...
Setting up libdevel-stacktrace-perl (2.0500-1) ...
Setting up libclass-xsaccessor-perl (1.19-4+b4) ...
Setting up libkrb5-3:amd64 (1.20.1-6+b1) ...
Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10) ...
Setting up libbio-perl-perl (1.7.8-1) ...
Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ...
update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode
Setting up libssh2-1t64:amd64 (1.11.0-5) ...
Setting up libexporter-tiny-perl (1.006002-1) ...
Setting up libfido2-1:amd64 (1.14.0-1+b2) ...
Setting up libde265-0:amd64 (1.0.15-1+b1) ...
Setting up libdivsufsort3:amd64 (2.0.1-6) ...
Setting up openssl (3.2.1-3) ...
Setting up libbsd0:amd64 (0.12.2-1) ...
Setting up tigr-glimmer (3.02b-6+b1) ...
Setting up libdrm-common (2.4.120-2) ...
Setting up libyuv0:amd64 (0.0.1888.20240509-4) ...
Setting up libxml2:amd64 (2.12.7+dfsg-2) ...
Setting up exonerate (2.4.0-5+b1) ...
Setting up bedtools (2.31.1+dfsg-2) ...
Setting up liburi-perl (5.28-1) ...
Setting up libfile-sort-perl (1.01-3) ...
Setting up raxml (8.2.13+dfsg-1) ...
Setting up libtext-csv-perl (2.04-1) ...
Setting up libnet-ssleay-perl:amd64 (1.94-1+b2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.0-1) ...
Setting up libbio-perl-run-perl (1.7.3-11) ...
Setting up libhttp-date-perl (6.06-1) ...
Setting up libhpdf-2.3.0:amd64 (2.3.0+dfsg-1+b2) ...
Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ...
Setting up liblapack3:amd64 (3.12.0-3) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
Setting up libxcb1:amd64 (1.17.0-2) ...
Setting up gettext (0.21-14+b1) ...
Setting up libmbedx509-1t64:amd64 (2.28.8-1) ...
Setting up libfile-listing-perl (6.16-1) ...
Setting up libtool (2.4.7-7) ...
Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ...
Setting up fontconfig-config (2.15.0-1.1) ...
Setting up wise (2.4.1-24) ...
Setting up libtest-warn-perl (0.37-2) ...
Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ...
Setting up libedit2:amd64 (3.1-20240517-1) ...
Setting up libtype-tiny-perl (2.004000-1) ...
Setting up libtest-differences-perl (0.71-1) ...
Setting up libnet-http-perl (6.23-1) ...
Setting up libexception-class-perl (1.45-1) ...
Setting up libdevel-callchecker-perl:amd64 (0.009-1+b1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libnl-route-3-200:amd64 (3.7.0-0.3) ...
Setting up dh-autoreconf (20) ...
Setting up libbio-tools-run-alignment-clustalw-perl (1.7.4-4) ...
Setting up ca-certificates (20240203) ...
Updating certificates in /etc/ssl/certs...
146 added, 0 removed; done.
Setting up libllvm17t64:amd64 (1:17.0.6-12) ...
Setting up libtest-exception-perl (0.43-3) ...
Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ...
Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ...
Setting up libgav1-1:amd64 (0.19.0-2+b1) ...
Setting up ucf (3.0043+nmu1) ...
Setting up dh-strip-nondeterminism (1.14.0-1) ...
Setting up libwww-robotrules-perl (6.02-1) ...
Setting up libdrm2:amd64 (2.4.120-2) ...
Setting up libmbedtls14t64:amd64 (2.28.8-1) ...
Setting up groff-base (1.23.0-4) ...
Setting up libhtml-parser-perl:amd64 (3.82-1+b1) ...
Setting up hmmer (3.4+dfsg-2) ...
Setting up libx11-6:amd64 (2:1.8.7-1+b1) ...
Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b1) ...
Setting up libfontconfig1:amd64 (2.15.0-1.1) ...
Setting up libio-socket-ssl-perl (2.085-1) ...
Setting up libpython3-stdlib:amd64 (3.11.8-1) ...
Setting up libhttp-message-perl (6.46-1) ...
Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ...
Setting up python3.11 (3.11.9-1) ...
Setting up libhttp-negotiate-perl (6.01-2) ...
Setting up libibverbs1:amd64 (50.0-2+b1) ...
Setting up libavif16:amd64 (1.0.4-3) ...
Setting up libxpm4:amd64 (1:3.5.17-1+b1) ...
Setting up ibverbs-providers:amd64 (50.0-2+b1) ...
Setting up libhttp-cookies-perl (6.11-1) ...
Setting up libtest-most-perl (0.38-1) ...
Setting up openssh-client (1:9.7p1-5) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhtml-tree-perl (5.07-3) ...
Setting up libparams-classify-perl:amd64 (0.015-2+b4) ...
Setting up libpq5:amd64 (16.3-1+b1) ...
Setting up libcurl3t64-gnutls:amd64 (8.8.0-1) ...
Setting up libxext6:amd64 (2:1.3.4-1+b1) ...
Setting up python3 (3.11.8-1) ...
Setting up hyphy-pt (2.5.62+dfsg-1) ...
Setting up man-db (2.12.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxml-sax-perl (1.02+dfsg-3) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...

Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up libxnvctrl0:amd64 (535.171.04-1) ...
Setting up ncbi-blast+ (2.12.0+ds-4+b1) ...
Setting up libmodule-runtime-perl (0.016-2) ...
Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-3+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 libhts3t64:amd64 (1.20+ds-1) ...
Setting up librdmacm1t64:amd64 (50.0-2+b1) ...
Setting up bedtools-test (2.31.1+dfsg-2) ...
Setting up libhsakmt1:amd64 (5.7.0-1) ...
Setting up python3-pkg-resources (68.1.2-2) ...
Setting up bioperl (1.7.8-1) ...
Setting up ncbi-blast+-legacy (2.12.0+ds-4) ...
Setting up libfabric1:amd64 (1.17.0-3+b1) ...
Setting up python3-pysam (0.22.1+ds-2) ...
Setting up libimport-into-perl (1.002005-2) ...
Setting up libmoo-perl (2.005005-1) ...
Setting up debhelper (13.15.3) ...
Setting up libhwloc-plugins:amd64 (2.10.0-1+b1) ...
Setting up samtools (1.20-3) ...
Setting up libarray-compare-perl (3.0.8-1) ...
Setting up libxml-simple-perl (2.25-2) ...
Setting up libpmix2t64:amd64 (5.0.2-3) ...
Setting up python3-numpy (1:1.26.4+ds-10) ...
Setting up libhsa-runtime64-1 (5.7.1-2) ...
Setting up python3-pybedtools (0.10.0-1) ...
Setting up libamdhip64-5 (5.7.1-3) ...
Setting up libucx0:amd64 (1.16.0+ds-5) ...
Setting up libopenmpi3t64:amd64 (4.1.6-13.3) ...
Setting up openmpi-bin (4.1.6-13.3) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up phyml (3:3.3.20220408-3+b1) ...
Setting up libheif-plugin-dav1d:amd64 (1.17.6-1+b2) ...
Setting up liblwp-protocol-https-perl (6.14-1) ...
Setting up libheif-plugin-libde265:amd64 (1.17.6-1+b2) ...
Setting up libwww-perl (6.77-1) ...
Setting up libheif1:amd64 (1.17.6-1+b2) ...
Setting up libgd3:amd64 (2.3.3-9+b3) ...
Setting up libbio-tools-run-remoteblast-perl (1.7.3-3) ...
Setting up emboss-lib (6.6.0+dfsg-15) ...
Setting up libxml-parser-perl (2.47-1+b3) ...
Setting up emboss (6.6.0+dfsg-15) ...
Setting up libxml-twig-perl (1:3.52-3) ...
Setting up libbio-variation-perl (1.7.5-3) ...
Setting up libxml-perl (0.08-4) ...
Setting up libbio-cluster-perl (1.7.3-6) ...
Setting up libxml-dom-perl (1.46-2) ...
Setting up libbio-asn1-entrezgene-perl (1.730-3) ...
Setting up libxml-dom-xpath-perl (0.14-4) ...
Setting up libbio-eutilities-perl (1.77-2) ...
Setting up libbio-featureio-perl (1.6.905-2) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.38-12) ...
Processing triggers for ca-certificates (20240203) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (amd64 included in all)

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) amd64 (x86_64)
Toolchain package versions: binutils_2.42-4 dpkg-dev_1.22.6 g++-13_13.2.0-25 gcc-13_13.2.0-25 libc6-dev_2.38-12 libstdc++-13-dev_13.2.0-25 libstdc++6_14.1.0-1 linux-libc-dev_6.8.12-1
Package versions: adduser_3.137 amap-align_2.2+git20080214.600fc29+dfsg-2 apt_2.9.4 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13.2 base-passwd_3.6.3 bash_5.2.21-2+b1 bedtools_2.31.1+dfsg-2 bedtools-test_2.31.1+dfsg-2 binutils_2.42-4 binutils-common_2.42-4 binutils-x86-64-linux-gnu_2.42-4 bioperl_1.7.8-1 bsdextrautils_2.40.1-7 bsdutils_1:2.40.1-7 build-essential_12.10 bzip2_1.0.8-5.1 ca-certificates_20240203 clustalw_2.1+lgpl-7 coreutils_9.4-3.1 cpp_4:13.2.0-7 cpp-13_13.2.0-25 cpp-13-x86-64-linux-gnu_13.2.0-25 cpp-x86-64-linux-gnu_4:13.2.0-7 dash_0.5.12-8 debconf_1.5.86 debhelper_13.15.3 debian-archive-keyring_2023.4 debianutils_5.17 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-7 dpkg_1.22.6 dpkg-dev_1.22.6 dwz_0.15-1+b1 eatmydata_131-2 emboss_6.6.0+dfsg-15 emboss-data_6.6.0+dfsg-15 emboss-lib_6.6.0+dfsg-15 exonerate_2.4.0-5+b1 fakeroot_1.34-1 fasttree_2.1.11-2 file_1:5.45-3 findutils_4.9.0-6 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wise_2.4.1-24 wise-data_2.4.1-24 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg+really1.3.1-1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

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Hash: SHA512

Format: 3.0 (quilt)
Source: bioperl-run
Binary: bioperl-run, libbio-perl-run-perl
Architecture: all
Version: 1.7.3-11
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>, Andreas Tille <tille@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: https://metacpan.org/release/BioPerl-Run
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/bioperl-run
Vcs-Git: https://salsa.debian.org/med-team/bioperl-run.git
Testsuite: autopkgtest-pkg-perl
Build-Depends: debhelper-compat (= 13), libmodule-build-perl
Build-Depends-Indep: perl, bioperl (>= 1.7.4), libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, libfile-sort-perl, libtest-most-perl, libarray-compare-perl, libtree-dagnode-perl, libbio-cluster-perl, libbio-featureio-perl, libconfig-any-perl, libbio-tools-run-alignment-clustalw-perl [any-amd64], libbio-eutilities-perl, libbio-tools-run-remoteblast-perl, amap-align, bedtools [any-amd64], bedtools-test, ncbi-blast+-legacy, clustalw [any-amd64], emboss [any-amd64 arm64 mips64el ppc64el riscv64], exonerate, hmmer [any-amd64 any-i386 powerpc ppc64], hyphy-pt | hyphy-mpi [any-amd64], infernal [any-amd64 any-i386], kalign, mafft, muscle, ncoils, phyml, primer3, probcons, python3-pybedtools [any-amd64], raxml, samtools [any-amd64], sim4, tigr-glimmer [any-amd64 arm64 mips64el ppc64el riscv64], wise, fasttree, lagan, pal2nal, pftools [any-amd64], libwww-perl
Package-List:
 bioperl-run deb science optional arch=all
 libbio-perl-run-perl deb perl optional arch=all
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Dgit: 0604168ee401c98a652249254a15606a29342506 debian archive/debian/1.7.3-11 https://git.dgit.debian.org/bioperl-run

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gpgv: Signature made Sat Apr 27 20:03:48 2024 UTC
gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv:                issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./bioperl-run_1.7.3-11.dsc: no acceptable signature found
dpkg-source: info: extracting bioperl-run in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking bioperl-run_1.7.3.orig.tar.gz
dpkg-source: info: unpacking bioperl-run_1.7.3-11.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying Extract_version_from_BEDTools_properly.patch
dpkg-source: info: applying skip_tests_for_RemoteBlast_rpsblast.patch
dpkg-source: info: applying skip_tests_for_RemoteBlast.patch
dpkg-source: info: applying kalign-input-via-piping.patch
dpkg-source: info: applying kalign-version-regex.patch
dpkg-source: info: applying skip_tests_for_wise.patch
dpkg-source: info: applying skip_tests_for_phylip.patch
dpkg-source: info: applying skip_tests_for_phyml.patch
dpkg-source: info: applying skip_tests_for_infernal.patch
dpkg-source: info: applying skip_tests_for_ncbi-blast+.patch
dpkg-source: info: applying hyphy.patch
dpkg-source: info: applying remove_tests_for_ensembl.patch
dpkg-source: info: applying skip_tests_for_soap.patch
dpkg-source: info: applying get-overlap.patch
dpkg-source: info: applying alternate-data.patch
dpkg-source: info: applying skip-test-for-kalign.patch
dpkg-source: info: applying fix-whatis-entries.patch
dpkg-source: info: applying unscramble-erpin.patch
dpkg-source: info: applying fix-pod-conversion.patch
dpkg-source: info: applying adjust-muscle-test.patch

Check disk space
----------------

Sufficient free space for build

+------------------------------------------------------------------------------+
| Starting Timed Build Commands                                                |
+------------------------------------------------------------------------------+


/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bioperl-run_1.7.3-11 perl-5.40-throwaway amd64
---------------------------------------------------------------------------------------------------------------------


I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bioperl-run_1.7.3-11 perl-5.40-throwaway amd64'.

Finished processing commands.
--------------------------------------------------------------------------------

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=en_GB.UTF-8
LANGUAGE=en_GB:en
LC_ALL=C.UTF-8
LD_LIBRARY_PATH=/usr/lib/libeatmydata
LD_PRELOAD=libeatmydata.so
LOGNAME=debomatic
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/<<PKGBUILDDIR>>
SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic
SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic
SCHROOT_COMMAND=env
SCHROOT_GID=110
SCHROOT_GROUP=sbuild
SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-50d3ded9-1036-4fe1-ba23-75bd170b246c
SCHROOT_UID=1002
SCHROOT_USER=debomatic
SHELL=/bin/sh
USER=debomatic

dpkg-buildpackage
-----------------

Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -Zxz
dpkg-buildpackage: info: source package bioperl-run
dpkg-buildpackage: info: source version 1.7.3-11
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
 dpkg-source -Zxz --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean
   dh_clean
 dpkg-source -Zxz -b .
dpkg-source: info: using source format '3.0 (quilt)'
dpkg-source: info: building bioperl-run using existing ./bioperl-run_1.7.3.orig.tar.gz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: building bioperl-run in bioperl-run_1.7.3-11.debian.tar.xz
dpkg-source: info: building bioperl-run in bioperl-run_1.7.3-11.dsc
 debian/rules binary
dh binary
   dh_update_autotools_config
   dh_autoreconf
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- --install_scripts 
	/usr/bin/perl Build.PL --installdirs vendor --config "optimize=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 '/<<PKGBUILDDIR>>'
   dh_auto_build
	/usr/bin/perl Build
Building BioPerl-Run
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir t.skip
for t in Blat Eponine Glimmer2 RepeatMasker Phyml Hyphy MCS ; do mv t/${t}.t t.skip ; done
PATH=$PATH:/usr/lib/emboss:/usr/lib/phylip/bin/:/usr/lib/tigr-glimmer:debian/test_hack_bin \
PHYLIPDIR=/usr/lib/phylip/bin HOME_4_TCOFFEE=/tmp COILSDIR=/usr/share/ncoils/ \
    dh_auto_test --no-parallel
	/usr/bin/perl Build test --verbose 1

AMAP version AMAP.2.2 - align multiple protein sequences and print to standard output
PROBCONS Written by Chuong Do
AMAP algorithm implemented by Ariel Schwartz

Using parameter set:
    initDistrib[] = { 0.400000006 0.3000000119 0.3000000119 }
        gapOpen[] = { 0.01993141696 0.01993141696 }
      gapExtend[] = { 0.7943345308 0.7943345308 }

Loading sequence file: t/data/cysprot.fa
Computing posterior matrices
Building DAG
Starting the sequence annealing process
Creating candidate edge list
Adding edges to the DAG

AMAP version AMAP.2.2 - align multiple protein sequences and print to standard output
PROBCONS Written by Chuong Do
AMAP algorithm implemented by Ariel Schwartz

Using parameter set:
    initDistrib[] = { 0.400000006 0.3000000119 0.3000000119 }
        gapOpen[] = { 0.01993141696 0.01993141696 }
      gapExtend[] = { 0.7943345308 0.7943345308 }

Loading sequence file: /tmp/S3iQLN0CH2
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/k1kM_dQ8ro/nOj4WfeKbV.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/YfdzZ1aiWl/qT8KSCelUa.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/HAvfPVm2Gc/G0CV8r1Tvf.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
ok 88 -  - number of lines # TODO maybe adapt reference results to Debian specific dataset
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/rHPgVpYkHo/9MaDbH9J12.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/aQlKOga8Wv/YE6ghPkAu_.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/jWLvfs5Iih/1LLirQ8sVV.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/CBvpBcqdMi/bGMLBVZ3ch.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/zvbMj3mhYy/gSb1jsUGxw.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/EjHHLKj0UJ/2PHqtfaXsN.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'
ok 280 - correct number of features for command 'closest' # TODO maybe adapt reference results to Debian specific dataset
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/4sddDFy6Ba/DzRNJyoqWP.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/pkFzDDoyr3/Fwzn6yoJ2j.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'
ok 333 - correct number of features for command 'complement' # TODO maybe adapt reference results to Debian specific dataset
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/yUftUEv32n/jfFonBrjrk.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/9rI3BjJAg2/IYfc0fYGDL.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/bb1otXpoSN/VOHZtN6Hty.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/eedrWf6u1b/lZAGY6l6oN.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 (3.4.0)

Copyright (C) 2006,2019,2020,2021,2023 Timo Lassmann

This program comes with ABSOLUTELY NO WARRANTY; for details type:
`kalign -showw'.
This is free software, and you are welcome to redistribute it
under certain conditions; consult the COPYING file for details.

Please cite:
  Lassmann, Timo.
  "Kalign 3: multiple sequence alignment of large data sets."
  Bioinformatics (2019) 
  https://doi.org/10.1093/bioinformatics/btz795

[2024-06-03 00:02:34] :     LOG : Detected protein sequences.
[2024-06-03 00:02:34] :     LOG : Read 7 sequences from standard input.
[2024-06-03 00:02:34] :     LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00
[2024-06-03 00:02:34] :     LOG : Calculating pairwise distances
[2024-06-03 00:02:34] :     LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00
[2024-06-03 00:02:34] :     LOG : Building guide tree.
[2024-06-03 00:02:34] :     LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00
[2024-06-03 00:02:34] :     LOG : Aligning
[2024-06-03 00:02:34] :     LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00
ok 5
ok 6

Kalign (3.4.0)

Copyright (C) 2006,2019,2020,2021,2023 Timo Lassmann

This program comes with ABSOLUTELY NO WARRANTY; for details type:
`kalign -showw'.
This is free software, and you are welcome to redistribute it
under certain conditions; consult the COPYING file for details.

Please cite:
  Lassmann, Timo.
  "Kalign 3: multiple sequence alignment of large data sets."
  Bioinformatics (2019) 
  https://doi.org/10.1093/bioinformatics/btz795

[2024-06-03 00:02:34] :     LOG : Detected protein sequences.
[2024-06-03 00:02:34] :     LOG : Read 7 sequences from standard input.
[2024-06-03 00:02:34] :     LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00
[2024-06-03 00:02:34] :     LOG : Calculating pairwise distances
[2024-06-03 00:02:34] :     LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00
[2024-06-03 00:02:34] :     LOG : Building guide tree.
[2024-06-03 00:02:34] :     LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00
[2024-06-03 00:02:34] :     LOG : Aligning
[2024-06-03 00:02:34] :     LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00
ok 7
ok
# Required executable for Bio::Tools::Run::Phylo::LVB is not present
t/LVB.t ....................... 
1..19
ok 1 - use Bio::Tools::Run::Phylo::LVB;
ok 2 - use Bio::AlignIO;
ok 3 - An object of class 'Bio::Tools::Run::Phylo::LVB' isa 'Bio::Tools::Run::Phylo::LVB'
ok 4 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
ok 5 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
ok 6 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
ok 7 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
ok 8 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
ok 9 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
ok 10 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
ok 11 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
ok 12 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
ok 13 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
ok 14 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
ok 15 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
ok 16 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
ok 17 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
ok 18 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
ok 19 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
ok
# Required executable for Bio::Tools::Run::Alignment::Lagan is not present
t/Lagan.t ..................... 
1..12
ok 1 - use Bio::AlignIO;
ok 2 - use Bio::Tools::Run::Alignment::Lagan;
ok 3 - use Bio::Root::IO;
ok 4 - use Bio::SeqIO;
ok 5 - use Bio::Seq;
ok 6 - use Bio::Matrix::Mlagan;
ok 7 - An object of class 'Bio::Tools::Run::Alignment::Lagan' isa 'Bio::Tools::Run::Alignment::Lagan'
ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present
ok 9 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present
ok 10 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present
ok 11 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present
ok 12 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present
ok
t/MAFFT.t ..................... 
1..23
ok 1 - use  Bio::Tools::Run::Alignment::MAFFT;
ok 2 - use  Bio::AlignIO;
ok 3 - use  Bio::SeqIO;
ok 4 - An object of class 'Bio::Tools::Run::Alignment::MAFFT' isa 'Bio::Tools::Run::Alignment::MAFFT'
ok 5
ok 6
ok 7
ok 8
ok 9 - 42 or 43 expected
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18 # skip Tests require version 6 of MAFFT
ok 19 # skip Tests require version 6 of MAFFT
ok 20 # skip Tests require version 6 of MAFFT
ok 21 # skip Tests require version 6 of MAFFT
ok 22 # skip Tests require version 6 of MAFFT
ok 23 # skip Tests require version 6 of MAFFT
ok
# Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
t/MSAProbs.t .................. 
1..19
ok 1 - use Bio::Tools::Run::Alignment::MSAProbs;
ok 2 - use Bio::Tools::GuessSeqFormat;
ok 3 - use Bio::AlignIO;
ok 4 - use Bio::SeqIO;
ok 5 - use Bio::Root::IO;
ok 6 - use POSIX;
ok 7
ok 8 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
ok 9 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
ok 10 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
ok 11 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
ok 12 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
ok 13 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
ok 14 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
ok 15 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
ok 16 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
ok 17 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
ok 18 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
ok 19 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
ok
# Required executable for Bio::Tools::Run::Match is not present
t/Match.t ..................... 
1..7
ok 1 - use Bio::Tools::Run::Match;
ok 2 - An object of class 'Bio::Tools::Run::Match' isa 'Bio::Tools::Run::Match'
ok 3 - mxlib parameter was set
ok 4 - program_dir returned correct default
ok 5 - Correct exe default name
ok 6 # skip Required executable for Bio::Tools::Run::Match is not present
ok 7 # skip Required executable for Bio::Tools::Run::Match is not present
ok
# Required executable for Bio::Tools::Run::Mdust is not present
t/Mdust.t ..................... 
1..5
ok 1 - use Bio::Tools::Run::Mdust;
ok 2 - use Bio::SeqIO;
ok 3 - An object of class 'Bio::Tools::Run::Mdust' isa 'Bio::Tools::Run::Mdust'
ok 4 # skip Required executable for Bio::Tools::Run::Mdust is not present
ok 5 # skip Required executable for Bio::Tools::Run::Mdust is not present
ok
# Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
t/Molphy.t .................... 
1..10
ok 1 - use Bio::Tools::Phylo::Molphy;
ok 2 - use Bio::Tools::Run::Phylo::Molphy::ProtML;
ok 3 - use Bio::AlignIO;
ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
ok
t/Muscle.t .................... 
1..16
ok 1 - use Bio::Tools::Run::Alignment::Muscle;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::SeqIO;
ok 4 - use Bio::Root::IO;
ok 5 - use POSIX;
ok 6
ok 7 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests
ok 8 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests
ok 9 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests
ok 10 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests
ok 11 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests
ok 12 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests
ok 13 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests
ok 14 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests
ok 15 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests
ok 16 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests
ok
# Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
t/Neighbor.t .................. 
1..19
ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtDist;
ok 2 - use Bio::Tools::Run::Phylo::Phylip::Neighbor;
ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
ok 15 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
ok
# Required executable for Bio::Tools::Run::Phylo::Njtree::Best is not present
t/Njtree.t .................... 
1..6
ok 1 - use Bio::Root::IO;
ok 2 - use Bio::Tools::Run::Phylo::Njtree::Best;
ok 3 - use Bio::AlignIO;
ok 4 - use Bio::TreeIO;
ok 5
ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Njtree::Best is not present
ok

--------------------- WARNING ---------------------
MSG: In sequence pseudogene residue count gives end value 183.  
Overriding value [178] with value 183 for Bio::LocatableSeq::end().
----LNCIVNDSQKMGIIRNGDLP*PQLKNKF2-FQRMTTPSSAEGKENLVFLIRKNWFSITEKNQPLKYIINLVVSRESKEPPQRPPFLD*SLGDALKRIEQLKLANKQDVFFTVGGSSVYKESMN*-DHFKLFVTWIMQDFQSDTFFS4EGDLEKYKLLPEYPQGVVSDVEEEKGIKYKFEVYEKND
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: In sequence pseudogene residue count gives end value 183.  
Overriding value [178] with value 183 for Bio::LocatableSeq::end().
----LNCIVNDSQKMGIIRNGDLP*PQLKNKF2-FQRMTTPSSAEGKENLVFLIRKNWFSITEKNQPLKYIINLVVSRESKEPPQRPPFLD*SLGDALKRIEQLKLANKQDVFFTVGGSSVYKESMN*-DHFKLFVTWIMQDFQSDTFFS4EGDLEKYKLLPEYPQGVVSDVEEEKGIKYKFEVYEKND
---------------------------------------------------
t/Pal2Nal.t ................... 
1..9
ok 1 - use Bio::Tools::Run::Alignment::Pal2Nal;
ok 2 - An object of class 'Bio::Tools::Run::Alignment::Pal2Nal' isa 'Bio::Tools::Run::Alignment::Pal2Nal'
ok 3 - program_dir returned correct default
ok 4 - Correct exe default name
ok 5
ok 6 - use Bio::AlignIO;
ok 7 - use Bio::SeqIO;
ok 8
ok 9
ok
# Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
t/PhastCons.t ................. 
1..181
ok 1 - use Bio::AlignIO;
ok 2 - use Bio::TreeIO;
ok 3 - use Bio::DB::Taxonomy;
ok 4 - Found input alignment file
ok 5 - Found input tree file
ok 6 - use Bio::Tools::Run::Phylo::Phast::PhastCons;
ok 7 - An object of class 'Bio::Tools::Run::Phylo::Phast::PhastCons' isa 'Bio::Tools::Run::Phylo::Phast::PhastCons'
ok 8 - has a created method not in args
ok 9 - dashed parameter with internal dash was set
ok 10 - wrong-case method wasn't created
ok 11 - dashless wrong-case parameter was set
ok 12 - synonym installed and accessed primary value
ok 13 - double-dashed parameter was set
ok 14 - program_dir returned correct default
ok 15 - Correct exe default name
ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 20 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 21 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 22 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 23 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 24 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 25 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 26 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 27 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 28 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 29 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 30 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 31 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 32 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 33 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 34 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 35 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 36 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 37 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 38 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 39 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 40 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 41 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 42 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 43 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 44 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 45 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 46 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 47 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 48 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 49 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 50 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 51 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 52 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 53 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 54 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 55 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 56 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 57 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 58 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 59 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 60 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 61 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 62 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 63 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 64 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 65 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 66 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 67 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 68 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 69 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 70 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 71 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 72 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 73 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 74 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 75 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 76 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 77 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 78 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 79 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 80 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 81 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 82 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 83 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 84 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 85 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 86 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 87 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 88 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 89 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 90 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 91 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 92 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 93 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 94 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 95 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 96 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 97 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 98 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 99 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 100 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 101 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 102 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 103 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 104 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 105 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 106 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 107 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 108 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 109 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 110 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 111 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 112 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 113 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 114 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 115 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 116 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 117 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 118 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 119 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 120 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 121 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 122 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 123 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 124 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 125 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 126 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 127 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 128 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 129 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 130 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 131 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 132 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 133 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 134 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 135 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 136 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 137 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 138 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 139 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 140 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 141 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 142 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 143 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 144 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 145 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 146 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 147 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 148 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 149 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 150 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 151 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 152 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 153 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 154 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 155 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 156 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 157 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 158 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 159 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 160 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 161 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 162 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 163 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 164 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 165 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 166 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 167 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 168 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 169 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 170 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 171 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 172 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 173 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 174 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 175 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 176 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 177 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 178 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 179 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 180 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok 181 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
ok
# Required executable for Bio::Tools::Run::Primate is not present
t/Primate.t ................... 
1..8
ok 1 - use Bio::Tools::Run::Primate;
ok 2 - use Bio::SeqIO;
ok 3 # skip Required executable for Bio::Tools::Run::Primate is not present
ok 4 # skip Required executable for Bio::Tools::Run::Primate is not present
ok 5 # skip Required executable for Bio::Tools::Run::Primate is not present
ok 6 # skip Required executable for Bio::Tools::Run::Primate is not present
ok 7 # skip Required executable for Bio::Tools::Run::Primate is not present
ok 8 # skip Required executable for Bio::Tools::Run::Primate is not present
ok
t/Primer3.t ................... 
1..9
ok 1 - use Bio::Tools::Run::Primer3;
ok 2 - use Bio::SeqIO;
ok 3
ok 4 # skip Primer3 wrapper only supports Primer3 v1
ok 5 # skip Primer3 wrapper only supports Primer3 v1
ok 6 # skip Primer3 wrapper only supports Primer3 v1
ok 7 # skip Primer3 wrapper only supports Primer3 v1
ok 8 # skip Primer3 wrapper only supports Primer3 v1
ok 9 # skip Primer3 wrapper only supports Primer3 v1
ok
# Required executable for Bio::Tools::Run::Prints is not present
t/Prints.t .................... 
1..7
ok 1 - use Bio::Tools::Run::Prints;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::Seq;
ok 4 - An object of class 'Bio::Tools::Run::Prints' isa 'Bio::Tools::Run::Prints'
ok 5 # skip Required executable for Bio::Tools::Run::Prints is not present
ok 6 # skip Required executable for Bio::Tools::Run::Prints is not present
ok 7 # skip Required executable for Bio::Tools::Run::Prints is not present
ok
# Required executable for Bio::Tools::Run::Alignment::Probalign is not present
t/Probalign.t ................. 
1..13
ok 1 - use Bio::Tools::Run::Alignment::Probalign;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::SeqIO;
ok 4 - use Cwd;
ok 5 - use POSIX;
ok 6 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present
ok 7 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present
ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present
ok 9 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present
ok 10 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present
ok 11 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present
ok 12 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present
ok 13 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present
ok

PROBCONS version 1.12 - align multiple protein sequences and print to standard output
Written by Chuong Do

Using parameter set:
    initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 }
        gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 }
      gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 }

Loading sequence file: t/data/cysprot.fa
Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA))



PROBCONS version 1.12 - align multiple protein sequences and print to standard output
Written by Chuong Do

Using parameter set:
    initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 }
        gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 }
      gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 }

Loading sequence file: /tmp/OhQDmrWrPQ
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/aZLoVqgPJU
Computing posterior matrix: (1) CYS1_DICDI vs. (2) ALEU_HORVU -- done.
Computing posterior matrix: (1) CYS1_DICDI vs. (3) CATH_HUMAN -- done.
Computing posterior matrix: (1) CYS1_DICDI vs. (4) CATH_RAT -- done.
Computing posterior matrix: (1) CYS1_DICDI vs. (5) CATL_HUMAN -- done.
Computing posterior matrix: (1) CYS1_DICDI vs. (6) CATL_RAT -- done.
Computing posterior matrix: (1) CYS1_DICDI vs. (7) PAPA_CARPA -- done.
Computing posterior matrix: (2) ALEU_HORVU vs. (3) CATH_HUMAN -- done.
Computing posterior matrix: (2) ALEU_HORVU vs. (4) CATH_RAT -- done.
Computing posterior matrix: (2) ALEU_HORVU vs. (5) CATL_HUMAN -- done.
Computing posterior matrix: (2) ALEU_HORVU vs. (6) CATL_RAT -- done.
Computing posterior matrix: (2) ALEU_HORVU vs. (7) PAPA_CARPA -- done.
Computing posterior matrix: (3) CATH_HUMAN vs. (4) CATH_RAT -- done.
Computing posterior matrix: (3) CATH_HUMAN vs. (5) CATL_HUMAN -- done.
Computing posterior matrix: (3) CATH_HUMAN vs. (6) CATL_RAT -- done.
Computing posterior matrix: (3) CATH_HUMAN vs. (7) PAPA_CARPA -- done.
Computing posterior matrix: (4) CATH_RAT vs. (5) CATL_HUMAN -- done.
Computing posterior matrix: (4) CATH_RAT vs. (6) CATL_RAT -- done.
Computing posterior matrix: (4) CATH_RAT vs. (7) PAPA_CARPA -- done.
Computing posterior matrix: (5) CATL_HUMAN vs. (6) CATL_RAT -- done.
Computing posterior matrix: (5) CATL_HUMAN vs. (7) PAPA_CARPA -- done.
Computing posterior matrix: (6) CATL_RAT vs. (7) PAPA_CARPA -- done.
Trained parameter set:
    initDistrib[] = { 0.8318762183 5.24617426e-05 5.24617426e-05 0.08400939405 0.08400939405 }
        gapOpen[] = { 0.01386300847 0.01386300847 0.006556313485 0.006556313485 }
      gapExtend[] = { 0.360332042 0.360332042 0.7831901312 0.7831901312 }


PROBCONS version 1.12 - align multiple protein sequences and print to standard output
Written by Chuong Do

Using parameter set:
    initDistrib[] = { 0.8318762183 5.246169894e-05 5.246169894e-05 0.08400939405 0.08400939405 }
        gapOpen[] = { 0.01386300847 0.01386300847 0.006556313485 0.006556313485 }
      gapExtend[] = { 0.360332042 0.360332042 0.7831901312 0.7831901312 }

Loading sequence file: /tmp/d88vGEHugY
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
#     You named your test '15'.  You shouldn't use numbers for your test names.
#     Very confusing.
#     You named your test '340'.  You shouldn't use numbers for your test names.
#     Very confusing.
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 - An object of class 'Bio::SeqFeature::FeaturePair' isa 'Bio::SeqFeatureI'
ok 6 - 15
ok 7 - 340
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, 88, 110, 155, 190, 208, 226
                262, 280, 315, 333, 405
Files=60, Tests=1652, 149 wallclock secs ( 0.24 usr  0.06 sys + 139.38 cusr  7.61 csys = 147.29 CPU)
Result: PASS
mv t.skip/* t
rm -rf t.skip
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   create-stamp debian/debhelper-build-stamp
   dh_prep
   dh_auto_install
	/usr/bin/perl Build install --destdir /<<PKGBUILDDIR>>/debian/tmp --create_packlist 0
Building BioPerl-Run
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1/bp_papplmaker.pl.1p
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1/bp_run_neighbor.pl.1p
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1/bp_run_protdist.pl.1p
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1/bp_panalysis.pl.1p
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1/bp_multi_hmmsearch.pl.1p
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/DB/ESoap.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/DB/ESoap/WSDL.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/Result.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/DocSumAdaptor.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/LinkAdaptor.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/GQueryAdaptor.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Factory/EMBOSS.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/tRNAscanSE.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/MCS.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSApplication.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primer3.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Infernal.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Ensembl.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Glimmer.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSacd.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genewise.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Vista.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Mdust.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Tmhmm.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primate.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Match.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Coil.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/ERPIN.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Simprot.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Eponine.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Hmmer.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Prints.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Seg.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Profile.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneWUBlast.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/FootPrinter.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Pseudowise.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genscan.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/TribeMCL.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneNCBIBlast.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/RNAMotif.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/RepeatMasker.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Signalp.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Promoterwise.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genemark.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools/Config.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Sim4.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Lagan.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/StandAloneFasta.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probalign.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Pal2Nal.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Blat.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Kalign.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Proda.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probcons.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MSAProbs.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Amap.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MAFFT.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/DBA.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Exonerate.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Muscle.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Gmap.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus/Config.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools/Config.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Analysis/soap.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/AnalysisFactory/soap.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/FastTree.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phyml.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/QuickTree.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/SLR.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Semphy.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Gerp.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/LVB.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Raxml.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Molphy/ProtML.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/REL.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Base.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/FEL.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Base.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Consense.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Njtree/Best.pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Neighbor.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Promoterwise.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BlastPlus.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::TribeMCL.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Coil.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Vista.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Molphy::ProtML.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawTree.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::EMBOSSApplication.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::RepeatMasker.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::DB::ESoap.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtDist.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::Result.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Sim4.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Pal2Nal.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Base.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::LinkAdaptor.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genscan.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genemark.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus::BlastMethods.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phast::PhastCons.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Muscle.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::PhylipConf.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::AnalysisFactory::soap.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Gerp.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Simprot.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Glimmer.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Gmap.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Exonerate.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Primate.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Factory::EMBOSS.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor::seq.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Semphy.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Raxml.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Kalign.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::ERPIN.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::StandAloneFasta.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::MAFFT.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneNCBIBlast.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Samtools::Config.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Samtools.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::SLR.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::FEL.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::QuickTree.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phast::PhyloFit.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Mdust.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::FastTree.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Pseudowise.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::DB::ESoap::WSDL.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::Base.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::DocSumAdaptor.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Proda.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Tmhmm.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::RNAMotif.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Hmmer.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::DBA.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::MSAProbs.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor::species.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Match.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Primer3.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Consense.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Probcons.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BEDTools::Config.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Ensembl.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Probalign.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawGram.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::MCS.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Eponine.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlast.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::Modeltest.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Profile.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genewise.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::BatchFile.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Prints.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Infernal.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::SeqBoot.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtPars.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phyml.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::LVB.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BEDTools.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::GQueryAdaptor.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::SLAC.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Lagan.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::FootPrinter.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Amap.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::REL.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::tRNAscanSE.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneWUBlast.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Seg.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Njtree::Best.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::EMBOSSacd.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Blat.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Signalp.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Analysis::soap.3pm
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/bin/bp_papplmaker.pl
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/bin/bp_run_protdist.pl
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/bin/bp_panalysis.pl
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/bin/bp_run_neighbor.pl
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/bin/bp_multi_hmmsearch.pl
   dh_install
   dh_installdocs
   dh_installchangelogs
   dh_installman
   dh_lintian
   dh_perl
   dh_link
   dh_strip_nondeterminism
   dh_compress
   dh_fixperms
   dh_missing
   dh_installdeb
   dh_gencontrol
   dh_md5sums
   dh_builddeb
dpkg-deb: building package 'bioperl-run' in '../bioperl-run_1.7.3-11_all.deb'.
dpkg-deb: building package 'libbio-perl-run-perl' in '../libbio-perl-run-perl_1.7.3-11_all.deb'.
 dpkg-genbuildinfo -O../bioperl-run_1.7.3-11_amd64.buildinfo
 dpkg-genchanges -O../bioperl-run_1.7.3-11_amd64.changes
dpkg-genchanges: info: not including original source code in upload
 dpkg-source -Zxz --after-build .
dpkg-buildpackage: info: binary and diff upload (original source NOT included)
--------------------------------------------------------------------------------
Build finished at 2024-06-03T00:03:02Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


bioperl-run_1.7.3-11_amd64.changes:
-----------------------------------

Format: 1.8
Date: Sat, 27 Apr 2024 21:48:57 +0200
Source: bioperl-run
Binary: bioperl-run libbio-perl-run-perl
Architecture: source all
Version: 1.7.3-11
Distribution: perl-5.40-throwaway
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
 bioperl-run - BioPerl wrappers: scripts
 libbio-perl-run-perl - BioPerl wrappers: modules
Changes:
 bioperl-run (1.7.3-11) unstable; urgency=medium
 .
   * d/control: restrict emboss build-dependency.
     emboss is not available anymore on 32-bit and big endian architectures.
     It is thus not possible anymore to test it in such context.
   * d/control: demote bioperl-run recommends to suggestions.
     emboss, hmmer and infernal are currently not available on some release
     architectures.  Demoting them helps getting the autodep8 perl test
     back on tracks at least on s390x.
   * d/control: demote tigr-glimmer to suggestion.
   * d/control: also restrict tigr-glimmer build-deps architecture set.
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 b7741a8a15bdb654b380bbc8a2dd4b631d470e07 36144 bioperl-run_1.7.3-11_all.deb
 6d356a7b7c3658a31857c6f49a37a5c773c365aa 13042 bioperl-run_1.7.3-11_amd64.buildinfo
 78d10db4fd4b2423ce5aaaf52a2ad3db2dc95223 527616 libbio-perl-run-perl_1.7.3-11_all.deb
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Files:
 3486d61299e7f12f82475daa7eb41dd8 2169 science optional bioperl-run_1.7.3-11.dsc
 c60f4ebba98758d7f3e9054953bb1423 19644 science optional bioperl-run_1.7.3-11.debian.tar.xz
 88830b1fd32fad5ffe1ac983c8f977a2 36144 science optional bioperl-run_1.7.3-11_all.deb
 a2fda5403b9424bc70d0e0684d3aa7a4 13042 science optional bioperl-run_1.7.3-11_amd64.buildinfo
 09b1da2ad760acec11acb0f5111c1ec3 527616 perl optional libbio-perl-run-perl_1.7.3-11_all.deb

+------------------------------------------------------------------------------+
| Buildinfo                                                                    |
+------------------------------------------------------------------------------+

Format: 1.0
Source: bioperl-run
Binary: bioperl-run libbio-perl-run-perl
Architecture: all source
Version: 1.7.3-11
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Build-Origin: Debian
Build-Architecture: amd64
Build-Date: Mon, 03 Jun 2024 00:03:01 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
 merged-usr-via-aliased-dirs
 usr-local-has-programs
Installed-Build-Depends:
 adduser (= 3.137),
 amap-align (= 2.2+git20080214.600fc29+dfsg-2),
 autoconf (= 2.71-3),
 automake (= 1:1.16.5-1.3),
 autopoint (= 0.21-14),
 autotools-dev (= 20220109.1),
 base-files (= 13.2),
 base-passwd (= 3.6.3),
 bash (= 5.2.21-2+b1),
 bedtools (= 2.31.1+dfsg-2),
 bedtools-test (= 2.31.1+dfsg-2),
 binutils (= 2.42-4),
 binutils-common (= 2.42-4),
 binutils-x86-64-linux-gnu (= 2.42-4),
 bioperl (= 1.7.8-1),
 bsdextrautils (= 2.40.1-7),
 bsdutils (= 1:2.40.1-7),
 build-essential (= 12.10),
 bzip2 (= 1.0.8-5.1),
 ca-certificates (= 20240203),
 clustalw (= 2.1+lgpl-7),
 coreutils (= 9.4-3.1),
 cpp (= 4:13.2.0-7),
 cpp-13 (= 13.2.0-25),
 cpp-13-x86-64-linux-gnu (= 13.2.0-25),
 cpp-x86-64-linux-gnu (= 4:13.2.0-7),
 dash (= 0.5.12-8),
 debconf (= 1.5.86),
 debhelper (= 13.15.3),
 debianutils (= 5.17),
 dh-autoreconf (= 20),
 dh-strip-nondeterminism (= 1.14.0-1),
 diffutils (= 1:3.10-1),
 dpkg (= 1.22.6),
 dpkg-dev (= 1.22.6),
 dwz (= 0.15-1+b1),
 emboss (= 6.6.0+dfsg-15),
 emboss-data (= 6.6.0+dfsg-15),
 emboss-lib (= 6.6.0+dfsg-15),
 exonerate (= 2.4.0-5+b1),
 fasttree (= 2.1.11-2),
 file (= 1:5.45-3),
 findutils (= 4.9.0-6),
 fontconfig-config (= 2.15.0-1.1),
 fonts-dejavu-core (= 2.37-8),
 fonts-dejavu-mono (= 2.37-8),
 g++ (= 4:13.2.0-7),
 g++-13 (= 13.2.0-25),
 g++-13-x86-64-linux-gnu (= 13.2.0-25),
 g++-x86-64-linux-gnu (= 4:13.2.0-7),
 gcc (= 4:13.2.0-7),
 gcc-13 (= 13.2.0-25),
 gcc-13-base (= 13.2.0-25),
 gcc-13-x86-64-linux-gnu (= 13.2.0-25),
 gcc-14-base (= 14.1.0-1),
 gcc-x86-64-linux-gnu (= 4:13.2.0-7),
 gettext (= 0.21-14+b1),
 gettext-base (= 0.21-14+b1),
 grep (= 3.11-4),
 groff-base (= 1.23.0-4),
 gzip (= 1.12-1.1),
 hmmer (= 3.4+dfsg-2),
 hostname (= 3.23+nmu2),
 hyphy-common (= 2.5.62+dfsg-1),
 hyphy-pt (= 2.5.62+dfsg-1),
 ibverbs-providers (= 50.0-2+b1),
 infernal (= 1.1.5-2),
 init-system-helpers (= 1.66),
 intltool-debian (= 0.35.0+20060710.6),
 kalign (= 1:3.4.0-1),
 lagan (= 2.0-10),
 libabsl20230802 (= 20230802.1-4),
 libacl1 (= 2.3.2-2),
 libalgorithm-diff-perl (= 1.201-1),
 libamd-comgr2 (= 6.0+git20231212.4510c28+dfsg-3+b1),
 libamdhip64-5 (= 5.7.1-3),
 libaom3 (= 3.8.2-2),
 libarchive-zip-perl (= 1.68-1),
 libarray-compare-perl (= 3.0.8-1),
 libasan8 (= 14.1.0-1),
 libatomic1 (= 14.1.0-1),
 libattr1 (= 1:2.5.2-1),
 libaudit-common (= 1:3.1.2-2.1),
 libaudit1 (= 1:3.1.2-2.1),
 libavif16 (= 1.0.4-3),
 libb-hooks-op-check-perl (= 0.22-3+b2),
 libbinutils (= 2.42-4),
 libbio-asn1-entrezgene-perl (= 1.730-3),
 libbio-cluster-perl (= 1.7.3-6),
 libbio-eutilities-perl (= 1.77-2),
 libbio-featureio-perl (= 1.6.905-2),
 libbio-perl-perl (= 1.7.8-1),
 libbio-perl-run-perl (= 1.7.3-11),
 libbio-tools-run-alignment-clustalw-perl (= 1.7.4-4),
 libbio-tools-run-remoteblast-perl (= 1.7.3-3),
 libbio-variation-perl (= 1.7.5-3),
 libblas3 (= 3.12.0-3),
 libblkid1 (= 2.40.1-7),
 libbrotli1 (= 1.1.0-2+b3),
 libbsd0 (= 0.12.2-1),
 libbz2-1.0 (= 1.0.8-5.1),
 libc-bin (= 2.38-12),
 libc-dev-bin (= 2.38-12),
 libc6 (= 2.38-12),
 libc6-dev (= 2.38-12),
 libcap-ng0 (= 0.8.5-1),
 libcap2 (= 1:2.66-5),
 libcapture-tiny-perl (= 0.48-2),
 libcbor0.10 (= 0.10.2-1.2),
 libcc1-0 (= 14.1.0-1),
 libclass-data-inheritable-perl (= 0.08-3),
 libclass-method-modifiers-perl (= 2.15-1),
 libclass-xsaccessor-perl (= 1.19-4+b4),
 libclone-perl (= 0.46-1+b3),
 libcom-err2 (= 1.47.1-1),
 libconfig-any-perl (= 0.33-1),
 libcrypt-dev (= 1:4.4.36-4),
 libcrypt1 (= 1:4.4.36-4),
 libctf-nobfd0 (= 2.42-4),
 libctf0 (= 2.42-4),
 libcurl3t64-gnutls (= 8.8.0-1),
 libdata-stag-perl (= 0.14-3),
 libdav1d7 (= 1.4.2-1),
 libdb5.3t64 (= 5.3.28+dfsg2-7),
 libde265-0 (= 1.0.15-1+b1),
 libdebconfclient0 (= 0.272),
 libdebhelper-perl (= 13.15.3),
 libdeflate0 (= 1.20-1),
 libdevel-callchecker-perl (= 0.009-1+b1),
 libdevel-stacktrace-perl (= 2.0500-1),
 libdivsufsort3 (= 2.0.1-6),
 libdpkg-perl (= 1.22.6),
 libdrm-amdgpu1 (= 2.4.120-2),
 libdrm-common (= 2.4.120-2),
 libdrm2 (= 2.4.120-2),
 libdynaloader-functions-perl (= 0.003-3),
 libedit2 (= 3.1-20240517-1),
 libelf1t64 (= 0.191-1+b1),
 libencode-locale-perl (= 1.05-3),
 libevent-core-2.1-7t64 (= 2.1.12-stable-10),
 libevent-pthreads-2.1-7t64 (= 2.1.12-stable-10),
 libexception-class-perl (= 1.45-1),
 libexpat1 (= 2.6.2-1),
 libexporter-tiny-perl (= 1.006002-1),
 libfabric1 (= 1.17.0-3+b1),
 libffi8 (= 3.4.6-1),
 libfido2-1 (= 1.14.0-1+b2),
 libfile-listing-perl (= 6.16-1),
 libfile-slurp-perl (= 9999.32-2),
 libfile-slurp-tiny-perl (= 0.004-2),
 libfile-sort-perl (= 1.01-3),
 libfile-stripnondeterminism-perl (= 1.14.0-1),
 libfontconfig1 (= 2.15.0-1.1),
 libfreetype6 (= 2.13.2+dfsg-1+b4),
 libgav1-1 (= 0.19.0-2+b1),
 libgcc-13-dev (= 13.2.0-25),
 libgcc-s1 (= 14.1.0-1),
 libgd3 (= 2.3.3-9+b3),
 libgdbm-compat4t64 (= 1.23-5.1+b1),
 libgdbm6t64 (= 1.23-5.1+b1),
 libgfortran5 (= 14.1.0-1),
 libglib2.0-0t64 (= 2.80.2-2),
 libgmp10 (= 2:6.3.0+dfsg-2+b1),
 libgnutls30t64 (= 3.8.5-4),
 libgomp1 (= 14.1.0-1),
 libgprofng0 (= 2.42-4),
 libgssapi-krb5-2 (= 1.20.1-6+b1),
 libheif-plugin-dav1d (= 1.17.6-1+b2),
 libheif-plugin-libde265 (= 1.17.6-1+b2),
 libheif1 (= 1.17.6-1+b2),
 libhogweed6t64 (= 3.9.1-2.2),
 libhpdf-2.3.0 (= 2.3.0+dfsg-1+b2),
 libhsa-runtime64-1 (= 5.7.1-2),
 libhsakmt1 (= 5.7.0-1),
 libhtml-parser-perl (= 3.82-1+b1),
 libhtml-tagset-perl (= 3.24-1),
 libhtml-tree-perl (= 5.07-3),
 libhts3t64 (= 1.20+ds-1),
 libhtscodecs2 (= 1.6.0-1+b1),
 libhttp-cookies-perl (= 6.11-1),
 libhttp-date-perl (= 6.06-1),
 libhttp-message-perl (= 6.46-1),
 libhttp-negotiate-perl (= 6.01-2),
 libhwasan0 (= 14.1.0-1),
 libhwloc-plugins (= 2.10.0-1+b1),
 libhwloc15 (= 2.10.0-1+b1),
 libibverbs1 (= 50.0-2+b1),
 libicu72 (= 72.1-4+b1),
 libidn2-0 (= 2.3.7-2),
 libimport-into-perl (= 1.002005-2),
 libio-html-perl (= 1.004-3),
 libio-pty-perl (= 1:1.20-1+b2),
 libio-socket-ssl-perl (= 2.085-1),
 libio-string-perl (= 1.08-4),
 libipc-run-perl (= 20231003.0-2),
 libisl23 (= 0.26-3+b2),
 libitm1 (= 14.1.0-1),
 libjansson4 (= 2.14-2+b2),
 libjbig0 (= 2.1-6.1+b1),
 libjpeg62-turbo (= 1:2.1.5-3),
 libk5crypto3 (= 1.20.1-6+b1),
 libkeyutils1 (= 1.6.3-3),
 libkrb5-3 (= 1.20.1-6+b1),
 libkrb5support0 (= 1.20.1-6+b1),
 liblapack3 (= 3.12.0-3),
 libldap-2.5-0 (= 2.5.17+dfsg-1+b1),
 liblerc4 (= 4.0.0+ds-4+b1),
 libllvm17t64 (= 1:17.0.6-12),
 liblmdb0 (= 0.9.31-1+b1),
 liblsan0 (= 14.1.0-1),
 liblwp-mediatypes-perl (= 6.04-2),
 liblwp-protocol-https-perl (= 6.14-1),
 liblzma5 (= 5.6.1+really5.4.5-1),
 libmagic-mgc (= 1:5.45-3),
 libmagic1t64 (= 1:5.45-3),
 libmariadb3 (= 1:10.11.8-1),
 libmbedcrypto7t64 (= 2.28.8-1),
 libmbedtls14t64 (= 2.28.8-1),
 libmbedx509-1t64 (= 2.28.8-1),
 libmd0 (= 1.1.0-2),
 libmodule-build-perl (= 0.423400-2),
 libmodule-pluggable-perl (= 5.2-5),
 libmodule-runtime-perl (= 0.016-2),
 libmoo-perl (= 2.005005-1),
 libmount1 (= 2.40.1-7),
 libmpc3 (= 1.3.1-1+b2),
 libmpfr6 (= 4.2.1-1+b1),
 libmunge2 (= 0.5.15-4),
 libncurses6 (= 6.5-2),
 libncursesw6 (= 6.5-2),
 libnet-http-perl (= 6.23-1),
 libnet-ssleay-perl (= 1.94-1+b2),
 libnettle8t64 (= 3.9.1-2.2),
 libnghttp2-14 (= 1.61.0-1+b1),
 libnl-3-200 (= 3.7.0-0.3),
 libnl-route-3-200 (= 3.7.0-0.3),
 libnuma1 (= 2.0.18-1),
 libopenmpi3t64 (= 4.1.6-13.3),
 libp11-kit0 (= 0.25.3-5),
 libpam-modules (= 1.5.3-7),
 libpam-modules-bin (= 1.5.3-7),
 libpam-runtime (= 1.5.3-7),
 libpam0g (= 1.5.3-7),
 libparams-classify-perl (= 0.015-2+b4),
 libpciaccess0 (= 0.17-3+b1),
 libpcre2-8-0 (= 10.42-4+b1),
 libperl5.40 (= 5.40.0~rc1-1),
 libpipeline1 (= 1.5.7-2),
 libpmix2t64 (= 5.0.2-3),
 libpng16-16t64 (= 1.6.43-5),
 libpq5 (= 16.3-1+b1),
 libpsl5t64 (= 0.21.2-1.1),
 libpsm-infinipath1 (= 3.3+20.604758e7-6.3),
 libpsm2-2 (= 11.2.185-2),
 libpython3-stdlib (= 3.11.8-1),
 libpython3.11-minimal (= 3.11.9-1),
 libpython3.11-stdlib (= 3.11.9-1),
 libquadmath0 (= 14.1.0-1),
 librav1e0 (= 0.7.1-2),
 librdmacm1t64 (= 50.0-2+b1),
 libreadline8t64 (= 8.2-4),
 librole-tiny-perl (= 2.002004-1),
 librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b4),
 libsasl2-2 (= 2.1.28+dfsg1-6),
 libsasl2-modules-db (= 2.1.28+dfsg1-6),
 libseccomp2 (= 2.5.5-1),
 libselinux1 (= 3.5-2+b2),
 libsemanage-common (= 3.5-1),
 libsemanage2 (= 3.5-1+b3),
 libsepol2 (= 3.5-2+b1),
 libsframe1 (= 2.42-4),
 libsharpyuv0 (= 1.4.0-0.1),
 libsmartcols1 (= 2.40.1-7),
 libsqlite3-0 (= 3.46.0-1),
 libssh2-1t64 (= 1.11.0-5),
 libssl3t64 (= 3.2.1-3),
 libstdc++-13-dev (= 13.2.0-25),
 libstdc++6 (= 14.1.0-1),
 libsub-quote-perl (= 2.006008-1),
 libsub-uplevel-perl (= 0.2800-3),
 libsvtav1enc1d1 (= 1.7.0+dfsg-2+b1),
 libsystemd0 (= 256~rc3-7),
 libtasn1-6 (= 4.19.0-3+b2),
 libtest-deep-perl (= 1.204-1),
 libtest-differences-perl (= 0.71-1),
 libtest-exception-perl (= 0.43-3),
 libtest-most-perl (= 0.38-1),
 libtest-warn-perl (= 0.37-2),
 libtext-csv-perl (= 2.04-1),
 libtext-diff-perl (= 1.45-2),
 libtiff6 (= 4.5.1+git230720-4),
 libtimedate-perl (= 2.3300-2),
 libtinfo6 (= 6.5-2),
 libtool (= 2.4.7-7),
 libtree-dagnode-perl (= 1.32-1),
 libtry-tiny-perl (= 0.31-2),
 libtsan2 (= 14.1.0-1),
 libtype-tiny-perl (= 2.004000-1),
 libubsan1 (= 14.1.0-1),
 libuchardet0 (= 0.0.8-1+b1),
 libucx0 (= 1.16.0+ds-5),
 libudev1 (= 256~rc3-7),
 libunistring5 (= 1.2-1),
 liburi-perl (= 5.28-1),
 libuuid1 (= 2.40.1-7),
 libwebp7 (= 1.4.0-0.1),
 libwww-perl (= 6.77-1),
 libwww-robotrules-perl (= 6.02-1),
 libx11-6 (= 2:1.8.7-1+b1),
 libx11-data (= 2:1.8.7-1),
 libxau6 (= 1:1.0.9-1+b1),
 libxcb1 (= 1.17.0-2),
 libxdmcp6 (= 1:1.1.2-3+b1),
 libxext6 (= 2:1.3.4-1+b1),
 libxml-dom-perl (= 1.46-2),
 libxml-dom-xpath-perl (= 0.14-4),
 libxml-libxml-perl (= 2.0207+dfsg+really+2.0134-3+b1),
 libxml-namespacesupport-perl (= 1.12-2),
 libxml-parser-perl (= 2.47-1+b3),
 libxml-perl (= 0.08-4),
 libxml-regexp-perl (= 0.04-1.1),
 libxml-sax-base-perl (= 1.09-3),
 libxml-sax-perl (= 1.02+dfsg-3),
 libxml-simple-perl (= 2.25-2),
 libxml-twig-perl (= 1:3.52-3),
 libxml-writer-perl (= 0.900-2),
 libxml-xpathengine-perl (= 0.14-2),
 libxml2 (= 2.12.7+dfsg-2),
 libxnvctrl0 (= 535.171.04-1),
 libxpm4 (= 1:3.5.17-1+b1),
 libyuv0 (= 0.0.1888.20240509-4),
 libz3-4 (= 4.8.12-3.1+b2),
 libzstd1 (= 1.5.5+dfsg2-2),
 linux-libc-dev (= 6.8.12-1),
 login (= 1:4.13+dfsg1-4),
 m4 (= 1.4.19-4),
 mafft (= 7.505-1),
 make (= 4.3-4.1),
 man-db (= 2.12.1-1),
 mariadb-common (= 1:10.11.8-1),
 mawk (= 1.3.4.20240123-1),
 media-types (= 10.1.0),
 muscle (= 1:5.1.0-1),
 mysql-common (= 5.8+1.1.0),
 ncbi-blast+ (= 2.12.0+ds-4+b1),
 ncbi-blast+-legacy (= 2.12.0+ds-4),
 ncbi-data (= 6.1.20170106+dfsg2-2),
 ncoils (= 2002-9),
 ncurses-base (= 6.5-2),
 ncurses-bin (= 6.5-2),
 netbase (= 6.4),
 ocl-icd-libopencl1 (= 2.3.2-1+b1),
 openmpi-bin (= 4.1.6-13.3),
 openmpi-common (= 4.1.6-13.3),
 openssh-client (= 1:9.7p1-5),
 openssl (= 3.2.1-3),
 pal2nal (= 14.1-3),
 passwd (= 1:4.13+dfsg1-4),
 patch (= 2.7.6-7),
 perl (= 5.40.0~rc1-1),
 perl-base (= 5.40.0~rc1-1),
 perl-modules-5.40 (= 5.40.0~rc1-1),
 perl-openssl-defaults (= 7+b2),
 pftools (= 3.2.12-1),
 phyml (= 3:3.3.20220408-3+b1),
 po-debconf (= 1.0.21+nmu1),
 primer3 (= 2.6.1-4),
 probcons (= 1.12-14),
 python3 (= 3.11.8-1),
 python3-minimal (= 3.11.8-1),
 python3-numpy (= 1:1.26.4+ds-10),
 python3-pkg-resources (= 68.1.2-2),
 python3-pybedtools (= 0.10.0-1),
 python3-pysam (= 0.22.1+ds-2),
 python3.11 (= 3.11.9-1),
 python3.11-minimal (= 3.11.9-1),
 raxml (= 8.2.13+dfsg-1),
 readline-common (= 8.2-4),
 rpcsvc-proto (= 1.4.3-1),
 samtools (= 1.20-3),
 sed (= 4.9-2),
 sensible-utils (= 0.0.22),
 sim4 (= 0.0.20121010-8),
 sysvinit-utils (= 3.09-1),
 tar (= 1.35+dfsg-3),
 tigr-glimmer (= 3.02b-6+b1),
 tzdata (= 2024a-4),
 ucf (= 3.0043+nmu1),
 usr-is-merged (= 39),
 util-linux (= 2.40.1-7),
 wise (= 2.4.1-24),
 wise-data (= 2.4.1-24),
 xz-utils (= 5.6.1+really5.4.5-1),
 zlib1g (= 1:1.3.dfsg+really1.3.1-1)
Environment:
 DEB_BUILD_OPTIONS="parallel=2"
 LANG="en_GB.UTF-8"
 LC_ALL="C.UTF-8"
 LC_COLLATE="C.UTF-8"
 LD_LIBRARY_PATH="/usr/lib/libeatmydata"
 SOURCE_DATE_EPOCH="1714247337"


+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


bioperl-run_1.7.3-11_all.deb
----------------------------

 new Debian package, version 2.0.
 size 36144 bytes: control archive=1348 bytes.
    1094 bytes,    15 lines      control
    1062 bytes,    15 lines      md5sums
 Package: bioperl-run
 Version: 1.7.3-11
 Architecture: all
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 89
 Depends: perl:any, bioperl (>= 1.7.4), libbio-perl-run-perl (= 1.7.3-11), libbio-featureio-perl, libbio-cluster-perl, libtest-requiresinternet-perl, libbio-eutilities-perl, libbio-tools-run-remoteblast-perl, libsoap-lite-perl, default-jdk-headless
 Recommends: amap-align, ncbi-blast+-legacy, bwa, exonerate, kalign, maq, mafft, muscle, ncoils, phylip, primer3, probalign, probcons, raxml, sim4, t-coffee, wise, lagan, pal2nal
 Suggests: gmap, fasta3, trnascan-se, bedtools, bowtie, clustalw, emboss, hmmer, hyphy-pt | hyphy-mpi, infernal, libbio-tools-run-alignment-clustalw-perl, pftools, phyml, samtools, tigr-glimmer
 Section: science
 Priority: optional
 Homepage: https://metacpan.org/release/BioPerl-Run
 Description: BioPerl wrappers: scripts
  Contains scripts from the BioPerl-Run package. This package will also install
  all wrappable applications packaged in Debian. The ones that are not Free are
  "Suggested" by this package.

drwxr-xr-x root/root         0 2024-04-27 19:48 ./
drwxr-xr-x root/root         0 2024-04-27 19:48 ./usr/
drwxr-xr-x root/root         0 2024-04-27 19:48 ./usr/bin/
-rwxr-xr-x root/root      3552 2024-04-27 19:48 ./usr/bin/bp_multi_hmmsearch.pl
-rwxr-xr-x root/root     23728 2024-04-27 19:48 ./usr/bin/bp_panalysis.pl
-rwxr-xr-x root/root     15037 2024-04-27 19:48 ./usr/bin/bp_papplmaker.pl
-rwxr-xr-x root/root      1324 2024-04-27 19:48 ./usr/bin/bp_run_neighbor.pl
-rwxr-xr-x root/root      2111 2024-04-27 19:48 ./usr/bin/bp_run_protdist.pl
drwxr-xr-x root/root         0 2024-04-27 19:48 ./usr/share/
drwxr-xr-x root/root         0 2024-04-27 19:48 ./usr/share/doc/
drwxr-xr-x root/root         0 2024-04-27 19:48 ./usr/share/doc/bioperl-run/
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libbio-perl-run-perl_1.7.3-11_all.deb
-------------------------------------

 new Debian package, version 2.0.
 size 527616 bytes: control archive=5628 bytes.
     614 bytes,    14 lines      control
   17160 bytes,   198 lines      md5sums
 Package: libbio-perl-run-perl
 Source: bioperl-run
 Version: 1.7.3-11
 Architecture: all
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 1721
 Depends: perl:any, libbio-perl-perl, libipc-run-perl, libfile-sort-perl
 Recommends: libalgorithm-diff-perl, libio-string-perl, libxml-twig-perl, libwww-perl
 Section: perl
 Priority: optional
 Homepage: https://metacpan.org/release/BioPerl-Run
 Description: BioPerl wrappers: modules
  Contains modules that provide a Perl interface to various bioinformatics
  applications to allow them to be used with common BioPerl objects.

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+------------------------------------------------------------------------------+
| Post Build                                                                   |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: amd64
Build Type: full
Build-Space: 19584
Build-Time: 156
Distribution: perl-5.40-throwaway
Host Architecture: amd64
Install-Time: 40
Job: /srv/debomatic/incoming/bioperl-run_1.7.3-11.dsc
Machine Architecture: amd64
Package: bioperl-run
Package-Time: 203
Source-Version: 1.7.3-11
Space: 19584
Status: successful
Version: 1.7.3-11
--------------------------------------------------------------------------------
Finished at 2024-06-03T00:03:02Z
Build needed 00:03:23, 19584k disk space