sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on carme.larted.org.uk +==============================================================================+ | bioperl-run 1.7.1-3 (amd64) Sun, 25 Jun 2017 18:55:02 +0000 | +==============================================================================+ Package: bioperl-run Version: 1.7.1-3 Source Version: 1.7.1-3 Distribution: experimental Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/experimental-amd64-debomatic-c0bdcbd5-3cae-4c86-9104-5e387c1c5151' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bioperl-run_1.7.1-3 experimental amd64 ------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bioperl-run_1.7.1-3 experimental amd64'. Finished processing commands. -------------------------------------------------------------------------------- +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian unstable InRelease [255 kB] Get:2 http://localhost:3142/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://localhost:3142/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://localhost:3142/debian unstable/main Sources 2017-06-20-2018.33.pdiff [25.0 kB] Get:5 http://localhost:3142/debian unstable/main Sources 2017-06-21-0217.08.pdiff [14.9 kB] Get:6 http://localhost:3142/debian unstable/main Sources 2017-06-21-0821.30.pdiff [15.3 kB] Get:7 http://localhost:3142/debian unstable/main Sources 2017-06-21-1417.59.pdiff [13.5 kB] Get:8 http://localhost:3142/debian unstable/main Sources 2017-06-21-2021.23.pdiff [20.5 kB] Get:9 http://localhost:3142/debian unstable/main Sources 2017-06-22-0218.25.pdiff [10.5 kB] Get:10 http://localhost:3142/debian unstable/main Sources 2017-06-22-0817.31.pdiff [6041 B] Get:11 http://localhost:3142/debian unstable/main Sources 2017-06-22-1416.20.pdiff [8348 B] Get:12 http://localhost:3142/debian unstable/main Sources 2017-06-22-2020.53.pdiff [19.5 kB] Get:13 http://localhost:3142/debian unstable/main Sources 2017-06-23-0215.59.pdiff [5519 B] Get:14 http://localhost:3142/debian unstable/main Sources 2017-06-23-0817.22.pdiff [6761 B] Get:15 http://localhost:3142/debian unstable/main Sources 2017-06-23-1418.00.pdiff [15.9 kB] Get:16 http://localhost:3142/debian unstable/main Sources 2017-06-23-2016.25.pdiff [25.0 kB] Get:17 http://localhost:3142/debian unstable/main Sources 2017-06-24-0216.35.pdiff [8422 B] Get:18 http://localhost:3142/debian unstable/main Sources 2017-06-24-0816.06.pdiff [5023 B] Get:19 http://localhost:3142/debian unstable/main Sources 2017-06-24-1416.41.pdiff [16.1 kB] Get:20 http://localhost:3142/debian unstable/main Sources 2017-06-24-2015.52.pdiff [17.3 kB] Get:21 http://localhost:3142/debian unstable/main Sources 2017-06-25-0217.07.pdiff [9236 B] Get:22 http://localhost:3142/debian unstable/main Sources 2017-06-25-0816.14.pdiff [8073 B] Get:23 http://localhost:3142/debian unstable/main Sources 2017-06-25-1416.46.pdiff [7833 B] Get:24 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-20-2018.33.pdiff [97.1 kB] Get:25 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-21-0217.08.pdiff [61.9 kB] Get:26 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-21-0821.30.pdiff [28.3 kB] Get:27 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-21-1417.59.pdiff [50.8 kB] Get:28 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-21-2021.23.pdiff [115 kB] Get:29 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-22-0218.25.pdiff [62.2 kB] Get:30 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-22-0817.31.pdiff [5496 B] Get:31 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-22-1416.20.pdiff [6955 B] Get:32 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-22-2020.53.pdiff [13.9 kB] Get:23 http://localhost:3142/debian unstable/main Sources 2017-06-25-1416.46.pdiff [7833 B] Get:33 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-23-0215.59.pdiff [16.6 kB] Get:34 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-23-0817.22.pdiff [3379 B] Get:35 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-23-1418.00.pdiff [47.6 kB] Get:36 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-23-2016.25.pdiff [28.4 kB] Get:37 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-24-0216.35.pdiff [14.9 kB] Get:38 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-24-0816.06.pdiff [4885 B] Get:39 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-24-1416.41.pdiff [17.5 kB] Get:40 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-24-2015.52.pdiff [12.3 kB] Get:41 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-25-0217.07.pdiff [7013 B] Get:42 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-25-0816.14.pdiff [4270 B] Get:43 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-25-1416.46.pdiff [7231 B] Get:43 http://localhost:3142/debian unstable/main amd64 Packages 2017-06-25-1416.46.pdiff [7231 B] Fetched 1175 kB in 0s (1534 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: dirmngr gnupg-l10n libffi6 libgnutls30 libhogweed4 libidn11 libidn2-0 libldap-2.4-2 libldap-common liblocale-gettext-perl libnettle6 libp11-kit0 libsasl2-2 libsasl2-modules libsasl2-modules-db libssl1.1 libtasn1-6 libunistring0 Use 'apt autoremove' to remove them. The following NEW packages will be installed: gcc-7-base libidn2-0 libunistring0 The following packages will be upgraded: cpp-6 findutils g++-6 gcc-6 gcc-6-base libasan3 libatomic1 libaudit-common libaudit1 libcc1-0 libcilkrts5 libgcc-6-dev libgcc1 libgnutls30 libgomp1 libitm1 liblsan0 libmpx2 libnpth0 libperl5.24 libquadmath0 libstdc++-6-dev libstdc++6 libtsan0 libubsan0 linux-libc-dev perl perl-base perl-modules-5.24 29 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 37.3 MB of archives. After this operation, 1992 kB of additional disk space will be used. Get:1 http://localhost:3142/debian unstable/main amd64 findutils amd64 4.6.0+git+20170606-2 [635 kB] Get:2 http://localhost:3142/debian unstable/main amd64 libperl5.24 amd64 5.24.1-4 [3528 kB] Get:3 http://localhost:3142/debian unstable/main amd64 perl amd64 5.24.1-4 [218 kB] Get:4 http://localhost:3142/debian unstable/main amd64 perl-base amd64 5.24.1-4 [1342 kB] Get:5 http://localhost:3142/debian unstable/main amd64 perl-modules-5.24 all 5.24.1-4 [2722 kB] Get:6 http://localhost:3142/debian unstable/main amd64 gcc-7-base amd64 7.1.0-7 [180 kB] Get:7 http://localhost:3142/debian unstable/main amd64 libgcc1 amd64 1:7.1.0-7 [39.3 kB] Get:8 http://localhost:3142/debian unstable/main amd64 libstdc++6 amd64 7.1.0-7 [398 kB] Get:9 http://localhost:3142/debian unstable/main amd64 libaudit-common all 1:2.7.7-1 [20.1 kB] Get:10 http://localhost:3142/debian unstable/main amd64 libaudit1 amd64 1:2.7.7-1 [54.2 kB] Get:11 http://localhost:3142/debian unstable/main amd64 libquadmath0 amd64 7.1.0-7 [132 kB] Get:12 http://localhost:3142/debian unstable/main amd64 libitm1 amd64 7.1.0-7 [27.2 kB] Get:13 http://localhost:3142/debian unstable/main amd64 libgomp1 amd64 7.1.0-7 [75.1 kB] Get:14 http://localhost:3142/debian unstable/main amd64 libatomic1 amd64 7.1.0-7 [8774 B] Get:15 http://localhost:3142/debian unstable/main amd64 libasan3 amd64 6.3.0-19 [310 kB] Get:16 http://localhost:3142/debian unstable/main amd64 liblsan0 amd64 7.1.0-7 [124 kB] Get:17 http://localhost:3142/debian unstable/main amd64 libtsan0 amd64 7.1.0-7 [270 kB] Get:18 http://localhost:3142/debian unstable/main amd64 libubsan0 amd64 7.1.0-7 [117 kB] Get:19 http://localhost:3142/debian unstable/main amd64 libcilkrts5 amd64 7.1.0-7 [42.0 kB] Get:20 http://localhost:3142/debian unstable/main amd64 libmpx2 amd64 7.1.0-7 [11.4 kB] Get:21 http://localhost:3142/debian unstable/main amd64 g++-6 amd64 6.3.0-19 [7085 kB] Get:22 http://localhost:3142/debian unstable/main amd64 libstdc++-6-dev amd64 6.3.0-19 [1420 kB] Get:23 http://localhost:3142/debian unstable/main amd64 gcc-6 amd64 6.3.0-19 [6895 kB] Get:24 http://localhost:3142/debian unstable/main amd64 libgcc-6-dev amd64 6.3.0-19 [2297 kB] Get:25 http://localhost:3142/debian unstable/main amd64 libcc1-0 amd64 7.1.0-7 [37.7 kB] Get:26 http://localhost:3142/debian unstable/main amd64 cpp-6 amd64 6.3.0-19 [6573 kB] Get:27 http://localhost:3142/debian unstable/main amd64 gcc-6-base amd64 6.3.0-19 [180 kB] Get:28 http://localhost:3142/debian unstable/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:29 http://localhost:3142/debian unstable/main amd64 libidn2-0 amd64 0.16-1 [60.6 kB] Get:30 http://localhost:3142/debian unstable/main amd64 libgnutls30 amd64 3.5.13-2 [914 kB] Get:31 http://localhost:3142/debian unstable/main amd64 libnpth0 amd64 1.5-2 [17.9 kB] Get:32 http://localhost:3142/debian unstable/main amd64 linux-libc-dev amd64 4.11.6-1 [1288 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 37.3 MB in 0s (140 MB/s) (Reading database ... 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Unpacking libgnutls30:amd64 (3.5.13-2) over (3.5.8-6) ... Preparing to unpack .../20-libnpth0_1.5-2_amd64.deb ... Unpacking libnpth0:amd64 (1.5-2) over (1.3-1) ... Preparing to unpack .../21-linux-libc-dev_4.11.6-1_amd64.deb ... Unpacking linux-libc-dev:amd64 (4.11.6-1) over (4.9.30-2) ... Setting up libquadmath0:amd64 (7.1.0-7) ... Setting up libnpth0:amd64 (1.5-2) ... Setting up libgomp1:amd64 (7.1.0-7) ... Setting up libatomic1:amd64 (7.1.0-7) ... Setting up perl-modules-5.24 (5.24.1-4) ... Setting up libperl5.24:amd64 (5.24.1-4) ... Setting up libcc1-0:amd64 (7.1.0-7) ... Setting up libcilkrts5:amd64 (7.1.0-7) ... Setting up libubsan0:amd64 (7.1.0-7) ... Setting up libtsan0:amd64 (7.1.0-7) ... Setting up gcc-6-base:amd64 (6.3.0-19) ... Setting up linux-libc-dev:amd64 (4.11.6-1) ... Setting up liblsan0:amd64 (7.1.0-7) ... Setting up perl (5.24.1-4) ... Setting up libmpx2:amd64 (7.1.0-7) ... Processing triggers for libc-bin (2.24-12) ... Setting up libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Setting up cpp-6 (6.3.0-19) ... Setting up libitm1:amd64 (7.1.0-7) ... Setting up libasan3:amd64 (6.3.0-19) ... Setting up libgcc-6-dev:amd64 (6.3.0-19) ... Setting up libidn2-0:amd64 (0.16-1) ... Setting up libstdc++-6-dev:amd64 (6.3.0-19) ... Setting up libgnutls30:amd64 (3.5.13-2) ... Setting up gcc-6 (6.3.0-19) ... Setting up g++-6 (6.3.0-19) ... Processing triggers for libc-bin (2.24-12) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/bioperl-run_1.7.1-3.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/bioperl-run-hZLCLI/bioperl-run-1.7.1' with '<>' I: NOTICE: Log filtering will replace 'build/bioperl-run-hZLCLI' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-V8rPeU/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-V8rPeU/apt_archive ./ InRelease Get:2 copy:/<>/resolver-V8rPeU/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-V8rPeU/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-V8rPeU/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-V8rPeU/apt_archive ./ Packages [428 B] Fetched 1734 B in 0s (0 B/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: dirmngr gnupg-l10n libffi6 libgnutls30 libhogweed4 libidn11 libidn2-0 libldap-2.4-2 libldap-common liblocale-gettext-perl libnettle6 libp11-kit0 libsasl2-2 libsasl2-modules libsasl2-modules-db libssl1.1 libtasn1-6 libunistring0 Use 'apt autoremove' to remove them. The following additional packages will be installed: fakeroot libfakeroot The following NEW packages will be installed: fakeroot libfakeroot sbuild-build-depends-core-dummy 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 132 kB of archives. After this operation, 374 kB of additional disk space will be used. Get:1 copy:/<>/resolver-V8rPeU/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [784 B] Get:2 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.21-3.1 [45.7 kB] Get:3 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.21-3.1 [85.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 kB in 0s (0 B/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... 14682 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.21-3.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.21-3.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.21-3.1_amd64.deb ... Unpacking fakeroot (1.21-3.1) ... Selecting previously unselected package sbuild-build-depends-core-dummy. Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.24-12) ... Setting up libfakeroot:amd64 (1.21-3.1) ... Setting up fakeroot (1.21-3.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.24-12) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 10), perl, libmodule-build-perl, bioperl, libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, libtest-most-perl, libarray-compare-perl, libtree-dagnode-perl, amap-align, bedtools, blast2, bowtie, bwa, clustalw, emboss, exonerate, hmmer, hyphy-mpi, infernal, kalign, maq, mafft, muscle, phylip, phyml, primer3, probcons, raxml, samtools, sim4, t-coffee, tigr-glimmer, wise, libwww-perl Filtered Build-Depends: debhelper (>= 10), perl, libmodule-build-perl, bioperl, libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, libtest-most-perl, libarray-compare-perl, libtree-dagnode-perl, amap-align, bedtools, blast2, bowtie, bwa, clustalw, emboss, exonerate, hmmer, hyphy-mpi, infernal, kalign, maq, mafft, muscle, phylip, phyml, primer3, probcons, raxml, samtools, sim4, t-coffee, tigr-glimmer, wise, libwww-perl dpkg-deb: building package 'sbuild-build-depends-bioperl-run-dummy' in '/<>/resolver-V8rPeU/apt_archive/sbuild-build-depends-bioperl-run-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-bioperl-run-dummy sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-V8rPeU/apt_archive ./ InRelease Get:2 copy:/<>/resolver-V8rPeU/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-V8rPeU/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-V8rPeU/apt_archive ./ Sources [717 B] Get:5 copy:/<>/resolver-V8rPeU/apt_archive ./ Packages [780 B] Fetched 2460 B in 0s (0 B/s) Reading package lists... Reading package lists... Install bioperl-run build dependencies (apt-based resolver) ----------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: dirmngr gnupg-l10n libidn11 liblocale-gettext-perl libsasl2-modules Use 'apt autoremove' to remove them. The following additional packages will be installed: amap-align autoconf automake autopoint autotools-dev bedtools beignet-opencl-icd bioperl blast2 bowtie bsdmainutils bwa ca-certificates clustalw debhelper dh-autoreconf dh-strip-nondeterminism emboss emboss-data emboss-lib exonerate file fontconfig-config fonts-dejavu-core gettext gettext-base groff-base hmmer hyphy-common hyphy-mpi infernal intltool-debian kalign libalgorithm-diff-perl libarchive-zip-perl libarray-compare-perl libbio-perl-perl libbsd0 libcapture-tiny-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libcroco3 libcurl3-gnutls libdata-stag-perl libdevel-globaldestruction-perl libdevel-stacktrace-perl libdivsufsort3 libdrm-intel1 libdrm2 libencode-locale-perl libexception-class-perl libexpat1 libexporter-tiny-perl libfabric1 libfile-listing-perl libfile-slurp-tiny-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgd3 libgfortran3 libglib2.0-0 libgssapi-krb5-2 libhmsbeagle1v5 libhpdf-2.2.1 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts2 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libhwloc-plugins libhwloc5 libibverbs1 libicu57 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 libltdl7 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1 libmariadbclient18 libmodule-build-perl libmodule-runtime-perl libmoo-perl libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi2 libparams-classify-perl libpciaccess0 libpipeline1 libpng16-16 libpq5 libpsl5 libpsm-infinipath1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib librdmacm1 librole-tiny-perl librtmp1 libsigsegv2 libssh2-1 libstrictures-perl libsub-exporter-progressive-perl libsub-quote-perl libsub-uplevel-perl libtbb2 libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-simple-perl libtest-warn-perl libtext-diff-perl libtiff5 libtimedate-perl libtool libtree-dagnode-perl libtype-tiny-perl liburi-perl libwebp6 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxfixes3 libxml-parser-perl libxml-twig-perl libxml2 libxpm4 m4 mafft man-db maq mime-support muscle mysql-common ncbi-blast+ ncbi-blast+-legacy ncbi-data netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssl perl-openssl-defaults phylip phyml po-debconf primer3 probcons python python-minimal python2.7 python2.7-minimal raxml samtools sim4 t-coffee tigr-glimmer ucf wise wise-data Suggested packages: autoconf-archive gnu-standards autoconf-doc filo bowtie-examples wamerican | wordlist whois vacation clustalx seaview dh-make emboss-doc emboss-test embassy gettext-doc libasprintf-dev libgettextpo-dev groff hmmer-doc libxml-sax-expatxs-perl libgd-tools krb5-doc krb5-user libdata-dump-perl libhwloc-contrib-plugins libcrypt-ssleay-perl libscalar-number-perl pciutils libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libtool-doc gfortran | fortran95-compiler gcj-jdk libauthen-ntlm-perl libunicode-map8-perl libunicode-string-perl xml-twig-tools m4-doc less www-browser gfortran phylip-doc libmail-box-perl ncbi-epcr probcons-extra python-doc python-tk python2.7-doc binfmt-support boxshade t-coffee-examples wise-doc Recommended packages: bioperl-run perl-doc libcache-cache-perl libbio-perl-run-perl libdbi-perl libgd-gd2-perl libapache-dbi-perl libxml-simple-perl libyaml-perl libace-perl liblist-moreutils-perl libset-scalar-perl dialign curl | wget | lynx-cur libalgorithm-diff-xs-perl bioperl-run | libbio-perl-run-perl libalgorithm-munkres-perl libbio-asn1-entrezgene-perl libclone-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-dom-xpath-perl libxml-sax-perl libxml-sax-writer-perl libxml-writer-perl libxml-libxml-perl perl-tk libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libxml-perl libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libhtml-format-perl krb5-locales libmodule-signature-perl libpod-readme-perl libsoftware-license-perl libclass-xsaccessor-perl libsub-name-perl publicsuffix libltdl-dev libdevel-lexalias-perl libtype-tiny-xs-perl libhtml-form-perl libhttp-daemon-perl libmailtools-perl libtext-iconv-perl libtie-ixhash-perl libxml-xpathengine-perl | libxml-xpath-perl xml-core lynx ruby libmail-sendmail-perl clustalo dialign-tx fsa mustang poa prank proda tm-align The following NEW packages will be installed: amap-align autoconf automake autopoint autotools-dev bedtools beignet-opencl-icd bioperl blast2 bowtie bsdmainutils bwa ca-certificates clustalw debhelper dh-autoreconf dh-strip-nondeterminism emboss emboss-data emboss-lib exonerate file fontconfig-config fonts-dejavu-core gettext gettext-base groff-base hmmer hyphy-common hyphy-mpi infernal intltool-debian kalign libalgorithm-diff-perl libarchive-zip-perl libarray-compare-perl libbio-perl-perl libbsd0 libcapture-tiny-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libcroco3 libcurl3-gnutls libdata-stag-perl libdevel-globaldestruction-perl libdevel-stacktrace-perl libdivsufsort3 libdrm-intel1 libdrm2 libencode-locale-perl libexception-class-perl libexpat1 libexporter-tiny-perl libfabric1 libfile-listing-perl libfile-slurp-tiny-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgd3 libgfortran3 libglib2.0-0 libgssapi-krb5-2 libhmsbeagle1v5 libhpdf-2.2.1 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts2 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libhwloc-plugins libhwloc5 libibverbs1 libicu57 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 libltdl7 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1 libmariadbclient18 libmodule-build-perl libmodule-runtime-perl libmoo-perl libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi2 libparams-classify-perl libpciaccess0 libpipeline1 libpng16-16 libpq5 libpsl5 libpsm-infinipath1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib librdmacm1 librole-tiny-perl librtmp1 libsigsegv2 libssh2-1 libstrictures-perl libsub-exporter-progressive-perl libsub-quote-perl libsub-uplevel-perl libtbb2 libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-simple-perl libtest-warn-perl libtext-diff-perl libtiff5 libtimedate-perl libtool libtree-dagnode-perl libtype-tiny-perl liburi-perl libwebp6 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxfixes3 libxml-parser-perl libxml-twig-perl libxml2 libxpm4 m4 mafft man-db maq mime-support muscle mysql-common ncbi-blast+ ncbi-blast+-legacy ncbi-data netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssl perl-openssl-defaults phylip phyml po-debconf primer3 probcons python python-minimal python2.7 python2.7-minimal raxml samtools sbuild-build-depends-bioperl-run-dummy sim4 t-coffee tigr-glimmer ucf wise wise-data 0 upgraded, 186 newly installed, 0 to remove and 0 not upgraded. Need to get 175 MB of archives. After this operation, 887 MB of additional disk space will be used. Get:1 copy:/<>/resolver-V8rPeU/apt_archive ./ sbuild-build-depends-bioperl-run-dummy 0.invalid.0 [1002 B] Get:2 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.22.3-9 [1160 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libbsd0 amd64 0.8.5-1 [89.6 kB] Get:4 http://localhost:3142/debian unstable/main amd64 bsdmainutils amd64 9.0.12+nmu1 [186 kB] Get:5 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.4.1-2 [27.6 kB] Get:6 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.7.6.1-2 [1044 kB] Get:7 http://localhost:3142/debian unstable/main amd64 libpython2.7-minimal amd64 2.7.13-2 [389 kB] Get:8 http://localhost:3142/debian unstable/main amd64 python2.7-minimal amd64 2.7.13-2 [1383 kB] Get:9 http://localhost:3142/debian unstable/main amd64 python-minimal amd64 2.7.13-2 [40.5 kB] Get:10 http://localhost:3142/debian unstable/main amd64 mime-support all 3.60 [36.7 kB] Get:11 http://localhost:3142/debian unstable/main amd64 libexpat1 amd64 2.2.1-2 [85.5 kB] Get:12 http://localhost:3142/debian unstable/main amd64 libpython2.7-stdlib amd64 2.7.13-2 [1895 kB] Get:13 http://localhost:3142/debian unstable/main amd64 python2.7 amd64 2.7.13-2 [285 kB] Get:14 http://localhost:3142/debian unstable/main amd64 libpython-stdlib amd64 2.7.13-2 [20.0 kB] Get:15 http://localhost:3142/debian unstable/main amd64 python amd64 2.7.13-2 [154 kB] Get:16 http://localhost:3142/debian unstable/main amd64 libxau6 amd64 1:1.0.8-1 [20.7 kB] Get:17 http://localhost:3142/debian unstable/main amd64 netbase all 5.4 [19.1 kB] Get:18 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.30-1 [222 kB] Get:19 http://localhost:3142/debian unstable/main amd64 libmagic1 amd64 1:5.30-1 [111 kB] Get:20 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.30-1 [63.9 kB] Get:21 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.19.8.1-2 [121 kB] Get:22 http://localhost:3142/debian unstable/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:23 http://localhost:3142/debian unstable/main amd64 libkrb5support0 amd64 1.15-1 [61.7 kB] Get:24 http://localhost:3142/debian unstable/main amd64 libk5crypto3 amd64 1.15-1 [119 kB] Get:25 http://localhost:3142/debian unstable/main amd64 libkrb5-3 amd64 1.15-1 [311 kB] Get:26 http://localhost:3142/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.15-1 [154 kB] Get:27 http://localhost:3142/debian unstable/main amd64 libicu57 amd64 57.1-6 [7701 kB] Get:28 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-2.2 [919 kB] Get:29 http://localhost:3142/debian unstable/main amd64 ucf all 3.0036 [70.2 kB] Get:30 http://localhost:3142/debian unstable/main amd64 amap-align amd64 2.2-6 [129 kB] Get:31 http://localhost:3142/debian unstable/main amd64 libsigsegv2 amd64 2.10-5 [28.9 kB] Get:32 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.18-1 [202 kB] Get:33 http://localhost:3142/debian unstable/main amd64 autoconf all 2.69-10 [338 kB] Get:34 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20161112.1 [73.4 kB] Get:35 http://localhost:3142/debian unstable/main amd64 automake all 1:1.15.1-1 [735 kB] Get:36 http://localhost:3142/debian unstable/main amd64 autopoint all 0.19.8.1-2 [433 kB] Get:37 http://localhost:3142/debian unstable/main amd64 bedtools amd64 2.26.0+dfsg-3 [584 kB] Get:38 http://localhost:3142/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:39 http://localhost:3142/debian unstable/main amd64 libdata-stag-perl all 0.14-2 [448 kB] Get:40 http://localhost:3142/debian unstable/main amd64 libbio-perl-perl all 1.7.1-2 [4605 kB] Get:41 http://localhost:3142/debian unstable/main amd64 bioperl all 1.7.1-2 [422 kB] Get:42 http://localhost:3142/debian unstable/main amd64 ncbi-data all 6.1.20170106-2 [3692 kB] Get:43 http://localhost:3142/debian unstable/main amd64 ncbi-blast+ amd64 2.6.0-1 [9591 kB] Get:44 http://localhost:3142/debian unstable/main amd64 ncbi-blast+-legacy all 2.6.0-1 [9604 B] Get:45 http://localhost:3142/debian unstable/main amd64 blast2 all 1:2.6.0-1 [9084 B] Get:46 http://localhost:3142/debian unstable/main amd64 bwa amd64 0.7.15-3 [193 kB] Get:47 http://localhost:3142/debian unstable/main amd64 openssl amd64 1.1.0f-3 [725 kB] Get:48 http://localhost:3142/debian unstable/main amd64 ca-certificates all 20161130+nmu1 [196 kB] Get:49 http://localhost:3142/debian unstable/main amd64 clustalw amd64 2.1+lgpl-5 [286 kB] Get:50 http://localhost:3142/debian unstable/main amd64 libtool all 2.4.6-2 [545 kB] Get:51 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 14 [15.9 kB] Get:52 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.59-1 [95.5 kB] Get:53 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.035-2 [17.0 kB] Get:54 http://localhost:3142/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:55 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 0.035-2 [10.7 kB] Get:56 http://localhost:3142/debian unstable/main amd64 libglib2.0-0 amd64 2.52.3-1 [2742 kB] Get:57 http://localhost:3142/debian unstable/main amd64 libcroco3 amd64 0.6.11-3 [143 kB] Get:58 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.19.8.1-2 [1495 kB] Get:59 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:60 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.20 [247 kB] Get:61 http://localhost:3142/debian unstable/main amd64 debhelper all 10.2.5 [961 kB] Get:62 http://localhost:3142/debian unstable/main amd64 libpng16-16 amd64 1.6.29-3 [281 kB] Get:63 http://localhost:3142/debian unstable/main amd64 libfreetype6 amd64 2.6.3-3.2 [438 kB] Get:64 http://localhost:3142/debian unstable/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get:65 http://localhost:3142/debian unstable/main amd64 fontconfig-config all 2.12.3-0.1 [303 kB] Get:66 http://localhost:3142/debian unstable/main amd64 libfontconfig1 amd64 2.12.3-0.1 [366 kB] Get:67 http://localhost:3142/debian unstable/main amd64 libjpeg62-turbo amd64 1:1.5.1-2 [134 kB] Get:68 http://localhost:3142/debian unstable/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:69 http://localhost:3142/debian unstable/main amd64 libtiff5 amd64 4.0.8-2 [237 kB] Get:70 http://localhost:3142/debian unstable/main amd64 libwebp6 amd64 0.5.2-1 [235 kB] Get:71 http://localhost:3142/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:72 http://localhost:3142/debian unstable/main amd64 libxcb1 amd64 1.12-1 [133 kB] Get:73 http://localhost:3142/debian unstable/main amd64 libx11-data all 2:1.6.4-3 [290 kB] Get:74 http://localhost:3142/debian unstable/main amd64 libx11-6 amd64 2:1.6.4-3 [747 kB] Get:75 http://localhost:3142/debian unstable/main amd64 libxpm4 amd64 1:3.5.12-1 [49.1 kB] Get:76 http://localhost:3142/debian unstable/main amd64 libgd3 amd64 2.2.4-2 [132 kB] Get:77 http://localhost:3142/debian unstable/main amd64 libhpdf-2.2.1 amd64 2.2.1-1.1+b1 [319 kB] Get:78 http://localhost:3142/debian unstable/main amd64 mysql-common all 5.8+1.0.2 [5608 B] Get:79 http://localhost:3142/debian unstable/main amd64 libmariadbclient18 amd64 10.1.24-6 [775 kB] Get:80 http://localhost:3142/debian unstable/main amd64 libpq5 amd64 9.6.3-3 [129 kB] Get:81 http://localhost:3142/debian unstable/main amd64 emboss-lib amd64 6.6.0+dfsg-6 [2773 kB] Get:82 http://localhost:3142/debian unstable/main amd64 emboss-data all 6.6.0+dfsg-6 [61.1 MB] Get:83 http://localhost:3142/debian unstable/main amd64 emboss amd64 6.6.0+dfsg-6 [1058 kB] Get:84 http://localhost:3142/debian unstable/main amd64 exonerate amd64 2.4.0-2 [1476 kB] Get:85 http://localhost:3142/debian unstable/main amd64 libdivsufsort3 amd64 2.0.1-2 [46.3 kB] Get:86 http://localhost:3142/debian unstable/main amd64 hmmer amd64 3.1b2+dfsg-5 [1122 kB] Get:87 http://localhost:3142/debian unstable/main amd64 hyphy-common all 2.2.7+dfsg-1 [619 kB] Get:88 http://localhost:3142/debian unstable/main amd64 libnghttp2-14 amd64 1.23.1-1 [80.1 kB] Get:89 http://localhost:3142/debian unstable/main amd64 libpsl5 amd64 0.17.0-4 [41.8 kB] Get:90 http://localhost:3142/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:91 http://localhost:3142/debian unstable/main amd64 libssh2-1 amd64 1.8.0-1 [138 kB] Get:92 http://localhost:3142/debian unstable/main amd64 libcurl3-gnutls amd64 7.52.1-5 [289 kB] Get:93 http://localhost:3142/debian unstable/main amd64 libnl-3-200 amd64 3.2.27-2 [61.5 kB] Get:94 http://localhost:3142/debian unstable/main amd64 libnl-route-3-200 amd64 3.2.27-2 [136 kB] Get:95 http://localhost:3142/debian unstable/main amd64 libibverbs1 amd64 1.2.1-2 [39.3 kB] Get:96 http://localhost:3142/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+19.g67c0807.open-3 [169 kB] Get:97 http://localhost:3142/debian unstable/main amd64 librdmacm1 amd64 1.1.0-2 [49.4 kB] Get:98 http://localhost:3142/debian unstable/main amd64 libfabric1 amd64 1.4.0-1 [259 kB] Get:99 http://localhost:3142/debian unstable/main amd64 libgfortran3 amd64 6.3.0-19 [265 kB] Get:100 http://localhost:3142/debian unstable/main amd64 libltdl7 amd64 2.4.6-2 [389 kB] Get:101 http://localhost:3142/debian unstable/main amd64 libnuma1 amd64 2.0.11-2.1 [33.3 kB] Get:102 http://localhost:3142/debian unstable/main amd64 libhwloc5 amd64 1.11.5-1 [105 kB] Get:103 http://localhost:3142/debian unstable/main amd64 libpciaccess0 amd64 0.13.4-1+b2 [50.0 kB] Get:104 http://localhost:3142/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.2.11-1 [36.8 kB] Get:105 http://localhost:3142/debian unstable/main amd64 libhwloc-plugins amd64 1.11.5-1 [16.1 kB] Get:106 http://localhost:3142/debian unstable/main amd64 libopenmpi2 amd64 2.1.1-6 [2062 kB] Get:107 http://localhost:3142/debian unstable/main amd64 hyphy-mpi amd64 2.2.7+dfsg-1+b2 [920 kB] Get:108 http://localhost:3142/debian unstable/main amd64 infernal amd64 1.1.2-1 [22.0 MB] Get:109 http://localhost:3142/debian unstable/main amd64 kalign amd64 1:2.03+20110620-3 [99.7 kB] Get:110 http://localhost:3142/debian unstable/main amd64 libalgorithm-diff-perl all 1.19.03-1 [48.7 kB] Get:111 http://localhost:3142/debian unstable/main amd64 libclass-method-modifiers-perl all 2.12-1 [18.6 kB] Get:112 http://localhost:3142/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:113 http://localhost:3142/debian unstable/main amd64 libdevel-globaldestruction-perl all 0.14-1 [8084 B] Get:114 http://localhost:3142/debian unstable/main amd64 libparams-classify-perl amd64 0.013-8 [24.4 kB] Get:115 http://localhost:3142/debian unstable/main amd64 libmodule-runtime-perl all 0.014-2 [18.0 kB] Get:116 http://localhost:3142/debian unstable/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB] Get:117 http://localhost:3142/debian unstable/main amd64 librole-tiny-perl all 2.000005-1 [19.0 kB] Get:118 http://localhost:3142/debian unstable/main amd64 libstrictures-perl all 2.000003-1 [18.1 kB] Get:119 http://localhost:3142/debian unstable/main amd64 libsub-quote-perl all 2.004000-1 [15.8 kB] Get:120 http://localhost:3142/debian unstable/main amd64 libmoo-perl all 2.003002-1 [57.0 kB] Get:121 http://localhost:3142/debian unstable/main amd64 libexporter-tiny-perl all 0.042-1 [32.4 kB] Get:122 http://localhost:3142/debian unstable/main amd64 libtype-tiny-perl all 1.000006-1 [242 kB] Get:123 http://localhost:3142/debian unstable/main amd64 libarray-compare-perl all 3.0.0-1 [14.0 kB] Get:124 http://localhost:3142/debian unstable/main amd64 libcapture-tiny-perl all 0.46-1 [25.7 kB] Get:125 http://localhost:3142/debian unstable/main amd64 libclass-data-inheritable-perl all 0.08-2 [9296 B] Get:126 http://localhost:3142/debian unstable/main amd64 libdevel-stacktrace-perl all 2.0200-1 [27.3 kB] Get:127 http://localhost:3142/debian unstable/main amd64 libdrm2 amd64 2.4.81-2 [38.4 kB] Get:128 http://localhost:3142/debian unstable/main amd64 libdrm-intel1 amd64 2.4.81-2 [69.5 kB] Get:129 http://localhost:3142/debian unstable/main amd64 libencode-locale-perl all 1.05-1 [13.7 kB] Get:130 http://localhost:3142/debian unstable/main amd64 libexception-class-perl all 1.42-1 [31.5 kB] Get:131 http://localhost:3142/debian unstable/main amd64 libhttp-date-perl all 6.02-1 [10.7 kB] Get:132 http://localhost:3142/debian unstable/main amd64 libfile-listing-perl all 6.04-1 [10.3 kB] Get:133 http://localhost:3142/debian unstable/main amd64 libfile-slurp-tiny-perl all 0.003-1 [6852 B] Get:134 http://localhost:3142/debian unstable/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:135 http://localhost:3142/debian unstable/main amd64 libxfixes3 amd64 1:5.0.3-1 [21.9 kB] Get:136 http://localhost:3142/debian unstable/main amd64 beignet-opencl-icd amd64 1.3.0-4 [12.8 MB] Get:137 http://localhost:3142/debian unstable/main amd64 libhmsbeagle1v5 amd64 2.1.2+20160831-5 [116 kB] Get:138 http://localhost:3142/debian unstable/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get:139 http://localhost:3142/debian unstable/main amd64 liburi-perl all 1.71-1 [88.6 kB] Get:140 http://localhost:3142/debian unstable/main amd64 libhtml-parser-perl amd64 3.72-3 [104 kB] Get:141 http://localhost:3142/debian unstable/main amd64 libhtml-tree-perl all 5.03-2 [210 kB] Get:142 http://localhost:3142/debian unstable/main amd64 libhts2 amd64 1.4.1-2 [294 kB] Get:143 http://localhost:3142/debian unstable/main amd64 libio-html-perl all 1.001-1 [17.6 kB] Get:144 http://localhost:3142/debian unstable/main amd64 liblwp-mediatypes-perl all 6.02-1 [22.1 kB] Get:145 http://localhost:3142/debian unstable/main amd64 libhttp-message-perl all 6.11-1 [75.9 kB] Get:146 http://localhost:3142/debian unstable/main amd64 libhttp-cookies-perl all 6.01-1 [17.4 kB] Get:147 http://localhost:3142/debian unstable/main amd64 libhttp-negotiate-perl all 6.00-2 [13.6 kB] Get:148 http://localhost:3142/debian unstable/main amd64 libio-pty-perl amd64 1:1.08-1.1+b2 [33.6 kB] Get:149 http://localhost:3142/debian unstable/main amd64 perl-openssl-defaults amd64 3 [6782 B] Get:150 http://localhost:3142/debian unstable/main amd64 libnet-ssleay-perl amd64 1.80-1 [285 kB] Get:151 http://localhost:3142/debian unstable/main amd64 libio-socket-ssl-perl all 2.049-1 [201 kB] Get:152 http://localhost:3142/debian unstable/main amd64 libipc-run-perl all 0.94-1 [102 kB] Get:153 http://localhost:3142/debian unstable/main amd64 libnet-http-perl all 6.12-1 [23.8 kB] Get:154 http://localhost:3142/debian unstable/main amd64 libwww-robotrules-perl all 6.01-1 [14.3 kB] Get:155 http://localhost:3142/debian unstable/main amd64 libwww-perl all 6.15-1 [195 kB] Get:156 http://localhost:3142/debian unstable/main amd64 liblwp-protocol-https-perl all 6.06-2 [9582 B] Get:157 http://localhost:3142/debian unstable/main amd64 libmodule-build-perl all 0.422400-1 [259 kB] Get:158 http://localhost:3142/debian unstable/main amd64 libsub-uplevel-perl all 0.2800-1 [16.3 kB] Get:159 http://localhost:3142/debian unstable/main amd64 libtest-deep-perl all 1.126-1 [48.4 kB] Get:160 http://localhost:3142/debian unstable/main amd64 libtext-diff-perl all 1.44-1 [27.4 kB] Get:161 http://localhost:3142/debian unstable/main amd64 libtest-differences-perl all 0.64-1 [18.0 kB] Get:162 http://localhost:3142/debian unstable/main amd64 libtest-exception-perl all 0.43-1 [18.7 kB] Get:163 http://localhost:3142/debian unstable/main amd64 libtest-warn-perl all 0.32-1 [15.1 kB] Get:164 http://localhost:3142/debian unstable/main amd64 libtest-simple-perl all 1.302075-1 [298 kB] Get:165 http://localhost:3142/debian unstable/main amd64 libtest-most-perl all 0.35-1 [24.5 kB] Get:166 http://localhost:3142/debian unstable/main amd64 libtree-dagnode-perl all 1.29-1 [60.6 kB] Get:167 http://localhost:3142/debian unstable/main amd64 libxml-parser-perl amd64 2.44-2+b1 [212 kB] Get:168 http://localhost:3142/debian unstable/main amd64 libxml-twig-perl all 1:3.50-1 [179 kB] Get:169 http://localhost:3142/debian unstable/main amd64 mafft amd64 7.307-1 [889 kB] Get:170 http://localhost:3142/debian unstable/main amd64 maq amd64 0.7.1-7 [311 kB] Get:171 http://localhost:3142/debian unstable/main amd64 muscle amd64 1:3.8.31+dfsg-2 [151 kB] Get:172 http://localhost:3142/debian unstable/main amd64 phylip amd64 1:3.696+dfsg-5 [942 kB] Get:173 http://localhost:3142/debian unstable/main amd64 openmpi-common all 2.1.1-6 [154 kB] Get:174 http://localhost:3142/debian unstable/main amd64 openmpi-bin amd64 2.1.1-6 [193 kB] Get:175 http://localhost:3142/debian unstable/main amd64 phyml amd64 3:3.2.0+dfsg-7+b1 [1298 kB] Get:176 http://localhost:3142/debian unstable/main amd64 primer3 amd64 2.3.7-3 [173 kB] Get:177 http://localhost:3142/debian unstable/main amd64 probcons amd64 1.12-11 [107 kB] Get:178 http://localhost:3142/debian unstable/main amd64 raxml amd64 8.2.10+dfsg-1 [1280 kB] Get:179 http://localhost:3142/debian unstable/main amd64 samtools amd64 1.4.1-1 [254 kB] Get:180 http://localhost:3142/debian unstable/main amd64 sim4 amd64 0.0.20121010-4 [396 kB] Get:181 http://localhost:3142/debian unstable/main amd64 t-coffee amd64 11.00.8cbe486-5 [1918 kB] Get:182 http://localhost:3142/debian unstable/main amd64 tigr-glimmer amd64 3.02b-1 [283 kB] Get:183 http://localhost:3142/debian unstable/main amd64 wise-data all 2.4.1-19 [108 kB] Get:184 http://localhost:3142/debian unstable/main amd64 wise amd64 2.4.1-19 [993 kB] Get:185 http://localhost:3142/debian unstable/main amd64 libtbb2 amd64 4.3~20150611-2 [136 kB] Get:186 http://localhost:3142/debian unstable/main amd64 bowtie amd64 1.2.0+dfsg-1 [1607 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 175 MB in 2s (85.0 MB/s) Selecting previously unselected package groff-base. (Reading database ... 14732 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-9_amd64.deb ... Unpacking groff-base (1.22.3-9) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../01-libbsd0_0.8.5-1_amd64.deb ... Unpacking libbsd0:amd64 (0.8.5-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../02-bsdmainutils_9.0.12+nmu1_amd64.deb ... Unpacking bsdmainutils (9.0.12+nmu1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.4.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.7.6.1-2_amd64.deb ... Unpacking man-db (2.7.6.1-2) ... Selecting previously unselected package libpython2.7-minimal:amd64. Preparing to unpack .../05-libpython2.7-minimal_2.7.13-2_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.13-2) ... 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Unpacking bedtools (2.26.0+dfsg-3) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../023-libio-string-perl_1.08-3_all.deb ... Unpacking libio-string-perl (1.08-3) ... Selecting previously unselected package libdata-stag-perl. Preparing to unpack .../024-libdata-stag-perl_0.14-2_all.deb ... Unpacking libdata-stag-perl (0.14-2) ... Selecting previously unselected package libbio-perl-perl. Preparing to unpack .../025-libbio-perl-perl_1.7.1-2_all.deb ... Unpacking libbio-perl-perl (1.7.1-2) ... Selecting previously unselected package bioperl. Preparing to unpack .../026-bioperl_1.7.1-2_all.deb ... Unpacking bioperl (1.7.1-2) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../027-ncbi-data_6.1.20170106-2_all.deb ... Unpacking ncbi-data (6.1.20170106-2) ... Selecting previously unselected package ncbi-blast+. Preparing to unpack .../028-ncbi-blast+_2.6.0-1_amd64.deb ... Unpacking ncbi-blast+ (2.6.0-1) ... 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Selecting previously unselected package probcons. Preparing to unpack .../162-probcons_1.12-11_amd64.deb ... Unpacking probcons (1.12-11) ... Selecting previously unselected package raxml. Preparing to unpack .../163-raxml_8.2.10+dfsg-1_amd64.deb ... Unpacking raxml (8.2.10+dfsg-1) ... Selecting previously unselected package samtools. Preparing to unpack .../164-samtools_1.4.1-1_amd64.deb ... Unpacking samtools (1.4.1-1) ... Selecting previously unselected package sim4. Preparing to unpack .../165-sim4_0.0.20121010-4_amd64.deb ... Unpacking sim4 (0.0.20121010-4) ... Selecting previously unselected package t-coffee. Preparing to unpack .../166-t-coffee_11.00.8cbe486-5_amd64.deb ... Unpacking t-coffee (11.00.8cbe486-5) ... Selecting previously unselected package tigr-glimmer. Preparing to unpack .../167-tigr-glimmer_3.02b-1_amd64.deb ... Unpacking tigr-glimmer (3.02b-1) ... Selecting previously unselected package wise-data. Preparing to unpack .../168-wise-data_2.4.1-19_all.deb ... Unpacking wise-data (2.4.1-19) ... Selecting previously unselected package wise. Preparing to unpack .../169-wise_2.4.1-19_amd64.deb ... Unpacking wise (2.4.1-19) ... Selecting previously unselected package libtbb2:amd64. Preparing to unpack .../170-libtbb2_4.3~20150611-2_amd64.deb ... Unpacking libtbb2:amd64 (4.3~20150611-2) ... Selecting previously unselected package bowtie. Preparing to unpack .../171-bowtie_1.2.0+dfsg-1_amd64.deb ... Unpacking bowtie (1.2.0+dfsg-1) ... Selecting previously unselected package sbuild-build-depends-bioperl-run-dummy. Preparing to unpack .../172-sbuild-build-depends-bioperl-run-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-bioperl-run-dummy (0.invalid.0) ... Setting up tigr-glimmer (3.02b-1) ... Setting up phylip (1:3.696+dfsg-5) ... Setting up libhtml-tagset-perl (3.20-3) ... Setting up mafft (7.307-1) ... Setting up libtest-deep-perl (1.126-1) ... Setting up kalign (1:2.03+20110620-3) ... Setting up libsub-exporter-progressive-perl (0.001013-1) ... Setting up libfile-slurp-tiny-perl (0.003-1) ... Setting up libexpat1:amd64 (2.2.1-2) ... Setting up libclass-method-modifiers-perl (2.12-1) ... Setting up bwa (0.7.15-3) ... Setting up maq (0.7.1-7) ... Setting up libjpeg62-turbo:amd64 (1:1.5.1-2) ... Setting up libclass-data-inheritable-perl (0.08-2) ... Setting up libarchive-zip-perl (1.59-1) ... Setting up libdivsufsort3:amd64 (2.0.1-2) ... Setting up libnghttp2-14:amd64 (1.23.1-1) ... Setting up bedtools (2.26.0+dfsg-3) ... Setting up mime-support (3.60) ... Setting up libio-pty-perl (1:1.08-1.1+b2) ... Setting up libencode-locale-perl (1.05-1) ... Setting up libpng16-16:amd64 (1.6.29-3) ... Setting up t-coffee (11.00.8cbe486-5) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libsigsegv2:amd64 (2.10-5) ... Setting up librole-tiny-perl (2.000005-1) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up perl-openssl-defaults:amd64 (3) ... Setting up libpsl5:amd64 (0.17.0-4) ... Setting up libnuma1:amd64 (2.0.11-2.1) ... Setting up libtbb2:amd64 (4.3~20150611-2) ... Setting up libdevel-stacktrace-perl (2.0200-1) ... Setting up libgfortran3:amd64 (6.3.0-19) ... Setting up groff-base (1.22.3-9) ... Setting up libglib2.0-0:amd64 (2.52.3-1) ... No schema files found: doing nothing. Setting up mysql-common (5.8+1.0.2) ... update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libcapture-tiny-perl (0.46-1) ... Setting up libio-html-perl (1.001-1) ... Setting up libexporter-tiny-perl (0.042-1) ... Setting up infernal (1.1.2-1) ... Setting up probcons (1.12-11) ... Setting up exonerate (2.4.0-2) ... Setting up libtiff5:amd64 (4.0.8-2) ... Setting up gettext-base (0.19.8.1-2) ... Setting up libpipeline1:amd64 (1.4.1-2) ... Setting up libmariadbclient18:amd64 (10.1.24-6) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Setting up m4 (1.4.18-1) ... Setting up libtest-simple-perl (1.302075-1) ... Setting up libicu57:amd64 (57.1-6) ... Setting up libbsd0:amd64 (0.8.5-1) ... Setting up ucf (3.0036) ... Setting up libxml2:amd64 (2.9.4+dfsg1-2.2) ... Setting up libfreetype6:amd64 (2.6.3-3.2) ... Setting up libmagic-mgc (1:5.30-1) ... Setting up libdrm2:amd64 (2.4.81-2) ... Setting up libmagic1:amd64 (1:5.30-1) ... Setting up libcroco3:amd64 (0.6.11-3) ... Setting up sim4 (0.0.20121010-4) ... Setting up libpsm-infinipath1 (3.3+19.g67c0807.open-3) ... Setting up raxml (8.2.10+dfsg-1) ... Setting up amap-align (2.2-6) ... Setting up libstrictures-perl (2.000003-1) ... Setting up ncbi-data (6.1.20170106-2) ... Setting up hmmer (3.1b2+dfsg-5) ... Setting up libssh2-1:amd64 (1.8.0-1) ... Setting up liblwp-mediatypes-perl (6.02-1) ... Setting up openmpi-common (2.1.1-6) ... Processing triggers for libc-bin (2.24-12) ... Setting up wise-data (2.4.1-19) ... Setting up autotools-dev (20161112.1) ... Setting up liburi-perl (1.71-1) ... Setting up primer3 (2.3.7-3) ... Setting up wise (2.4.1-19) ... Setting up libltdl7:amd64 (2.4.6-2) ... Setting up libhtml-parser-perl (3.72-3) ... Setting up libipc-run-perl (0.94-1) ... Setting up openssl (1.1.0f-3) ... Setting up libdevel-globaldestruction-perl (0.14-1) ... Setting up libio-string-perl (1.08-3) ... Setting up libalgorithm-diff-perl (1.19.03-1) ... Setting up emboss-data (6.6.0+dfsg-6) ... Setting up libpciaccess0:amd64 (0.13.4-1+b2) ... Setting up libnet-http-perl (6.12-1) ... Setting up muscle (1:3.8.31+dfsg-2) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up ocl-icd-libopencl1:amd64 (2.2.11-1) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up bsdmainutils (9.0.12+nmu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libmodule-build-perl (0.422400-1) ... Setting up libnl-3-200:amd64 (3.2.27-2) ... Setting up libsub-uplevel-perl (0.2800-1) ... Setting up clustalw (2.1+lgpl-5) ... Setting up ca-certificates (20161130+nmu1) ... Updating certificates in /etc/ssl/certs... 166 added, 0 removed; done. Setting up libparams-classify-perl (0.013-8) ... Setting up libsub-quote-perl (2.004000-1) ... Setting up libtree-dagnode-perl (1.29-1) ... Setting up libwww-robotrules-perl (6.01-1) ... Setting up libx11-data (2:1.6.4-3) ... Setting up libpython2.7-stdlib:amd64 (2.7.13-2) ... Setting up libdata-stag-perl (0.14-2) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up autopoint (0.19.8.1-2) ... Setting up hyphy-common (2.2.7+dfsg-1) ... Setting up libtest-warn-perl (0.32-1) ... Setting up netbase (5.4) ... Setting up libwebp6:amd64 (0.5.2-1) ... Setting up libfile-stripnondeterminism-perl (0.035-2) ... Setting up libhpdf-2.2.1 (2.2.1-1.1+b1) ... Setting up fontconfig-config (2.12.3-0.1) ... Setting up libhttp-date-perl (6.02-1) ... Setting up libbio-perl-perl (1.7.1-2) ... Setting up libexception-class-perl (1.42-1) ... Setting up gettext (0.19.8.1-2) ... Setting up libnet-ssleay-perl (1.80-1) ... Setting up libtype-tiny-perl (1.000006-1) ... Setting up libmodule-runtime-perl (0.014-2) ... Setting up libtext-diff-perl (1.44-1) ... Setting up libtest-exception-perl (0.43-1) ... Setting up python2.7 (2.7.13-2) ... Setting up libnl-route-3-200:amd64 (3.2.27-2) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.30-1) ... Setting up libhwloc5:amd64 (1.11.5-1) ... Setting up libkrb5support0:amd64 (1.15-1) ... Setting up libio-socket-ssl-perl (2.049-1) ... Setting up libhtml-tree-perl (5.03-2) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up libhwloc-plugins (1.11.5-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libdrm-intel1:amd64 (2.4.81-2) ... Setting up automake (1:1.15.1-1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up bioperl (1.7.1-2) ... Setting up libfile-listing-perl (6.04-1) ... Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libhttp-message-perl (6.11-1) ... Setting up libxcb1:amd64 (1.12-1) ... Setting up python (2.7.13-2) ... Setting up libhttp-negotiate-perl (6.00-2) ... Setting up libtool (2.4.6-2) ... Setting up libibverbs1 (1.2.1-2) ... Setting up libfontconfig1:amd64 (2.12.3-0.1) ... Setting up libk5crypto3:amd64 (1.15-1) ... Setting up bowtie (1.2.0+dfsg-1) ... Setting up libtest-differences-perl (0.64-1) ... Setting up libimport-into-perl (1.002005-1) ... Setting up po-debconf (1.0.20) ... Setting up libhttp-cookies-perl (6.01-1) ... Setting up ncbi-blast+ (2.6.0-1) ... Setting up libx11-6:amd64 (2:1.6.4-3) ... Setting up librdmacm1 (1.1.0-2) ... Setting up libxpm4:amd64 (1:3.5.12-1) ... Setting up libmoo-perl (2.003002-1) ... Setting up libkrb5-3:amd64 (1.15-1) ... Setting up libtest-most-perl (0.35-1) ... Setting up ncbi-blast+-legacy (2.6.0-1) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libxfixes3:amd64 (1:5.0.3-1) ... Setting up libfabric1 (1.4.0-1) ... Setting up blast2 (1:2.6.0-1) ... Setting up libarray-compare-perl (3.0.0-1) ... Setting up libgd3:amd64 (2.2.4-2) ... Setting up libgssapi-krb5-2:amd64 (1.15-1) ... Setting up libpq5:amd64 (9.6.3-3) ... Setting up emboss-lib (6.6.0+dfsg-6) ... Setting up libopenmpi2:amd64 (2.1.1-6) ... Setting up beignet-opencl-icd:amd64 (1.3.0-4) ... Setting up libcurl3-gnutls:amd64 (7.52.1-5) ... Setting up libhmsbeagle1v5 (2.1.2+20160831-5) ... Setting up openmpi-bin (2.1.1-6) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode Setting up emboss (6.6.0+dfsg-6) ... Setting up phyml (3:3.2.0+dfsg-7+b1) ... Setting up libhts2:amd64 (1.4.1-2) ... Setting up hyphy-mpi (2.2.7+dfsg-1+b2) ... Setting up samtools (1.4.1-1) ... Setting up dh-autoreconf (14) ... Setting up liblwp-protocol-https-perl (6.06-2) ... Setting up dh-strip-nondeterminism (0.035-2) ... Setting up libwww-perl (6.15-1) ... Setting up debhelper (10.2.5) ... Setting up libxml-parser-perl (2.44-2+b1) ... Setting up libxml-twig-perl (1:3.50-1) ... Setting up sbuild-build-depends-bioperl-run-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.24-12) ... Processing triggers for ca-certificates (20161130+nmu1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-3-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.28-6 dpkg-dev_1.18.24 g++-5_5.4.1-11 g++-6_6.3.0-19 gcc-5_5.4.1-11 gcc-6_6.3.0-19 libc6-dev_2.24-12 libstdc++-5-dev_5.4.1-11 libstdc++-6-dev_6.3.0-19 libstdc++6_7.1.0-7 linux-libc-dev_4.11.6-1 Package versions: adduser_3.115 amap-align_2.2-6 apt_1.4.6 autoconf_2.69-10 automake_1:1.15.1-1 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_9.9 base-passwd_3.5.43 bash_4.4-5 bedtools_2.26.0+dfsg-3 beignet-opencl-icd_1.3.0-4 binutils_2.28-6 bioperl_1.7.1-2 blast2_1:2.6.0-1 bowtie_1.2.0+dfsg-1 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-1 build-essential_12.3 bwa_0.7.15-3 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 clustalw_2.1+lgpl-5 coreutils_8.26-3 cpp_4:6.3.0-4 cpp-5_5.4.1-11 cpp-6_6.3.0-19 dash_0.5.8-2.4 debconf_1.5.61 debhelper_10.2.5 debian-archive-keyring_2017.5 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.035-2 diffutils_1:3.5-3 dirmngr_2.1.18-8 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 emboss_6.6.0+dfsg-6 emboss-data_6.6.0+dfsg-6 emboss-lib_6.6.0+dfsg-6 exonerate_2.4.0-2 fakeroot_1.21-3.1 file_1:5.30-1 findutils_4.6.0+git+20170606-2 fontconfig-config_2.12.3-0.1 fonts-dejavu-core_2.37-1 g++_4:6.3.0-4 g++-5_5.4.1-11 g++-6_6.3.0-19 gcc_4:6.3.0-4 gcc-4.9-base_4.9.3-14 gcc-5_5.4.1-11 gcc-5-base_5.4.1-11 gcc-6_6.3.0-19 gcc-6-base_6.3.0-19 gcc-7-base_7.1.0-7 gettext_0.19.8.1-2 gettext-base_0.19.8.1-2 gnupg_2.1.18-8 gnupg-agent_2.1.18-8 gnupg-l10n_2.1.18-8 gpgv_2.1.18-8 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5+b1 hmmer_3.1b2+dfsg-5 hostname_3.18+b1 hyphy-common_2.2.7+dfsg-1 hyphy-mpi_2.2.7+dfsg-1+b2 infernal_1.1.2-1 init-system-helpers_1.48 initscripts_2.88dsf-59.9 insserv_1.14.0-5.4+b1 intltool-debian_0.35.0+20060710.4 kalign_1:2.03+20110620-3 libacl1_2.2.52-3+b1 libalgorithm-diff-perl_1.19.03-1 libapt-pkg5.0_1.4.6 libarchive-zip-perl_1.59-1 libarray-compare-perl_3.0.0-1 libasan2_5.4.1-11 libasan3_6.3.0-19 libassuan0_2.4.3-2 libatomic1_7.1.0-7 libattr1_1:2.4.47-2+b2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1 libbio-perl-perl_1.7.1-2 libblkid1_2.29.2-1 libbsd0_0.8.5-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-12 libc-dev-bin_2.24-12 libc6_2.24-12 libc6-dev_2.24-12 libcap-ng0_0.7.7-3+b1 libcapture-tiny-perl_0.46-1 libcc1-0_7.1.0-7 libcilkrts5_7.1.0-7 libclass-data-inheritable-perl_0.08-2 libclass-method-modifiers-perl_2.12-1 libcomerr2_1.43.4-2 libcroco3_0.6.11-3 libcurl3-gnutls_7.52.1-5 libdata-stag-perl_0.14-2 libdb5.3_5.3.28-12+b1 libdebconfclient0_0.228 libdevel-globaldestruction-perl_0.14-1 libdevel-stacktrace-perl_2.0200-1 libdivsufsort3_2.0.1-2 libdpkg-perl_1.18.24 libdrm-intel1_2.4.81-2 libdrm2_2.4.81-2 libencode-locale-perl_1.05-1 libexception-class-perl_1.42-1 libexpat1_2.2.1-2 libexporter-tiny-perl_0.042-1 libfabric1_1.4.0-1 libfakeroot_1.21-3.1 libfdisk1_2.29.2-1 libffi6_3.2.1-6 libfile-listing-perl_6.04-1 libfile-slurp-tiny-perl_0.003-1 libfile-stripnondeterminism-perl_0.035-2 libfontconfig1_2.12.3-0.1 libfreetype6_2.6.3-3.2 libgcc-5-dev_5.4.1-11 libgcc-6-dev_6.3.0-19 libgcc1_1:7.1.0-7 libgcrypt20_1.7.7-2 libgd3_2.2.4-2 libgdbm3_1.8.3-14 libgfortran3_6.3.0-19 libglib2.0-0_2.52.3-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.13-2 libgomp1_7.1.0-7 libgpg-error0_1.26-2 libgssapi-krb5-2_1.15-1 libhmsbeagle1v5_2.1.2+20160831-5 libhogweed4_3.3-1+b1 libhpdf-2.2.1_2.2.1-1.1+b1 libhtml-parser-perl_3.72-3 libhtml-tagset-perl_3.20-3 libhtml-tree-perl_5.03-2 libhts2_1.4.1-2 libhttp-cookies-perl_6.01-1 libhttp-date-perl_6.02-1 libhttp-message-perl_6.11-1 libhttp-negotiate-perl_6.00-2 libhwloc-plugins_1.11.5-1 libhwloc5_1.11.5-1 libibverbs1_1.2.1-2 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_0.16-1 libimport-into-perl_1.002005-1 libio-html-perl_1.001-1 libio-pty-perl_1:1.08-1.1+b2 libio-socket-ssl-perl_2.049-1 libio-string-perl_1.08-3 libipc-run-perl_0.94-1 libisl15_0.18-1 libitm1_7.1.0-7 libjbig0_2.1-3.1+b2 libjpeg62-turbo_1:1.5.1-2 libk5crypto3_1.15-1 libkeyutils1_1.5.9-9 libkrb5-3_1.15-1 libkrb5support0_1.15-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.44+dfsg-5 libldap-common_2.4.44+dfsg-5 liblocale-gettext-perl_1.07-3+b1 liblsan0_7.1.0-7 libltdl7_2.4.6-2 liblwp-mediatypes-perl_6.02-1 liblwp-protocol-https-perl_6.06-2 liblz4-1_0.0~r131-2+b1 liblzma5_5.2.2-1.2+b1 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmariadbclient18_10.1.24-6 libmodule-build-perl_0.422400-1 libmodule-runtime-perl_0.014-2 libmoo-perl_2.003002-1 libmount1_2.29.2-1 libmpc3_1.0.3-1+b2 libmpfr4_3.1.5-1 libmpx0_5.4.1-11 libmpx2_7.1.0-7 libncurses5_6.0+20161126-1 libncursesw5_6.0+20161126-1 libnet-http-perl_6.12-1 libnet-ssleay-perl_1.80-1 libnettle6_3.3-1+b1 libnghttp2-14_1.23.1-1 libnl-3-200_3.2.27-2 libnl-route-3-200_3.2.27-2 libnpth0_1.5-2 libnuma1_2.0.11-2.1 libopenmpi2_2.1.1-6 libp11-kit0_0.23.3-5 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libparams-classify-perl_0.013-8 libpciaccess0_0.13.4-1+b2 libpcre3_2:8.39-3 libperl5.22_5.22.2-1 libperl5.24_5.24.1-4 libpipeline1_1.4.1-2 libpng16-16_1.6.29-3 libpq5_9.6.3-3 libpsl5_0.17.0-4 libpsm-infinipath1_3.3+19.g67c0807.open-3 libpython-stdlib_2.7.13-2 libpython2.7-minimal_2.7.13-2 libpython2.7-stdlib_2.7.13-2 libquadmath0_7.1.0-7 librdmacm1_1.1.0-2 libreadline6_6.3-9 libreadline7_7.0-3 librole-tiny-perl_2.000005-1 librtmp1_2.4+20151223.gitfa8646d.1-1+b1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libselinux1_2.6-3+b1 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.10-5 libsmartcols1_2.29.2-1 libsqlite3-0_3.16.2-5 libss2_1.43.4-2 libssh2-1_1.8.0-1 libssl1.1_1.1.0f-3 libstdc++-5-dev_5.4.1-11 libstdc++-6-dev_6.3.0-19 libstdc++6_7.1.0-7 libstrictures-perl_2.000003-1 libsub-exporter-progressive-perl_0.001013-1 libsub-quote-perl_2.004000-1 libsub-uplevel-perl_0.2800-1 libsystemd0_233-9 libtasn1-6_4.12-2 libtbb2_4.3~20150611-2 libtest-deep-perl_1.126-1 libtest-differences-perl_0.64-1 libtest-exception-perl_0.43-1 libtest-most-perl_0.35-1 libtest-simple-perl_1.302075-1 libtest-warn-perl_0.32-1 libtext-diff-perl_1.44-1 libtiff5_4.0.8-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20161126-1 libtool_2.4.6-2 libtree-dagnode-perl_1.29-1 libtsan0_7.1.0-7 libtype-tiny-perl_1.000006-1 libubsan0_7.1.0-7 libudev1_233-9 libunistring0_0.9.6+really0.9.3-0.1 liburi-perl_1.71-1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-1 libwebp6_0.5.2-1 libwww-perl_6.15-1 libwww-robotrules-perl_6.01-1 libx11-6_2:1.6.4-3 libx11-data_2:1.6.4-3 libxau6_1:1.0.8-1 libxcb1_1.12-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxfixes3_1:5.0.3-1 libxml-parser-perl_2.44-2+b1 libxml-twig-perl_1:3.50-1 libxml2_2.9.4+dfsg1-2.2 libxpm4_1:3.5.12-1 linux-libc-dev_4.11.6-1 login_1:4.4-4.1 lsb-base_9.20161125 m4_1.4.18-1 mafft_7.307-1 make_4.1-9.1 man-db_2.7.6.1-2 maq_0.7.1-7 mawk_1.3.3-17+b3 mime-support_3.60 mount_2.29.2-1 multiarch-support_2.24-12 muscle_1:3.8.31+dfsg-2 mysql-common_5.8+1.0.2 ncbi-blast+_2.6.0-1 ncbi-blast+-legacy_2.6.0-1 ncbi-data_6.1.20170106-2 ncurses-base_6.0+20161126-1 ncurses-bin_6.0+20161126-1 netbase_5.4 ocl-icd-libopencl1_2.2.11-1 openmpi-bin_2.1.1-6 openmpi-common_2.1.1-6 openssl_1.1.0f-3 passwd_1:4.4-4.1 patch_2.7.5-1+b2 perl_5.24.1-4 perl-base_5.24.1-4 perl-modules-5.22_5.22.2-1 perl-modules-5.24_5.24.1-4 perl-openssl-defaults_3 phylip_1:3.696+dfsg-5 phyml_3:3.2.0+dfsg-7+b1 pinentry-curses_1.0.0-2 po-debconf_1.0.20 primer3_2.3.7-3 probcons_1.12-11 python_2.7.13-2 python-minimal_2.7.13-2 python2.7_2.7.13-2 python2.7-minimal_2.7.13-2 raxml_8.2.10+dfsg-1 readline-common_7.0-3 samtools_1.4.1-1 sbuild-build-depends-bioperl-run-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 sim4_0.0.20121010-4 startpar_0.59-3.1 sysv-rc_2.88dsf-59.9 sysvinit-utils_2.88dsf-59.9 t-coffee_11.00.8cbe486-5 tar_1.29b-1.1 tigr-glimmer_3.02b-1 tzdata_2017b-2 ucf_3.0036 util-linux_2.29.2-1 wise_2.4.1-19 wise-data_2.4.1-19 xz-utils_5.2.2-1.2+b1 zlib1g_1:1.2.8.dfsg-5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Jan 13 07:30:49 2017 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bioperl-run_1.7.1-3.dsc dpkg-source: info: extracting bioperl-run in /<> dpkg-source: info: unpacking bioperl-run_1.7.1.orig.tar.gz dpkg-source: info: unpacking bioperl-run_1.7.1-3.debian.tar.xz 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_t-coffee.patch dpkg-source: info: applying skip_tests_for_bowtie.patch dpkg-source: info: applying skip_tests_for_infernal.patch dpkg-source: info: applying skip_tests_for_muscle.patch dpkg-source: info: applying skip_tests_for_ncbi-blast+.patch dpkg-source: info: applying skip_tests_for_maq.patch dpkg-source: info: applying hyphy.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bioperl-run_1.7.1-3 experimental amd64 ------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bioperl-run_1.7.1-3 experimental amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LC_ALL=POSIX LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=experimental-amd64-debomatic SCHROOT_CHROOT_NAME=experimental-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=112 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=experimental-amd64-debomatic-c0bdcbd5-3cae-4c86-9104-5e387c1c5151 SCHROOT_UID=1001 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic XDG_RUNTIME_DIR=/run/user/1001 XDG_SESSION_ID=c33779 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package bioperl-run dpkg-buildpackage: info: source version 1.7.1-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source -Zxz --before-build bioperl-run-1.7.1 dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean dh_autoreconf_clean dh_clean dpkg-source -Zxz -b bioperl-run-1.7.1 dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building bioperl-run using existing ./bioperl-run_1.7.1.orig.tar.gz dpkg-source: info: building bioperl-run in bioperl-run_1.7.1-3.debian.tar.xz dpkg-source: info: building bioperl-run in bioperl-run_1.7.1-3.dsc debian/rules build dh build dh_testdir dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- --install_scripts perl -I. Build.PL --installdirs vendor --config "optimize=-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro" --install_scripts Checking prerequisites... recommends: * Config::Any is not installed * File::Sort is not installed ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Run 'Build installdeps' to install missing prerequisites. 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 '1.007001' make[1]: Leaving directory '/<>' dh_auto_build perl Build Building BioPerl-Run debian/rules override_dh_auto_test make[1]: Entering directory '/<>' mkdir t.skip for t in Blat Eponine Glimmer2 Gumby RepeatMasker BWA 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 \ HOME_4_TCOFFEE=/tmp \ dh_auto_test 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/WZc_JTPgOk 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/AnalysisFactory_soap.t ...... skipped: Network tests have not been requested t/Analysis_soap.t ............. skipped: Network tests have not been requested t/BEDTools.t .................. skipped: The optional module Bio::Tools::Run::BEDTools (or dependencies thereof) was not installed ------------- EXCEPTION ------------- MSG: /usr/bin/bowtie call crashed: There was a problem running /usr/bin/bowtie : Encountered a space parsing the quality string for read r1 If this is a FASTQ file with integer (non-ASCII-encoded) qualities, please re-run Bowtie with the --integer-quals option. TBB Warning: Exact exception propagation is requested by application but the linked library is built without support for it Command: bowtie-align --wrapper basic-0 -e 70 -l 28 -n 2 -S --12 t/data/bowtie/reads/e_coli.cb t/data/bowtie/indexes/e_coli /tmp/UGEC21nEC7/LPOjob2y33.sam STACK Bio::Tools::Run::WrapperBase::_run /<>/blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm:1032 STACK Bio::Tools::Run::Bowtie::run /<>/blib/lib/Bio/Tools/Run/Bowtie.pm:358 STACK toplevel t/Bowtie.t:234 ------------------------------------- # Looks like your test exited with 29 just after 57. t/Bowtie.t .................... 1..70 ok 1 - make a factory using command 'assemble' 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 - set an exclusive group parameter ok 16 - parameter really set ok 17 - set an incompatible parameter ok 18 - parameter really set ok 19 - original exclusive parameter really unset ok 20 - parameters changed ok 21 - all available options ok 22 - available parameters ok 23 - available switches ok 24 - parameters changed ok 25 - all available options ok 26 - available parameters ok 27 - available switches ok 28 - get_parameters correct ok 29 - command attribute set ok 30 - internal command array set ok 31 - internal prefix hash set ok 32 - commands filtered by prefix ok 33 - translate_params: options correct ok 34 - make unpaired reads bowtie factory ok 35 - read raw sequence ok 36 - bowtie success ok 37 - read fasta sequence ok 38 - bowtie success ok 39 - read fastq sequence ok 40 - bowtie success ok 41 - make paired reads bowtie factory ok 42 - read paired fasta sequence ok 43 - bowtie success ok 44 - read paired fastq sequence ok 45 - bowtie success ok 46 - make a single alignment factory ok 47 - command attribute set ok 48 - seed mismatch param set ok 49 - seed length param set ok 50 - quality mismatch param set ok 51 - return type set ok 52 - make file based alignment ok 53 - make readable output ok 54 - number of alignments ok 55 - change mode ok 56 - make a crossbow alignment factory ok 57 - command attribute set Dubious, test returned 29 (wstat 7424, 0x1d00) Failed 13/70 subtests # Required executable for Bio::Tools::Run::Cap3 is not present t/Cap3.t ...................... 1..91 ok 1 - use Bio::SeqIO; ok 2 ok 3 - An object of class 'Bio::Tools::Run::Cap3' isa 'Bio::Tools::Run::Cap3' ok 4 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 ok 48 ok 49 ok 50 ok 51 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 52 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 53 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 54 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 55 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 56 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 57 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 58 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 59 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 60 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 61 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 62 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 63 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 64 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 65 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 66 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 67 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 68 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 69 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 70 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 71 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 72 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 73 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 74 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 75 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 76 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 77 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 78 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 79 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 80 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 81 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 82 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 83 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 84 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 85 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 86 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 87 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 88 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 89 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 90 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 91 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok t/Clustalw.t .................. 1..45 ok 1 - use Bio::Tools::Run::Alignment::Clustalw; ok 2 - use Bio::SimpleAlign; ok 3 - use Bio::AlignIO; ok 4 - use Bio::SeqIO; ok 5 - use File::Spec; ok 6 - Found input file ok 7 - Found profile1 file ok 8 - Found profile2 file ok 9 - An object of class 'Bio::Tools::Run::Alignment::Clustalw' isa 'Bio::Tools::Run::Alignment::Clustalw' ok 10 - program_dir returned correct default ok 11 - error_string returned correct default ok 12 - outfile_name returned correct default ok 13 - bootstrap returned correct default ok 14 - Correct exe default name ok 15 - Supported program version 2.1 ok 16 - No error occured ok 17 - outfile_name returned something ok 18 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 19 - Correct number of seqs returned ok 20 - Score ok 21 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 22 - Correct number of seqs returned ok 23 - Got correct sequence by position ok 24 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::Tree' ok 25 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 26 - Correct number of seqs returned ok 27 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 28 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::Tree' ok 29 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 30 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::Tree' ok 31 - footprinting worked ok 32 - Got correct sequence by position ok 33 - Got correct sequence by position ok 34 - Set and got ktuple correctly ok 35 - Set and got topdiags correctly ok 36 - Set and got window correctly ok 37 - Set and got pairgap correctly ok 38 - Set and got fixedgap correctly ok 39 - Set and got floatgap correctly ok 40 - Set and got matrix correctly ok 41 - Set and got type correctly ok 42 - Set and got output correctly ok 43 - Set and got outfile correctly ok 44 - set and got quiet correctly ok 45 - set and got bootstrap correctly ok # Required executable for Bio::Tools::Run::Coil is not present t/Coil.t ...................... 1..6 ok 1 - use Bio::Tools::Run::Coil; ok 2 - use Bio::SeqIO; ok 3 # skip Required executable for Bio::Tools::Run::Coil is not present ok 4 # skip Required executable for Bio::Tools::Run::Coil is not present ok 5 # skip Required executable for Bio::Tools::Run::Coil is not present ok 6 # skip Required executable for Bio::Tools::Run::Coil is not present ok t/Consense.t .................. 1..8 ok 1 - use Bio::Tools::Run::Phylo::Phylip::Consense; ok 2 - use Bio::AlignIO; ok 3 - An object of class 'Bio::Tools::Run::Phylo::Phylip::Consense' isa 'Bio::Tools::Run::Phylo::Phylip::Consense' ok 4 - could not set rooted option consense: can't find input tree file "intree" Please enter a new file name>  Consensus tree program, version 3.696 Settings for this run: C Consensus type (MRe, strict, MR, Ml): Majority rule (extended) O Outgroup root: No, use as outgroup species 1 R Trees to be treated as Rooted: No T Terminal type (IBM PC, ANSI, none): ANSI 1 Print out the sets of species: Yes 2 Print indications of progress of run: Yes 3 Print out tree: Yes 4 Write out trees onto tree file: Yes Are these settings correct? (type Y or the letter for one to change)  Consensus tree program, version 3.696 Settings for this run: C Consensus type (MRe, strict, MR, Ml): Majority rule (extended) R Trees to be treated as Rooted: Yes T Terminal type (IBM PC, ANSI, none): ANSI 1 Print out the sets of species: Yes 2 Print indications of progress of run: Yes 3 Print out tree: Yes 4 Write out trees onto tree file: Yes Are these settings correct? (type Y or the letter for one to change) Consensus tree written to file "outtree" Output written to file "outfile" Done. ok 5 ok 6 ok 7 ok 8 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 t/DrawGram.t .................. 1..6 ok 1 - use Bio::Tools::Run::Phylo::Phylip::DrawGram; ok 2 - use Bio::TreeIO; ok 3 ok 4 ok 5 ok 6 ok t/DrawTree.t .................. 1..6 ok 1 - use Bio::Tools::Run::Phylo::Phylip::DrawTree; ok 2 - use Bio::TreeIO; ok 3 ok 4 ok 5 ok 6 ok -- namet is "-sequence" associated seqall qualifiers -- namet is "-outfile" associated outfile qualifiers t/EMBOSS.t .................... 1..32 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 ok 15 - SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE 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 t/Ensembl.t ................... skipped: Network tests have not been requested 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 # Required executable for Bio::Tools::Run::Phylo::FastTree is not present 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 # skip Required executable for Bio::Tools::Run::Phylo::FastTree is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::FastTree is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::FastTree is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::FastTree is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::FastTree is not present 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 beignet-opencl-icd: no supported GPU found, this is probably the wrong opencl-icd package for this hardware (If you have multiple ICDs installed and OpenCL works, you can ignore this message) beignet-opencl-icd: no supported GPU found, this is probably the wrong opencl-icd package for this hardware (If you have multiple ICDs installed and OpenCL works, you can ignore this message) beignet-opencl-icd: no supported GPU found, this is probably the wrong opencl-icd package for this hardware (If you have multiple ICDs installed and OpenCL works, you can ignore this message) beignet-opencl-icd: no supported GPU found, this is probably the wrong opencl-icd package for this hardware (If you have multiple ICDs installed and OpenCL works, you can ignore this message) beignet-opencl-icd: no supported GPU found, this is probably the wrong opencl-icd package for this hardware (If you have multiple ICDs installed and OpenCL works, you can ignore this message) beignet-opencl-icd: no supported GPU found, this is probably the wrong opencl-icd package for this hardware (If you have multiple ICDs installed and OpenCL works, you can ignore this message) --------------------- WARNING --------------------- MSG: HYPHYMP reported error 0 - see error_string for the program output --------------------------------------------------- beignet-opencl-icd: no supported GPU found, this is probably the wrong opencl-icd package for this hardware (If you have multiple ICDs installed and OpenCL works, you can ignore this message) beignet-opencl-icd: no supported GPU found, this is probably the wrong opencl-icd package for this hardware (If you have multiple ICDs installed and OpenCL works, you can ignore this message) beignet-opencl-icd: no supported GPU found, this is probably the wrong opencl-icd package for this hardware (If you have multiple ICDs installed and OpenCL works, you can ignore this message) beignet-opencl-icd: no supported GPU found, this is probably the wrong opencl-icd package for this hardware (If you have multiple ICDs installed and OpenCL works, you can ignore this message) t/Hyphy.t ..................... 1..9 ok 1 - use Bio::Tools::Run::Phylo::Hyphy::SLAC; ok 2 - use Bio::Tools::Run::Phylo::Hyphy::FEL; ok 3 - use Bio::Tools::Run::Phylo::Hyphy::REL; ok 4 - use Bio::Tools::Run::Phylo::Hyphy::Modeltest; ok 5 - use Bio::Tools::Run::Phylo::Hyphy::BatchFile; ok 6 - REL module ok 7 - FEL module ok 8 - Batchfile module ok 9 - SLAC module ok t/Infernal.t .................. 1..3 ok 1 - use Bio::Tools::Run::Infernal; ok 2 - use Bio::SeqIO; ok 3 - use Bio::AlignIO; ok Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann Kalign is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation. reading from STDIN: found 0 sequences reading from t/data/cysprot.fa: found 7 sequences Output file: /tmp/uNpryjwoyd/GiP_nUftTi, in (null) format. Aligning 7 protein sequences with these parameters: 54.94940948 gap open penalty 8.52492046 gap extension 4.42409992 terminal gap penalty 0.20000000 bonus Alignment will be written to file:'/tmp/uNpryjwoyd/GiP_nUftTi'. Distance Calculation: 5 percent done 10 percent done 14 percent done 19 percent done 24 percent done 29 percent done 33 percent done 38 percent done 43 percent done 48 percent done 52 percent done 57 percent done 62 percent done 67 percent done 71 percent done 76 percent done 81 percent done 86 percent done 90 percent done 95 percent done 100 percent done Alignment: 0 percent done 14 percent done 29 percent done 43 percent done 57 percent done 71 percent done 100 percent done Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann Kalign is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation. reading from STDIN: found 0 sequences reading from /tmp/1yXYHndovr: found 7 sequences Output file: /tmp/uNpryjwoyd/GiP_nUftTi, in (null) format. Aligning 7 protein sequences with these parameters: 54.94940948 gap open penalty 8.52492046 gap extension 4.42409992 terminal gap penalty 0.20000000 bonus Alignment will be written to file:'/tmp/uNpryjwoyd/GiP_nUftTi'. Distance Calculation: 5 percent done 10 percent done 14 percent done 19 percent done 24 percent done 29 percent done 33 percent done 38 percent done 43 percent done 48 percent done 52 percent done 57 percent done 62 percent done 67 percent done 71 percent done 76 percent done 81 percent done 86 percent done 90 percent done 95 percent done 100 percent done Alignment: 0 percent done 14 percent done 29 percent done 43 percent done 57 percent done 71 percent done 100 percent done t/Kalign.t .................... 1..8 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 ok 5 ok 6 ok 7 ok 8 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 t/Maq.t ....................... 1..52 ok 1 - make a factory using command 'assemble' 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 - make fasta2bfa conversion factory ok 27 - convert refseq to bfa ok 28 - maq success ok 29 - make fastq2bfq conversion factory ok 30 - convert r1.fq to bfa ok 31 - maq success ok 32 - convert r2.fq to bfa ok 33 - maq success ok 34 - make map factory ok 35 - map single-end reads ok 36 - map paired-end reads ok 37 - make mapmerge factory ok 38 - merge maps ok 39 - make assemble factory ok 40 - assemble consensus ok 41 - make mapview converter ok 42 - convert mmap ok 43 - make consensus->fastq converter ok 44 - convert consensus -> fastq ok 45 - make an assembly factory ok 46 - command attribute set ok 47 - map param set ok 48 - asm param set ok 49 - c2q param set ok 50 - make full assy ok 51 - number of contigs ok 52 - number of singlets ok t/Match.t ..................... skipped: The optional module Config::Any (or dependencies thereof) was not installed # 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::Meme is not present t/Meme.t ...................... 1..25 ok 1 - use Bio::Tools::Run::Meme; ok 2 - An object of class 'Bio::Tools::Run::Meme' isa 'Bio::Tools::Run::Meme' ok 3 - has a created method not in args ok 4 - mod param was set ok 5 - dna 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::Meme is not present ok 9 # skip Required executable for Bio::Tools::Run::Meme is not present ok 10 # skip Required executable for Bio::Tools::Run::Meme is not present ok 11 # skip Required executable for Bio::Tools::Run::Meme is not present ok 12 # skip Required executable for Bio::Tools::Run::Meme is not present ok 13 # skip Required executable for Bio::Tools::Run::Meme is not present ok 14 # skip Required executable for Bio::Tools::Run::Meme is not present ok 15 # skip Required executable for Bio::Tools::Run::Meme is not present ok 16 # skip Required executable for Bio::Tools::Run::Meme is not present ok 17 # skip Required executable for Bio::Tools::Run::Meme is not present ok 18 # skip Required executable for Bio::Tools::Run::Meme is not present ok 19 # skip Required executable for Bio::Tools::Run::Meme is not present ok 20 # skip Required executable for Bio::Tools::Run::Meme is not present ok 21 # skip Required executable for Bio::Tools::Run::Meme is not present ok 22 # skip Required executable for Bio::Tools::Run::Meme is not present ok 23 # skip Required executable for Bio::Tools::Run::Meme is not present ok 24 # skip Required executable for Bio::Tools::Run::Meme is not present ok 25 # skip Required executable for Bio::Tools::Run::Meme is not present ok # Required executable for Bio::Tools::Run::Minimo is not present t/Minimo.t .................... 1..72 ok 1 - use Bio::SeqIO; ok 2 ok 3 - An object of class 'Bio::Tools::Run::Minimo' isa 'Bio::Tools::Run::Minimo' ok 4 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 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 26 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 27 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 28 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 29 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 30 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 31 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 32 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 33 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 34 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 35 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 36 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 37 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 38 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 39 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 40 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 41 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 42 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 43 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 44 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 45 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 46 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 47 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 48 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 49 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 50 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 51 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 52 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 53 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 54 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 55 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 56 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 57 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 58 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 59 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 60 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 61 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 62 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 63 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 64 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 65 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 66 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 67 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 68 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 69 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 70 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 71 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 72 # skip Required executable for Bio::Tools::Run::Minimo is not present ok # Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present t/Molphy.t .................... 1..10 ok 1 - use Bio::Tools::Phylo::Molphy; ok 2 - use Bio::Tools::Run::Phylo::Molphy::ProtML; ok 3 - use Bio::AlignIO; ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok t/Muscle.t .................... 1..8 ok 1 - use Bio::Tools::Run::Alignment::Muscle; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - use Bio::Root::IO; ok 5 - use POSIX; ok 6 ok 7 - Code tested only on muscle versions > 3.6 ok 8 - log file ok 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 - An object of class 'Bio::Tools::Run::Phylo::Phylip::Neighbor' isa 'Bio::Tools::Run::Phylo::Phylip::Neighbor' ok 4 - couldn't set factory parameter ok 5 - couldn't set factory parameter ok 6 - couldn't set factory parameter ok 7 - couldn't set factory parameter ok 8 - couldn't set factory parameter ok 9 - couldn't set factory parameter ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 - failed creating tree by neighbor protdist: can't find input file "infile" Please enter a new file name>  Protein distance algorithm, version 3.696 Settings for this run: P Use JTT, PMB, PAM, Kimura, categories model? Jones-Taylor-Thornton matrix G Gamma distribution of rates among positions? No C One category of substitution rates? Yes W Use weights for positions? No M Analyze multiple data sets? No I Input sequences interleaved? Yes 0 Terminal type (IBM PC, ANSI)? ANSI 1 Print out the data at start of run No 2 Print indications of progress of run Yes Are these settings correct? (type Y or the letter for one to change) Computing distances: S01 S02 . S03 .. S04 ... S05 .... S06 ..... S07 ...... S08 ....... S09 ........ S10 ......... S11 .......... S12 ........... S13 ............ S14 ............. Output written to file "outfile" Done. ok 18 - failed to assign serial names ok 19 - failed to restore original names ok # Required executable for Bio::Tools::Run::Newbler is not present t/Newbler.t ................... 1..98 ok 1 - use Bio::SeqIO; ok 2 ok 3 - An object of class 'Bio::Tools::Run::Newbler' isa 'Bio::Tools::Run::Newbler' ok 4 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 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 54 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 55 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 56 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 57 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 58 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 59 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 60 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 61 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 62 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 63 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 64 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 65 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 66 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 67 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 68 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 69 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 70 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 71 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 72 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 73 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 74 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 75 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 76 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 77 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 78 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 79 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 80 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 81 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 82 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 83 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 84 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 85 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 86 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 87 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 88 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 89 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 90 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 91 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 92 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 93 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 94 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 95 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 96 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 97 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 98 # skip Required executable for Bio::Tools::Run::Newbler 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 # Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present t/PAML.t ...................... 1..28 ok 1 - use Bio::Tools::Phylo::PAML; ok 2 - use Bio::Tools::Run::Phylo::PAML::Codeml; ok 3 - use Bio::Tools::Run::Phylo::PAML::Yn00; ok 4 - use Bio::AlignIO; ok 5 ok 6 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 12 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 14 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 15 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 16 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 17 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 18 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 19 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 20 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 21 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 22 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 23 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 24 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 25 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 26 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 27 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok 28 # skip Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present ok # Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present 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 # skip Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present ok 6 # skip Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present ok 7 # skip Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present ok 9 # skip Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present ok t/PhastCons.t ................. skipped: The optional module Clone (or dependencies thereof) was not installed # Required executable for Bio::Tools::Run::Phrap is not present t/Phrap.t ..................... 1..127 ok 1 - use Bio::SeqIO; ok 2 ok 3 - An object of class 'Bio::Tools::Run::Phrap' isa 'Bio::Tools::Run::Phrap' ok 4 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 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 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 90 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 91 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 92 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 93 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 94 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 95 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 96 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 97 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 98 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 99 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 100 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 101 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 102 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 103 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 104 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 105 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 106 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 107 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 108 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 109 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 110 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 111 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 112 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 113 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 114 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 115 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 116 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 117 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 118 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 119 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 120 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 121 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 122 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 123 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 124 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 125 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 126 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 127 # skip Required executable for Bio::Tools::Run::Phrap is not present ok t/Phyml.t ..................... 1..42 ok 1 - use Bio::Tools::Run::Phylo::Phyml; ok 2 - use Bio::AlignIO; ok 3 - Found protein input file ok 4 - An object of class 'Bio::Tools::Run::Phylo::Phyml' isa 'Bio::Tools::Run::Phylo::Phyml' ok 5 - program_dir returned correct default ok 6 - Correct exe default name ok 7 - data_format, default ok 8 - data_format, sequential ok 9 - data_format, interleaved ok 10 - dataset_count, default ok 11 - data_count, 2 ok 12 - kappa, default ok 13 - kappa ok 14 - invar, default ok 15 - invar ok 16 - category_number, default ok 17 - category_number ok 18 - alpha, default ok 19 - alpha ok 20 - alpha ok 21 - tree, default ok 22 - tree ok 23 - tree ok 24 - version ok 25 - data_type, default ok 26 - data_type, dna ok 27 - data_type, protein ok 28 - model, default ok 29 - opt_topology, default ok 30 - opt_topology ok 31 - opt_topology ok 32 - opt_lengths, default ok 33 - opt_lengths ok 34 - opt_lengths ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 - tree_string() ok 42 - Found DNA input file 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 ................... skipped: The optional module Clone (or dependencies thereof) was not installed # Required executable for Bio::Tools::Run::Prints is not present t/Prints.t .................... 1..7 ok 1 - use Bio::Tools::Run::Prints; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Prints' isa 'Bio::Tools::Run::Prints' ok 5 # skip Required executable for Bio::Tools::Run::Prints is not present ok 6 # skip Required executable for Bio::Tools::Run::Prints is not present ok 7 # skip Required executable for Bio::Tools::Run::Prints is not present ok # Required executable for Bio::Tools::Run::Alignment::Probalign is not present t/Probalign.t ................. 1..13 ok 1 - use Bio::Tools::Run::Alignment::Probalign; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - use Cwd; ok 5 - use POSIX; ok 6 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 7 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 9 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 10 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 11 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 12 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 13 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok PROBCONS version 1.12 - align multiple protein sequences and print to standard output Written by Chuong Do Using parameter set: initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } Loading sequence file: t/data/cysprot.fa Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) PROBCONS version 1.12 - align multiple protein sequences and print to standard output Written by Chuong Do Using parameter set: initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } Loading sequence file: /tmp/PsZHWQmBay 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/C9il84bhPI 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/xv0EmggAQU Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) t/Probcons.t .................. 1..11 ok 1 - use Bio::Tools::Run::Alignment::Probcons; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - Code tested only on probcons versions > 1.09 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok # Required executable for Bio::Tools::Run::Profile is not present t/Profile.t ................... 1..7 ok 1 - use Bio::Tools::Run::Profile; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Profile' isa 'Bio::Tools::Run::Profile' ok 5 # skip Required executable for Bio::Tools::Run::Profile is not present ok 6 # skip Required executable for Bio::Tools::Run::Profile is not present ok 7 # skip Required executable for Bio::Tools::Run::Profile is not present ok t/Promoterwise.t .............. 1..9 ok 1 - use Bio::Tools::Run::Promoterwise; ok 2 - use Bio::Seq; ok 3 - An object of class 'Bio::Tools::Run::Promoterwise' isa 'Bio::Tools::Run::Promoterwise' ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok t/ProtDist.t .................. 1..14 ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtDist; ok 2 - use Bio::Tools::Run::Alignment::Clustalw; ok 3 - An object of class 'Bio::Tools::Run::Phylo::Phylip::ProtDist' isa 'Bio::Tools::Run::Phylo::Phylip::ProtDist' ok 4 - set factory parameter ok 5 - set factory parameter ok 6 - set factory parameter ok 7 - set factory parameter ok 8 - set factory parameter ok 9 - set factory parameter ok 10 ok 11 - creating distance matrix ok 12 ok 13 - failed creating matrix on safe names ok 14 ok t/ProtPars.t .................. 1..9 ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtPars; ok 2 - use Bio::Tools::Run::Alignment::Clustalw; ok 3 - An object of class 'Bio::Tools::Run::Phylo::Phylip::ProtPars' isa 'Bio::Tools::Run::Phylo::Phylip::ProtPars' ok 4 - set factory parameter ok 5 - set factory parameter ok 6 - set factory parameter ok 7 - creating tree by protpars ok 8 - creating tree by protpars ok 9 - creating tree by protpars 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 t/SeqBoot.t ................... 1..9 ok 1 - use Bio::Tools::Run::Phylo::Phylip::SeqBoot; ok 2 - use Bio::AlignIO; ok 3 - An object of class 'Bio::Tools::Run::Phylo::Phylip::SeqBoot' isa 'Bio::Tools::Run::Phylo::Phylip::SeqBoot' ok 4 - couldn't set datatype parameter ok 5 - coludn't set number of replicates ok 6 ok 7 ok 8 - ailed to assign serial names ok 9 - fail to restore original names 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 t/TCoffee.t ................... 1..25 ok 1 - use Bio::Tools::Run::Alignment::TCoffee; 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::TCoffee' isa 'Bio::Tools::Run::Alignment::TCoffee' ok 6 - set factory parameter ok 7 - get factory parameter ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 - expect 21 >= val >= 23 ok 19 - expect 47 or 48 ok 20 - simple generic run ok 21 ok 22 ok 23 ok 24 - expect 13 or 14 ok 25 - expect 41 or 42 rmdir /tmp/IROS_go3Mb ok # Required executable for Bio::Tools::Run::TigrAssembler is not present # Required executable for Bio::Tools::Run::TigrAssembler is not present t/TigrAssembler.t ............. 1..88 ok 1 - use Bio::SeqIO; ok 2 ok 3 - An object of class 'Bio::Tools::Run::TigrAssembler' isa 'Bio::Tools::Run::TigrAssembler' ok 4 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 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 38 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 39 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 40 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 41 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 42 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 43 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 44 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 45 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 46 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 47 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 48 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 49 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 50 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 51 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 52 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 53 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 54 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 55 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 56 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 57 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 58 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 59 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 60 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 61 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 62 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 63 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 64 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 65 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 66 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 67 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 68 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 69 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 70 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 71 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 72 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 73 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 74 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 75 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 76 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 77 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 78 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 79 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 80 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 81 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 82 ok 83 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 84 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 85 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 86 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 87 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 88 # skip Required executable for Bio::Tools::Run::TigrAssembler 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 Test Summary Report ------------------- t/Bowtie.t (Wstat: 7424 Tests: 57 Failed: 0) Non-zero exit status: 29 Parse errors: Bad plan. You planned 70 tests but ran 57. Files=76, Tests=1783, 98 wallclock secs ( 0.21 usr 0.06 sys + 91.28 cusr 3.72 csys = 95.27 CPU) Result: FAIL Failed 1/76 test programs. 0/1783 subtests failed. dh_auto_test: perl Build test --verbose 1 returned exit code 255 debian/rules:32: recipe for target 'override_dh_auto_test' failed make[1]: *** [override_dh_auto_test] Error 2 make[1]: Leaving directory '/<>' debian/rules:26: recipe for target 'build' failed make: *** [build] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 2017-06-25T18:57:21Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 33964 Build-Time: 100 Distribution: experimental Fail-Stage: build Host Architecture: amd64 Install-Time: 27 Job: /srv/debomatic/incoming/bioperl-run_1.7.1-3.dsc Machine Architecture: amd64 Package: bioperl-run Package-Time: 139 Source-Version: 1.7.1-3 Space: 33964 Status: attempted Version: 1.7.1-3 -------------------------------------------------------------------------------- Finished at 2017-06-25T18:57:21Z Build needed 00:02:19, 33964k disk space