https://launchpad.net/ubuntu/+source/bioperl-run/1.7.3-6/+build/20778089 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lgw01-amd64-026 4.15.0-129-generic #132-Ubuntu SMP Thu Dec 10 14:02:26 UTC 2020 x86_64 Buildd toolchain package versions: launchpad-buildd_193~468~ubuntu18.04.1 python3-lpbuildd_193~468~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.7 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 7 Jan 13:37:18 ntpdate[1797]: adjust time server 10.211.37.1 offset -0.000023 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20778089 --image-type chroot /home/buildd/filecache-default/720a8366e1260e086c1691fe6381a3f2b1c21d81 Creating target for build PACKAGEBUILD-20778089 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20778089 Starting target for build PACKAGEBUILD-20778089 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20778089 'deb http://ftpmaster.internal/ubuntu hirsute main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-security main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-updates main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-20778089 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20778089 Updating target for build PACKAGEBUILD-20778089 Get:1 http://ftpmaster.internal/ubuntu hirsute InRelease [269 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute-proposed InRelease [121 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main amd64 Packages [1386 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main Translation-en [509 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/universe amd64 Packages [13.0 MB] Get:8 http://ftpmaster.internal/ubuntu hirsute/universe Translation-en [5395 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 Packages [139 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main Translation-en [53.0 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/universe amd64 Packages [828 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/universe Translation-en [345 kB] Fetched 22.2 MB in 4s (5647 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: libisl22 libperl5.30 perl-modules-5.30 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libisl23 libperl5.32 libxxhash0 perl-modules-5.32 The following packages will be upgraded: adduser apt base-files base-passwd bash binutils binutils-common binutils-x86-64-linux-gnu bsdutils coreutils cpp-10 dash dpkg dpkg-dev fakeroot g++-10 gcc-10 gcc-10-base grep init init-system-helpers libacl1 libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libgcc-10-dev libgcc-s1 libgcrypt20 libgomp1 libgssapi-krb5-2 libidn2-0 libip4tc2 libitm1 libk5crypto3 libkrb5-3 libkrb5support0 liblsan0 liblz4-1 libmount1 libmpc3 libncurses6 libncursesw6 libnpth0 libp11-kit0 libpcre2-8-0 libquadmath0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libssl1.1 libstdc++-10-dev libstdc++6 libsystemd0 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login mount ncurses-base ncurses-bin openssl passwd perl perl-base readline-common systemd systemd-sysv systemd-timesyncd sysvinit-utils tar tzdata util-linux 105 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 86.0 MB of archives. After this operation, 54.5 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcrypt-dev amd64 1:4.4.17-1ubuntu1 [105 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc6-dev amd64 2.32-0ubuntu6 [2131 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc-dev-bin amd64 2.32-0ubuntu6 [30.9 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcrypt1 amd64 1:4.4.17-1ubuntu1 [78.8 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 linux-libc-dev amd64 5.8.0-34.37+21.04.1 [1138 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main amd64 libtirpc-common all 1.3.1-1 [7452 B] Get:7 http://ftpmaster.internal/ubuntu hirsute/main amd64 libk5crypto3 amd64 1.17-10ubuntu1 [79.2 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute/main amd64 libgssapi-krb5-2 amd64 1.17-10ubuntu1 [121 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute/main amd64 libkrb5-3 amd64 1.17-10ubuntu1 [332 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute/main amd64 libkrb5support0 amd64 1.17-10ubuntu1 [30.7 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libssl1.1 amd64 1.1.1f-1ubuntu5 [1324 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute/main amd64 libtirpc-dev amd64 1.3.1-1 [183 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main amd64 libtirpc3 amd64 1.3.1-1 [76.9 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute/main amd64 libisl23 amd64 0.23-1 [652 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libcc1-0 amd64 10.2.1-2ubuntu3 [48.7 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libctf0 amd64 2.35.50.20210106-1ubuntu2 [95.1 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libctf-nobfd0 amd64 2.35.50.20210106-1ubuntu2 [97.1 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.35.50.20210106-1ubuntu2 [1838 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libbinutils amd64 2.35.50.20210106-1ubuntu2 [584 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 binutils-common amd64 2.35.50.20210106-1ubuntu2 [216 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 binutils amd64 2.35.50.20210106-1ubuntu2 [3396 B] Get:22 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 gcc-10-base amd64 10.2.1-2ubuntu3 [19.3 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libgcc-s1 amd64 10.2.1-2ubuntu3 [41.7 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libgomp1 amd64 10.2.1-2ubuntu3 [102 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libitm1 amd64 10.2.1-2ubuntu3 [26.3 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libatomic1 amd64 10.2.1-2ubuntu3 [9288 B] Get:27 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libasan6 amd64 10.2.1-2ubuntu3 [2060 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 liblsan0 amd64 10.2.1-2ubuntu3 [834 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtsan0 amd64 10.2.1-2ubuntu3 [2009 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libubsan1 amd64 10.2.1-2ubuntu3 [784 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libquadmath0 amd64 10.2.1-2ubuntu3 [146 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 g++-10 amd64 10.2.1-2ubuntu3 [9759 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libstdc++-10-dev amd64 10.2.1-2ubuntu3 [1754 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libgcc-10-dev amd64 10.2.1-2ubuntu3 [2344 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 gcc-10 amd64 10.2.1-2ubuntu3 [17.4 MB] Get:36 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 cpp-10 amd64 10.2.1-2ubuntu3 [8575 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libstdc++6 amd64 10.2.1-2ubuntu3 [501 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute/main amd64 libmpc3 amd64 1.2.0-1 [44.3 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute/main amd64 libzstd1 amd64 1.4.8+dfsg-1 [304 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc6 amd64 2.32-0ubuntu6 [2683 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main amd64 base-files amd64 11ubuntu16 [60.5 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/main amd64 bash amd64 5.1-1ubuntu1 [673 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/main amd64 bsdutils amd64 1:2.36.1-1ubuntu2 [86.8 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute/main amd64 coreutils amd64 8.32-4ubuntu2 [1353 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute/main amd64 tar amd64 1.32+dfsg-1 [279 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute/main amd64 dpkg amd64 1.20.5ubuntu3 [1172 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main amd64 dash amd64 0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1 [87.1 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/main amd64 grep amd64 3.6-1 [155 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main amd64 login amd64 1:4.8.1-1ubuntu7 [220 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main amd64 libncurses6 amd64 6.2+20201114-2 [102 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main amd64 libncursesw6 amd64 6.2+20201114-2 [132 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main amd64 libtinfo6 amd64 6.2+20201114-2 [87.3 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/main amd64 ncurses-bin amd64 6.2+20201114-2 [173 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute/main amd64 perl-modules-5.32 all 5.32.0-6 [2754 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute/main amd64 libperl5.32 amd64 5.32.0-6 [4064 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute/main amd64 perl amd64 5.32.0-6 [225 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute/main amd64 perl-base amd64 5.32.0-6 [1562 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/main amd64 util-linux amd64 2.36.1-1ubuntu2 [1073 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libdebconfclient0 amd64 0.256ubuntu1 [6220 B] Get:60 http://ftpmaster.internal/ubuntu hirsute/main amd64 base-passwd amd64 3.5.48 [47.5 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 init-system-helpers all 1.60 [37.8 kB] Get:62 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc-bin amd64 2.32-0ubuntu6 [642 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute/main amd64 ncurses-base all 6.2+20201114-2 [18.4 kB] Get:64 http://ftpmaster.internal/ubuntu hirsute/main amd64 sysvinit-utils amd64 2.96-5ubuntu1 [20.8 kB] Get:65 http://ftpmaster.internal/ubuntu hirsute/main amd64 libxxhash0 amd64 0.8.0-1 [16.1 kB] Get:66 http://ftpmaster.internal/ubuntu hirsute/main amd64 libgcrypt20 amd64 1.8.7-2ubuntu1 [424 kB] Get:67 http://ftpmaster.internal/ubuntu hirsute/main amd64 liblz4-1 amd64 1.9.3-0ubuntu1 [56.0 kB] Get:68 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 systemd-sysv amd64 247.1-4ubuntu1 [10.3 kB] Get:69 http://ftpmaster.internal/ubuntu hirsute/main amd64 libaudit-common all 1:2.8.5-3ubuntu3 [4048 B] Get:70 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcap-ng0 amd64 0.7.9-2.2build1 [11.0 kB] Get:71 http://ftpmaster.internal/ubuntu hirsute/main amd64 libaudit1 amd64 1:2.8.5-3ubuntu3 [39.0 kB] Get:72 http://ftpmaster.internal/ubuntu hirsute/main amd64 libpcre2-8-0 amd64 10.35-2ubuntu1 [204 kB] Get:73 http://ftpmaster.internal/ubuntu hirsute/main amd64 libselinux1 amd64 3.1-2build2 [69.4 kB] Get:74 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsemanage-common all 3.1-1build2 [10.0 kB] Get:75 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsemanage1 amd64 3.1-1build2 [86.9 kB] Get:76 http://ftpmaster.internal/ubuntu hirsute/main amd64 passwd amd64 1:4.8.1-1ubuntu7 [797 kB] Get:77 http://ftpmaster.internal/ubuntu hirsute/main amd64 adduser all 3.118ubuntu4 [163 kB] Get:78 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 systemd-timesyncd amd64 247.1-4ubuntu1 [28.1 kB] Get:79 http://ftpmaster.internal/ubuntu hirsute/main amd64 libapparmor1 amd64 3.0.0-0ubuntu5 [35.5 kB] Get:80 http://ftpmaster.internal/ubuntu hirsute/main amd64 libblkid1 amd64 2.36.1-1ubuntu2 [132 kB] Get:81 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libudev1 amd64 247.1-4ubuntu1 [69.1 kB] Get:82 http://ftpmaster.internal/ubuntu hirsute/main amd64 libdevmapper1.02.1 amd64 2:1.02.167-1ubuntu4 [128 kB] Get:83 http://ftpmaster.internal/ubuntu hirsute/main amd64 libuuid1 amd64 2.36.1-1ubuntu2 [21.6 kB] Get:84 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcryptsetup12 amd64 2:2.3.4-1ubuntu1 [195 kB] Get:85 http://ftpmaster.internal/ubuntu hirsute/main amd64 libip4tc2 amd64 1.8.5-3ubuntu4 [18.7 kB] Get:86 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libseccomp2 amd64 2.4.3-1ubuntu6 [41.9 kB] Get:87 http://ftpmaster.internal/ubuntu hirsute/main amd64 mount amd64 2.36.1-1ubuntu2 [121 kB] Get:88 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 systemd amd64 247.1-4ubuntu1 [3988 kB] Get:89 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libsystemd0 amd64 247.1-4ubuntu1 [276 kB] Get:90 http://ftpmaster.internal/ubuntu hirsute/main amd64 libapt-pkg6.0 amd64 2.1.15 [851 kB] Get:91 http://ftpmaster.internal/ubuntu hirsute/main amd64 apt amd64 2.1.15 [1318 kB] Get:92 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 init amd64 1.60 [6040 B] Get:93 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libacl1 amd64 2.2.53-9 [17.6 kB] Get:94 http://ftpmaster.internal/ubuntu hirsute/main amd64 libattr1 amd64 1:2.4.48-6 [12.9 kB] Get:95 http://ftpmaster.internal/ubuntu hirsute/main amd64 libmount1 amd64 2.36.1-1ubuntu2 [147 kB] Get:96 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsmartcols1 amd64 2.36.1-1ubuntu2 [94.6 kB] Get:97 http://ftpmaster.internal/ubuntu hirsute/main amd64 libidn2-0 amd64 2.3.0-4 [52.4 kB] Get:98 http://ftpmaster.internal/ubuntu hirsute/main amd64 libp11-kit0 amd64 0.23.22-1 [191 kB] Get:99 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcap2 amd64 1:2.44-1 [17.2 kB] Get:100 http://ftpmaster.internal/ubuntu hirsute/main amd64 readline-common all 8.1-1 [54.1 kB] Get:101 http://ftpmaster.internal/ubuntu hirsute/main amd64 libreadline8 amd64 8.1-1 [137 kB] Get:102 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsqlite3-0 amd64 3.34.0-1 [589 kB] Get:103 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 openssl amd64 1.1.1f-1ubuntu5 [621 kB] Get:104 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 tzdata all 2020f-1ubuntu1 [294 kB] Get:105 http://ftpmaster.internal/ubuntu hirsute/main amd64 dpkg-dev all 1.20.5ubuntu3 [758 kB] Get:106 http://ftpmaster.internal/ubuntu hirsute/main amd64 libdpkg-perl all 1.20.5ubuntu3 [232 kB] Get:107 http://ftpmaster.internal/ubuntu hirsute/main amd64 libfakeroot amd64 1.25.3-1.1 [26.8 kB] Get:108 http://ftpmaster.internal/ubuntu hirsute/main amd64 fakeroot amd64 1.25.3-1.1 [62.9 kB] Get:109 http://ftpmaster.internal/ubuntu hirsute/main amd64 libnpth0 amd64 1.6-3 [8220 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 86.0 MB in 7s (12.8 MB/s) (Reading database ... 12980 files and directories currently installed.) 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Setting up libquadmath0:amd64 (10.2.1-2ubuntu3) ... Setting up libmpc3:amd64 (1.2.0-1) ... Setting up libatomic1:amd64 (10.2.1-2ubuntu3) ... Setting up libncursesw6:amd64 (6.2+20201114-2) ... Setting up libk5crypto3:amd64 (1.17-10ubuntu1) ... Setting up libperl5.32:amd64 (5.32.0-6) ... Setting up libubsan1:amd64 (10.2.1-2ubuntu3) ... Setting up libcrypt-dev:amd64 (1:4.4.17-1ubuntu1) ... Setting up libkrb5-3:amd64 (1.17-10ubuntu1) ... Setting up libbinutils:amd64 (2.35.50.20210106-1ubuntu2) ... Setting up libisl23:amd64 (0.23-1) ... Setting up libc-dev-bin (2.32-0ubuntu6) ... Setting up openssl (1.1.1f-1ubuntu5) ... Setting up readline-common (8.1-1) ... Setting up libcc1-0:amd64 (10.2.1-2ubuntu3) ... Setting up liblsan0:amd64 (10.2.1-2ubuntu3) ... Setting up cpp-10 (10.2.1-2ubuntu3) ... Setting up libitm1:amd64 (10.2.1-2ubuntu3) ... Setting up libtsan0:amd64 (10.2.1-2ubuntu3) ... Setting up libctf0:amd64 (2.35.50.20210106-1ubuntu2) ... Setting up libgcc-10-dev:amd64 (10.2.1-2ubuntu3) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up perl (5.32.0-6) ... Setting up libgssapi-krb5-2:amd64 (1.17-10ubuntu1) ... Setting up libdpkg-perl (1.20.5ubuntu3) ... Setting up binutils-x86-64-linux-gnu (2.35.50.20210106-1ubuntu2) ... Setting up libtirpc3:amd64 (1.3.1-1) ... Setting up binutils (2.35.50.20210106-1ubuntu2) ... Setting up dpkg-dev (1.20.5ubuntu3) ... Setting up libtirpc-dev:amd64 (1.3.1-1) ... Setting up gcc-10 (10.2.1-2ubuntu3) ... Setting up libc6-dev:amd64 (2.32-0ubuntu6) ... Setting up libstdc++-10-dev:amd64 (10.2.1-2ubuntu3) ... Setting up g++-10 (10.2.1-2ubuntu3) ... Processing triggers for libc-bin (2.32-0ubuntu6) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-20778089 amd64 hirsute-proposed -c chroot:build-PACKAGEBUILD-20778089 --arch=amd64 --dist=hirsute-proposed --nolog -A bioperl-run_1.7.3-6.dsc Initiating build PACKAGEBUILD-20778089 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-129-generic #132-Ubuntu SMP Thu Dec 10 14:02:26 UTC 2020 x86_64 sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on lgw01-amd64-026.buildd +==============================================================================+ | bioperl-run 1.7.3-6 (amd64) Thu, 07 Jan 2021 13:38:06 +0000 | +==============================================================================+ Package: bioperl-run Version: 1.7.3-6 Source Version: 1.7.3-6 Distribution: hirsute-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-20778089/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- bioperl-run_1.7.3-6.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/bioperl-run-HWwZzq/bioperl-run-1.7.3' with '<>' I: NOTICE: Log filtering will replace 'build/bioperl-run-HWwZzq' 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-80qfGU/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-80qfGU/apt_archive ./ InRelease Get:2 copy:/<>/resolver-80qfGU/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-80qfGU/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-80qfGU/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-80qfGU/apt_archive ./ Packages [431 B] Fetched 1737 B in 0s (42.6 kB/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: libisl22 libperl5.30 perl-modules-5.30 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-80qfGU/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14926 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), perl, libmodule-build-perl, bioperl (>= 1.7.4), libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, libfile-sort-perl, libtest-most-perl, libarray-compare-perl, libtree-dagnode-perl, libbio-cluster-perl, libbio-featureio-perl, libconfig-any-perl, libbio-tools-run-alignment-clustalw-perl, libbio-eutilities-perl, libbio-tools-run-remoteblast-perl, amap-align, bedtools, bedtools-test, ncbi-blast+-legacy, clustalw, emboss, exonerate, hmmer, hyphy-pt | hyphy-mpi, infernal, kalign, mafft, muscle, ncoils, phyml, primer3, probcons, python3-pybedtools, raxml, samtools, sim4, tigr-glimmer, wise, fasttree, lagan, pal2nal, pftools, libwww-perl Filtered Build-Depends: debhelper-compat (= 13), perl, libmodule-build-perl, bioperl (>= 1.7.4), libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, libfile-sort-perl, libtest-most-perl, libarray-compare-perl, libtree-dagnode-perl, libbio-cluster-perl, libbio-featureio-perl, libconfig-any-perl, libbio-tools-run-alignment-clustalw-perl, libbio-eutilities-perl, libbio-tools-run-remoteblast-perl, amap-align, bedtools, bedtools-test, ncbi-blast+-legacy, clustalw, emboss, exonerate, hmmer, hyphy-pt | hyphy-mpi, infernal, kalign, mafft, muscle, ncoils, phyml, primer3, probcons, python3-pybedtools, raxml, samtools, sim4, tigr-glimmer, wise, fasttree, lagan, pal2nal, pftools, libwww-perl dpkg-deb: building package 'sbuild-build-depends-bioperl-run-dummy' in '/<>/resolver-80qfGU/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-80qfGU/apt_archive ./ InRelease Get:2 copy:/<>/resolver-80qfGU/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-80qfGU/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-80qfGU/apt_archive ./ Sources [854 B] Get:5 copy:/<>/resolver-80qfGU/apt_archive ./ Packages [889 B] Fetched 2706 B in 0s (152 kB/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: libisl22 libperl5.30 perl-modules-5.30 Use 'apt autoremove' to remove them. The following additional packages will be installed: amap-align autoconf automake autopoint autotools-dev bedtools bedtools-test bioperl bsdextrautils clustalw debhelper dh-autoreconf dh-strip-nondeterminism dwz emboss emboss-data emboss-lib exonerate fasttree file fontconfig-config fonts-dejavu-core gettext gettext-base groff-base hmmer hyphy-common hyphy-pt ibverbs-providers infernal intltool-debian kalign lagan libalgorithm-diff-perl libarchive-zip-perl libarray-compare-perl libasn1-8-heimdal libb-hooks-op-check-perl libbio-asn1-entrezgene-perl libbio-cluster-perl libbio-db-ncbihelper-perl libbio-eutilities-perl libbio-featureio-perl libbio-perl-perl libbio-perl-run-perl libbio-tools-run-alignment-clustalw-perl libbio-tools-run-remoteblast-perl libbio-variation-perl libbrotli1 libbsd0 libcache-cache-perl libcapture-tiny-perl libcbor0.6 libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libconfig-any-perl libcurl3-gnutls libdata-stag-perl libdebhelper-perl libdeflate0 libdevel-callchecker-perl libdevel-stacktrace-perl libdivsufsort3 libdynaloader-functions-perl libedit2 libelf1 libencode-locale-perl liberror-perl libevent-core-2.1-7 libevent-pthreads-2.1-7 libexception-class-perl libexpat1 libexporter-tiny-perl libfabric1 libfido2-1 libfile-listing-perl libfile-slurp-perl libfile-slurp-tiny-perl libfile-sort-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgd3 libgfortran5 libglib2.0-0 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhpdf-2.3.0 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts3 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libhwloc-plugins libhwloc15 libhx509-5-heimdal libibverbs1 libicu67 libimport-into-perl libio-html-perl libio-pty-perl libio-socket-ssl-perl libio-string-perl libipc-run-perl libipc-sharelite-perl libjbig0 libjpeg-turbo8 libjpeg8 libkrb5-26-heimdal libldap-2.4-2 liblmdb0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmodule-build-perl libmodule-pluggable-perl libmodule-runtime-perl libmoo-perl libmysqlclient21 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3 libparams-classify-perl libpciaccess0 libpipeline1 libpmix2 libpq5 libpsl5 libpsm-infinipath1 libpsm2-2 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librdmacm1 libroken18-heimdal librole-tiny-perl librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libstrictures-perl libsub-override-perl libsub-quote-perl libsub-uplevel-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-csv-perl libtext-diff-perl libtiff5 libtimedate-perl libtool libtree-dagnode-perl libtry-tiny-perl libtype-tiny-perl libuchardet0 libucx0 liburi-perl libwebp6 libwind0-heimdal libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml-dom-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-namespacesupport-perl libxml-parser-perl libxml-perl libxml-regexp-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libxml-xpathengine-perl libxml2 libxnvctrl0 libxpm4 m4 mafft mailcap man-db media-types mime-support muscle mysql-common ncbi-blast+ ncbi-blast+-legacy ncbi-data ncoils netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pal2nal perl-openssl-defaults pftools phyml po-debconf primer3 probcons python3 python3-minimal python3-pybedtools python3-pysam python3-six python3.9 python3.9-minimal raxml samtools sim4 tigr-glimmer ucf wise wise-data Suggested packages: autoconf-archive gnu-standards autoconf-doc clustalx seaview dh-make emboss-doc emboss-test embassy gettext-doc libasprintf-dev libgettextpo-dev groff hmmer-doc libxml-sax-expatxs-perl libgd-tools 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 libdevel-lexalias-perl libauthen-ntlm-perl libunicode-map8-perl libunicode-string-perl xml-twig-tools m4-doc apparmor less www-browser gnuplot opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl ncbi-epcr probcons-extra python3-doc python3-tk python3-venv python-pybedtools-doc python3.9-venv python3.9-doc binfmt-support cwltool wise-doc Recommended packages: bioperl-run perl-doc libdbi-perl libgd-gd2-perl libapache-dbi-perl libyaml-perl libace-perl liblist-moreutils-perl libset-scalar-perl dialign curl | wget | lynx libalgorithm-diff-xs-perl libalgorithm-munkres-perl 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-sax-writer-perl libcgi-fast-perl libconfig-general-perl libconfig-tiny-perl libyaml-libyaml-perl | libyaml-syck-perl | libyaml-perl perl-tk libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libhtml-format-perl libldap-common libmodule-signature-perl libpod-readme-perl libsoftware-license-perl libclass-xsaccessor-perl libnamespace-clean-perl libsub-name-perl publicsuffix libsasl2-modules libtext-csv-xs-perl libltdl-dev libref-util-perl libtype-tiny-xs-perl libdata-dump-perl libhtml-form-perl libhttp-daemon-perl libmailtools-perl libxml-sax-expat-perl libtext-iconv-perl libtie-ixhash-perl blast2 lynx ruby xauth paml libmail-sendmail-perl The following NEW packages will be installed: amap-align autoconf automake autopoint autotools-dev bedtools bedtools-test bioperl bsdextrautils clustalw debhelper dh-autoreconf dh-strip-nondeterminism dwz emboss emboss-data emboss-lib exonerate fasttree file fontconfig-config fonts-dejavu-core gettext gettext-base groff-base hmmer hyphy-common hyphy-pt ibverbs-providers infernal intltool-debian kalign lagan libalgorithm-diff-perl libarchive-zip-perl libarray-compare-perl libasn1-8-heimdal libb-hooks-op-check-perl libbio-asn1-entrezgene-perl libbio-cluster-perl libbio-db-ncbihelper-perl libbio-eutilities-perl libbio-featureio-perl libbio-perl-perl libbio-perl-run-perl libbio-tools-run-alignment-clustalw-perl libbio-tools-run-remoteblast-perl libbio-variation-perl libbrotli1 libbsd0 libcache-cache-perl libcapture-tiny-perl libcbor0.6 libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libconfig-any-perl libcurl3-gnutls libdata-stag-perl libdebhelper-perl libdeflate0 libdevel-callchecker-perl libdevel-stacktrace-perl libdivsufsort3 libdynaloader-functions-perl libedit2 libelf1 libencode-locale-perl liberror-perl libevent-core-2.1-7 libevent-pthreads-2.1-7 libexception-class-perl libexpat1 libexporter-tiny-perl libfabric1 libfido2-1 libfile-listing-perl libfile-slurp-perl libfile-slurp-tiny-perl libfile-sort-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgd3 libgfortran5 libglib2.0-0 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhpdf-2.3.0 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts3 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libhwloc-plugins libhwloc15 libhx509-5-heimdal libibverbs1 libicu67 libimport-into-perl libio-html-perl libio-pty-perl libio-socket-ssl-perl libio-string-perl libipc-run-perl libipc-sharelite-perl libjbig0 libjpeg-turbo8 libjpeg8 libkrb5-26-heimdal libldap-2.4-2 liblmdb0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmodule-build-perl libmodule-pluggable-perl libmodule-runtime-perl libmoo-perl libmysqlclient21 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3 libparams-classify-perl libpciaccess0 libpipeline1 libpmix2 libpq5 libpsl5 libpsm-infinipath1 libpsm2-2 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librdmacm1 libroken18-heimdal librole-tiny-perl librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libstrictures-perl libsub-override-perl libsub-quote-perl libsub-uplevel-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-csv-perl libtext-diff-perl libtiff5 libtimedate-perl libtool libtree-dagnode-perl libtry-tiny-perl libtype-tiny-perl libuchardet0 libucx0 liburi-perl libwebp6 libwind0-heimdal libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml-dom-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-namespacesupport-perl libxml-parser-perl libxml-perl libxml-regexp-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libxml-xpathengine-perl libxml2 libxnvctrl0 libxpm4 m4 mafft mailcap man-db media-types mime-support muscle mysql-common ncbi-blast+ ncbi-blast+-legacy ncbi-data ncoils netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pal2nal perl-openssl-defaults pftools phyml po-debconf primer3 probcons python3 python3-minimal python3-pybedtools python3-pysam python3-six python3.9 python3.9-minimal raxml samtools sbuild-build-depends-bioperl-run-dummy sim4 tigr-glimmer ucf wise wise-data 0 upgraded, 240 newly installed, 0 to remove and 0 not upgraded. Need to get 213 MB of archives. After this operation, 1030 MB of additional disk space will be used. Get:1 copy:/<>/resolver-80qfGU/apt_archive ./ sbuild-build-depends-bioperl-run-dummy 0.invalid.0 [1176 B] Get:2 http://ftpmaster.internal/ubuntu hirsute/main amd64 libpython3.9-minimal amd64 3.9.1-1 [753 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute/main amd64 libexpat1 amd64 2.2.10-1 [76.0 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3.9-minimal amd64 3.9.1-1 [1909 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 python3-minimal amd64 3.9.1-1 [24.0 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 media-types all 2.0.0 [21.8 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/main amd64 mailcap all 3.68ubuntu1 [24.1 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute/main amd64 mime-support all 3.66 [3696 B] Get:9 http://ftpmaster.internal/ubuntu hirsute/main amd64 libpython3.9-stdlib amd64 3.9.1-1 [1754 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3.9 amd64 3.9.1-1 [414 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libpython3-stdlib amd64 3.9.1-1 [7244 B] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 python3 amd64 3.9.1-1 [48.8 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main amd64 bsdextrautils amd64 2.36.1-1ubuntu2 [77.3 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute/main amd64 libuchardet0 amd64 0.0.7-1 [68.0 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute/main amd64 groff-base amd64 1.22.4-5 [847 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute/main amd64 libpipeline1 amd64 1.5.3-1 [27.8 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute/main amd64 man-db amd64 2.9.3-2 [1117 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute/main amd64 libmagic-mgc amd64 1:5.39-3 [228 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute/main amd64 libmagic1 amd64 1:5.39-3 [80.6 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute/main amd64 file amd64 1:5.39-3 [23.7 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute/main amd64 libbsd0 amd64 0.10.0-1 [45.4 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute/main amd64 libelf1 amd64 0.182-3 [44.4 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libglib2.0-0 amd64 2.66.4-1 [1307 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute/main amd64 libicu67 amd64 67.1-5 [8618 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute/main amd64 libxml2 amd64 2.9.10+dfsg-6.3build1 [623 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute/main amd64 netbase all 6.2 [13.0 kB] Get:27 http://ftpmaster.internal/ubuntu hirsute/main amd64 ucf all 3.0043 [56.1 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 gettext-base amd64 0.21-3 [40.0 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcbor0.6 amd64 0.6.0-0ubuntu3 [21.7 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute/main amd64 libedit2 amd64 3.1-20191231-2 [87.8 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute/main amd64 libfido2-1 amd64 1.5.0-2 [52.2 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute/main amd64 liblmdb0 amd64 0.9.24-1 [44.6 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute/main amd64 libnuma1 amd64 2.0.12-1build1 [21.2 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute/main amd64 libpsl5 amd64 0.21.0-1.1ubuntu1 [52.3 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute/main amd64 libxau6 amd64 1:1.0.9-0ubuntu1 [7488 B] Get:36 http://ftpmaster.internal/ubuntu hirsute/main amd64 libxdmcp6 amd64 1:1.1.3-0ubuntu1 [10.6 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute/main amd64 libxcb1 amd64 1.14-2.1 [45.1 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libx11-data all 2:1.7.0-1 [112 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libx11-6 amd64 2:1.7.0-1 [574 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute/main amd64 libxext6 amd64 2:1.3.4-0ubuntu1 [29.1 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main amd64 openssh-client amd64 1:8.4p1-3 [695 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/universe amd64 amap-align amd64 2.2+git20080214.600fc29+dfsg-2 [133 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libsigsegv2 amd64 2.12-3 [14.0 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute/main amd64 m4 amd64 1.4.18-5 [200 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute/main amd64 autoconf all 2.69-14 [293 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute/main amd64 autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main amd64 automake all 1:1.16.3-2ubuntu1 [552 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 autopoint all 0.21-3 [423 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute-proposed/universe amd64 bedtools amd64 2.29.2+dfsg-5 [690 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute-proposed/universe amd64 bedtools-test all 2.29.2+dfsg-5 [10.9 MB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main amd64 libio-string-perl all 1.08-3.1 [10.7 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libdata-stag-perl all 0.14-2 [369 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libbio-perl-perl all 1.7.7-2 [2570 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute/main amd64 libclass-data-inheritable-perl all 0.08-3 [8084 B] Get:55 http://ftpmaster.internal/ubuntu hirsute/main amd64 libdevel-stacktrace-perl all 2.0400-1 [22.7 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute/main amd64 libexception-class-perl all 1.44-1 [25.9 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libtest-deep-perl all 1.130-1 [41.5 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcapture-tiny-perl all 0.48-1 [20.4 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute/main amd64 libalgorithm-diff-perl all 1.201-1 [41.8 kB] Get:60 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libtext-diff-perl all 1.45-1 [25.7 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libtest-differences-perl all 0.67-1 [16.3 kB] Get:62 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libsub-uplevel-perl all 0.2800-1.1 [13.6 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libtest-exception-perl all 0.43-1 [14.7 kB] Get:64 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libtest-warn-perl all 0.36-1 [14.0 kB] Get:65 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libtest-most-perl all 0.37-1 [22.5 kB] Get:66 http://ftpmaster.internal/ubuntu hirsute/universe amd64 bioperl all 1.7.7-2 [208 kB] Get:67 http://ftpmaster.internal/ubuntu hirsute/universe amd64 clustalw amd64 2.1+lgpl-7 [275 kB] Get:68 http://ftpmaster.internal/ubuntu hirsute/main amd64 libtool all 2.4.6-14 [161 kB] Get:69 http://ftpmaster.internal/ubuntu hirsute/main amd64 dh-autoreconf all 19 [16.1 kB] Get:70 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libdebhelper-perl all 13.3ubuntu4 [63.8 kB] Get:71 http://ftpmaster.internal/ubuntu hirsute/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:72 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsub-override-perl all 0.09-2 [9532 B] Get:73 http://ftpmaster.internal/ubuntu hirsute/main amd64 libfile-stripnondeterminism-perl all 1.9.0-1 [17.2 kB] Get:74 http://ftpmaster.internal/ubuntu hirsute/main amd64 dh-strip-nondeterminism all 1.9.0-1 [5192 B] Get:75 http://ftpmaster.internal/ubuntu hirsute/main amd64 dwz amd64 0.13+20201015-2 [173 kB] Get:76 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 gettext amd64 0.21-3 [824 kB] Get:77 http://ftpmaster.internal/ubuntu hirsute/main amd64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:78 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:79 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 debhelper all 13.3ubuntu4 [881 kB] Get:80 http://ftpmaster.internal/ubuntu hirsute/main amd64 libbrotli1 amd64 1.0.9-2build2 [274 kB] Get:81 http://ftpmaster.internal/ubuntu hirsute/main amd64 libfreetype6 amd64 2.10.4+dfsg-1 [349 kB] Get:82 http://ftpmaster.internal/ubuntu hirsute/main amd64 fonts-dejavu-core all 2.37-2 [1041 kB] Get:83 http://ftpmaster.internal/ubuntu hirsute/main amd64 fontconfig-config all 2.13.1-4.2ubuntu2 [28.6 kB] Get:84 http://ftpmaster.internal/ubuntu hirsute/main amd64 libfontconfig1 amd64 2.13.1-4.2ubuntu2 [117 kB] Get:85 http://ftpmaster.internal/ubuntu hirsute/main amd64 libjpeg-turbo8 amd64 2.0.3-0ubuntu2 [118 kB] Get:86 http://ftpmaster.internal/ubuntu hirsute/main amd64 libjpeg8 amd64 8c-2ubuntu8 [2194 B] Get:87 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libdeflate0 amd64 1.7-1 [52.7 kB] Get:88 http://ftpmaster.internal/ubuntu hirsute/main amd64 libjbig0 amd64 2.1-3.1build1 [26.7 kB] Get:89 http://ftpmaster.internal/ubuntu hirsute/main amd64 libwebp6 amd64 0.6.1-2 [185 kB] Get:90 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtiff5 amd64 4.2.0-1 [168 kB] Get:91 http://ftpmaster.internal/ubuntu hirsute/main amd64 libxpm4 amd64 1:3.5.12-1 [34.0 kB] Get:92 http://ftpmaster.internal/ubuntu hirsute/main amd64 libgd3 amd64 2.3.0-2 [118 kB] Get:93 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libhpdf-2.3.0 amd64 2.3.0+dfsg-1build1 [335 kB] Get:94 http://ftpmaster.internal/ubuntu hirsute/main amd64 mysql-common all 5.8+1.0.5ubuntu2 [7496 B] Get:95 http://ftpmaster.internal/ubuntu hirsute/main amd64 libmysqlclient21 amd64 8.0.22-0ubuntu0.20.10.2 [1221 kB] Get:96 http://ftpmaster.internal/ubuntu hirsute/main amd64 libroken18-heimdal amd64 7.7.0+dfsg-2 [41.8 kB] Get:97 http://ftpmaster.internal/ubuntu hirsute/main amd64 libasn1-8-heimdal amd64 7.7.0+dfsg-2 [181 kB] Get:98 http://ftpmaster.internal/ubuntu hirsute/main amd64 libheimbase1-heimdal amd64 7.7.0+dfsg-2 [29.7 kB] Get:99 http://ftpmaster.internal/ubuntu hirsute/main amd64 libhcrypto4-heimdal amd64 7.7.0+dfsg-2 [88.0 kB] Get:100 http://ftpmaster.internal/ubuntu hirsute/main amd64 libwind0-heimdal amd64 7.7.0+dfsg-2 [47.6 kB] Get:101 http://ftpmaster.internal/ubuntu hirsute/main amd64 libhx509-5-heimdal amd64 7.7.0+dfsg-2 [107 kB] Get:102 http://ftpmaster.internal/ubuntu hirsute/main amd64 libkrb5-26-heimdal amd64 7.7.0+dfsg-2 [207 kB] Get:103 http://ftpmaster.internal/ubuntu hirsute/main amd64 libheimntlm0-heimdal amd64 7.7.0+dfsg-2 [15.1 kB] Get:104 http://ftpmaster.internal/ubuntu hirsute/main amd64 libgssapi3-heimdal amd64 7.7.0+dfsg-2 [96.5 kB] Get:105 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2ubuntu1 [14.7 kB] Get:106 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2ubuntu1 [49.3 kB] Get:107 http://ftpmaster.internal/ubuntu hirsute/main amd64 libldap-2.4-2 amd64 2.4.56+dfsg-1ubuntu1 [156 kB] Get:108 http://ftpmaster.internal/ubuntu hirsute/main amd64 libpq5 amd64 13.1-1build1 [174 kB] Get:109 http://ftpmaster.internal/ubuntu hirsute/universe amd64 emboss-lib amd64 6.6.0+dfsg-7ubuntu2 [2695 kB] Get:110 http://ftpmaster.internal/ubuntu hirsute/universe amd64 emboss-data all 6.6.0+dfsg-7ubuntu2 [61.0 MB] Get:111 http://ftpmaster.internal/ubuntu hirsute/universe amd64 emboss amd64 6.6.0+dfsg-7ubuntu2 [994 kB] Get:112 http://ftpmaster.internal/ubuntu hirsute/universe amd64 exonerate amd64 2.4.0-5 [1608 kB] Get:113 http://ftpmaster.internal/ubuntu hirsute/universe amd64 hyphy-common all 2.5.24+dfsg-2 [562 kB] Get:114 http://ftpmaster.internal/ubuntu hirsute/main amd64 libnghttp2-14 amd64 1.42.0-1 [72.1 kB] Get:115 http://ftpmaster.internal/ubuntu hirsute/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build2 [55.0 kB] Get:116 http://ftpmaster.internal/ubuntu hirsute/main amd64 libssh-4 amd64 0.9.5-1 [172 kB] Get:117 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcurl3-gnutls amd64 7.72.0-1ubuntu1 [236 kB] Get:118 http://ftpmaster.internal/ubuntu hirsute/universe amd64 hyphy-pt amd64 2.5.24+dfsg-2 [916 kB] Get:119 http://ftpmaster.internal/ubuntu hirsute/main amd64 libnl-3-200 amd64 3.4.0-1 [53.9 kB] Get:120 http://ftpmaster.internal/ubuntu hirsute/main amd64 libnl-route-3-200 amd64 3.4.0-1 [149 kB] Get:121 http://ftpmaster.internal/ubuntu hirsute/main amd64 libibverbs1 amd64 33.0-1 [57.5 kB] Get:122 http://ftpmaster.internal/ubuntu hirsute/main amd64 ibverbs-providers amd64 33.0-1 [250 kB] Get:123 http://ftpmaster.internal/ubuntu hirsute/universe amd64 infernal amd64 1.1.4-1 [5522 kB] Get:124 http://ftpmaster.internal/ubuntu hirsute/universe amd64 kalign amd64 1:3.3-1 [134 kB] Get:125 http://ftpmaster.internal/ubuntu hirsute/universe amd64 lagan amd64 2.0-6 [181 kB] Get:126 http://ftpmaster.internal/ubuntu hirsute/main amd64 libclass-method-modifiers-perl all 2.13-1 [16.2 kB] Get:127 http://ftpmaster.internal/ubuntu hirsute/main amd64 libb-hooks-op-check-perl amd64 0.22-1build3 [10.3 kB] Get:128 http://ftpmaster.internal/ubuntu hirsute/main amd64 libdynaloader-functions-perl all 0.003-1.1 [12.1 kB] Get:129 http://ftpmaster.internal/ubuntu hirsute/main amd64 libdevel-callchecker-perl amd64 0.008-1ubuntu2 [14.5 kB] Get:130 http://ftpmaster.internal/ubuntu hirsute/main amd64 libparams-classify-perl amd64 0.015-1build3 [21.1 kB] Get:131 http://ftpmaster.internal/ubuntu hirsute/main amd64 libmodule-runtime-perl all 0.016-1 [16.2 kB] Get:132 http://ftpmaster.internal/ubuntu hirsute/main amd64 libimport-into-perl all 1.002005-1 [11.0 kB] Get:133 http://ftpmaster.internal/ubuntu hirsute/main amd64 librole-tiny-perl all 2.001004-1 [16.5 kB] Get:134 http://ftpmaster.internal/ubuntu hirsute/main amd64 libstrictures-perl all 2.000006-1 [16.3 kB] Get:135 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsub-quote-perl all 2.006006-1 [19.5 kB] Get:136 http://ftpmaster.internal/ubuntu hirsute/main amd64 libmoo-perl all 2.004004-1 [46.9 kB] Get:137 http://ftpmaster.internal/ubuntu hirsute/main amd64 libexporter-tiny-perl all 1.002002-1 [36.2 kB] Get:138 http://ftpmaster.internal/ubuntu hirsute/main amd64 libtype-tiny-perl all 1.012000-1 [316 kB] Get:139 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libarray-compare-perl all 3.0.8-1 [13.2 kB] Get:140 http://ftpmaster.internal/ubuntu hirsute/main amd64 liberror-perl all 0.17029-1 [26.5 kB] Get:141 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libipc-sharelite-perl amd64 0.17-4build4 [22.2 kB] Get:142 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libcache-cache-perl all 1.08-2 [72.8 kB] Get:143 http://ftpmaster.internal/ubuntu hirsute/main amd64 libhtml-tagset-perl all 3.20-4 [12.5 kB] Get:144 http://ftpmaster.internal/ubuntu hirsute/main amd64 liburi-perl all 5.05-1 [77.5 kB] Get:145 http://ftpmaster.internal/ubuntu hirsute/main amd64 libhtml-parser-perl amd64 3.75-1build1 [85.5 kB] Get:146 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcgi-pm-perl all 4.51-1 [186 kB] Get:147 http://ftpmaster.internal/ubuntu hirsute/main amd64 libencode-locale-perl all 1.05-1.1 [11.8 kB] Get:148 http://ftpmaster.internal/ubuntu hirsute/main amd64 libtimedate-perl all 2.3300-1 [33.9 kB] Get:149 http://ftpmaster.internal/ubuntu hirsute/main amd64 libhttp-date-perl all 6.05-1 [9920 B] Get:150 http://ftpmaster.internal/ubuntu hirsute/main amd64 libio-html-perl all 1.001-1.1 [14.4 kB] Get:151 http://ftpmaster.internal/ubuntu hirsute/main amd64 liblwp-mediatypes-perl all 6.04-1 [19.5 kB] Get:152 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libhttp-message-perl all 6.27-1 [75.7 kB] Get:153 http://ftpmaster.internal/ubuntu hirsute/main amd64 libfile-listing-perl all 6.14-1 [11.2 kB] Get:154 http://ftpmaster.internal/ubuntu hirsute/main amd64 libhtml-tree-perl all 5.07-2 [200 kB] Get:155 http://ftpmaster.internal/ubuntu hirsute/main amd64 libhttp-cookies-perl all 6.10-1 [18.4 kB] Get:156 http://ftpmaster.internal/ubuntu hirsute/main amd64 libhttp-negotiate-perl all 6.01-1 [12.5 kB] Get:157 http://ftpmaster.internal/ubuntu hirsute/main amd64 perl-openssl-defaults amd64 5 [7404 B] Get:158 http://ftpmaster.internal/ubuntu hirsute/main amd64 libnet-ssleay-perl amd64 1.88-2ubuntu2 [291 kB] Get:159 http://ftpmaster.internal/ubuntu hirsute/main amd64 libio-socket-ssl-perl all 2.068-1 [179 kB] Get:160 http://ftpmaster.internal/ubuntu hirsute/main amd64 libnet-http-perl all 6.19-1 [22.8 kB] Get:161 http://ftpmaster.internal/ubuntu hirsute/main amd64 liblwp-protocol-https-perl all 6.10-1 [10.9 kB] Get:162 http://ftpmaster.internal/ubuntu hirsute/main amd64 libtry-tiny-perl all 0.30-1 [20.5 kB] Get:163 http://ftpmaster.internal/ubuntu hirsute/main amd64 libwww-robotrules-perl all 6.02-1 [12.6 kB] Get:164 http://ftpmaster.internal/ubuntu hirsute/main amd64 libwww-perl all 6.51-1 [140 kB] Get:165 http://ftpmaster.internal/ubuntu hirsute/main amd64 libxml-parser-perl amd64 2.46-2 [192 kB] Get:166 http://ftpmaster.internal/ubuntu hirsute/main amd64 libxml-twig-perl all 1:3.52-1 [157 kB] Get:167 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libbio-db-ncbihelper-perl all 1.7.6-2 [57.2 kB] Get:168 http://ftpmaster.internal/ubuntu hirsute/main amd64 libxml-writer-perl all 0.900-1 [25.1 kB] Get:169 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libbio-variation-perl all 1.7.5-1 [72.1 kB] Get:170 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libbio-cluster-perl all 1.7.3-5 [53.0 kB] Get:171 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libbio-asn1-entrezgene-perl all 1.730-1 [46.6 kB] Get:172 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libtext-csv-perl all 2.00-1 [101 kB] Get:173 http://ftpmaster.internal/ubuntu hirsute/main amd64 libxml-namespacesupport-perl all 1.12-1.1 [13.2 kB] Get:174 http://ftpmaster.internal/ubuntu hirsute/main amd64 libxml-sax-base-perl all 1.09-1.1 [19.0 kB] Get:175 http://ftpmaster.internal/ubuntu hirsute/main amd64 libxml-sax-perl all 1.02+dfsg-1 [56.2 kB] Get:176 http://ftpmaster.internal/ubuntu hirsute/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-2build1 [312 kB] Get:177 http://ftpmaster.internal/ubuntu hirsute/main amd64 libxml-simple-perl all 2.25-1 [64.9 kB] Get:178 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libbio-eutilities-perl all 1.77-1 [123 kB] Get:179 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libfile-slurp-tiny-perl all 0.004-1 [6940 B] Get:180 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libtree-dagnode-perl all 1.31-1 [54.7 kB] Get:181 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libxml-perl all 0.08-3.1 [91.1 kB] Get:182 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libxml-regexp-perl all 0.04-1.1 [7208 B] Get:183 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libxml-dom-perl all 1.46-1 [144 kB] Get:184 http://ftpmaster.internal/ubuntu hirsute/main amd64 libxml-xpathengine-perl all 0.14-1 [31.8 kB] Get:185 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libxml-dom-xpath-perl all 0.14-3 [8002 B] Get:186 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libbio-featureio-perl all 1.6.905-2 [52.8 kB] Get:187 http://ftpmaster.internal/ubuntu hirsute/main amd64 libio-pty-perl amd64 1:1.15-2 [32.7 kB] Get:188 http://ftpmaster.internal/ubuntu hirsute/main amd64 libipc-run-perl all 20200505.0-1 [89.8 kB] Get:189 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libfile-sort-perl all 1.01-2 [21.2 kB] Get:190 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libbio-perl-run-perl all 1.7.3-5 [602 kB] Get:191 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libbio-tools-run-alignment-clustalw-perl all 1.7.4-2 [24.0 kB] Get:192 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libbio-tools-run-remoteblast-perl all 1.7.3-3 [17.3 kB] Get:193 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libmodule-pluggable-perl all 5.2-1 [21.9 kB] Get:194 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libconfig-any-perl all 0.32-1 [28.4 kB] Get:195 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libdivsufsort3 amd64 2.0.1-5 [42.8 kB] Get:196 http://ftpmaster.internal/ubuntu hirsute/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-1 [89.4 kB] Get:197 http://ftpmaster.internal/ubuntu hirsute/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-1 [7364 B] Get:198 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.1 [170 kB] Get:199 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libpsm2-2 amd64 11.2.185-1 [182 kB] Get:200 http://ftpmaster.internal/ubuntu hirsute/main amd64 librdmacm1 amd64 33.0-1 [65.9 kB] Get:201 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libfabric1 amd64 1.11.0-2 [522 kB] Get:202 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libfile-slurp-perl all 9999.32-1 [21.5 kB] Get:203 http://ftpmaster.internal/ubuntu 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Selecting previously unselected package libpython3.9-minimal:amd64. 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Adding 'diversion of /usr/bin/config_data to /usr/bin/config_data.diverted by libmodule-build-perl' Adding 'diversion of /usr/share/man/man1/config_data.1.gz to /usr/share/man/man1/config_data.diverted.1.gz by libmodule-build-perl' Unpacking libmodule-build-perl (0.423100-1) ... Selecting previously unselected package libpciaccess0:amd64. Preparing to unpack .../198-libpciaccess0_0.16-1_amd64.deb ... Unpacking libpciaccess0:amd64 (0.16-1) ... Selecting previously unselected package libxnvctrl0:amd64. Preparing to unpack .../199-libxnvctrl0_440.82-0ubuntu1_amd64.deb ... Unpacking libxnvctrl0:amd64 (440.82-0ubuntu1) ... Selecting previously unselected package ocl-icd-libopencl1:amd64. Preparing to unpack .../200-ocl-icd-libopencl1_2.2.13-1_amd64.deb ... Unpacking ocl-icd-libopencl1:amd64 (2.2.13-1) ... Selecting previously unselected package libhwloc-plugins:amd64. Preparing to unpack .../201-libhwloc-plugins_2.4.0+dfsg-3_amd64.deb ... Unpacking libhwloc-plugins:amd64 (2.4.0+dfsg-3) ... 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Setting up libxau6:amd64 (1:1.0.9-0ubuntu1) ... Setting up libhpdf-2.3.0:amd64 (2.3.0+dfsg-1build1) ... Setting up libpsl5:amd64 (0.21.0-1.1ubuntu1) ... Setting up libfile-slurp-perl (9999.32-1) ... Setting up bsdextrautils (2.36.1-1ubuntu2) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up probcons (1.12-13) ... Setting up libicu67:amd64 (67.1-5) ... Setting up libdynaloader-functions-perl (0.003-1.1) ... Setting up libtest-deep-perl (1.130-1) ... Setting up libclass-method-modifiers-perl (2.13-1) ... Setting up libxml-regexp-perl (0.04-1.1) ... Setting up libio-pty-perl (1:1.15-2) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up mafft (7.475-1) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.66.4-1) ... No schema files found: doing nothing. Setting up libhtml-tagset-perl (3.20-4) ... Setting up libdebhelper-perl (13.3ubuntu4) ... 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Setting up infernal (1.1.4-1) ... Setting up libxml-sax-base-perl (1.09-1.1) ... Setting up libio-string-perl (1.08-3.1) ... Setting up primer3 (2.4.0-4) ... Setting up kalign (1:3.3-1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up lagan (2.0-6) ... Setting up libfreetype6:amd64 (2.10.4+dfsg-1) ... Setting up libx11-data (2:1.7.0-1) ... Setting up libtext-diff-perl (1.45-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build2) ... Setting up libxml-xpathengine-perl (0.14-1) ... Setting up sim4 (0.0.20121010-8) ... Setting up libxml-writer-perl (0.900-1) ... Setting up libsigsegv2:amd64 (2.12-3) ... Setting up libhwloc15:amd64 (2.4.0+dfsg-3) ... Setting up libevent-core-2.1-7:amd64 (2.1.12-stable-1) ... Setting up libio-html-perl (1.001-1.1) ... Setting up autopoint (0.21-3) ... Setting up libwebp6:amd64 (0.6.1-2) ... Setting up libb-hooks-op-check-perl (0.22-1build3) ... 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Setting up openmpi-common (4.0.5-7ubuntu1) ... Setting up libconfig-any-perl (0.32-1) ... Setting up clustalw (2.1+lgpl-7) ... Setting up libmbedcrypto3:amd64 (2.16.9-0.1ubuntu1) ... Setting up libsub-uplevel-perl (0.2800-1.1) ... Setting up libsub-override-perl (0.09-2) ... Setting up fasttree (2.1.11-2) ... Setting up netbase (6.2) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006006-1) ... Setting up libdevel-stacktrace-perl (2.0400-1) ... Setting up libbio-perl-perl (1.7.7-2) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.1) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up bedtools-test (2.29.2+dfsg-5) ... Setting up libexporter-tiny-perl (1.002002-1) ... Setting up libfido2-1:amd64 (1.5.0-2) ... Setting up libdivsufsort3:amd64 (2.0.1-5) ... Setting up libbsd0:amd64 (0.10.0-1) ... 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Setting up libfile-listing-perl (6.14-1) ... Setting up mime-support (3.66) ... Setting up libcache-cache-perl (1.08-2) ... Setting up libtool (2.4.6-14) ... Setting up libmbedx509-0:amd64 (2.16.9-0.1ubuntu1) ... Setting up fontconfig-config (2.13.1-4.2ubuntu2) ... Setting up wise (2.4.1-23) ... Setting up libtest-warn-perl (0.36-1) ... Setting up libasn1-8-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libedit2:amd64 (3.1-20191231-2) ... Setting up libmbedtls12:amd64 (2.16.9-0.1ubuntu1) ... Setting up libtype-tiny-perl (1.012000-1) ... Setting up libtest-differences-perl (0.67-1) ... Setting up libnet-http-perl (6.19-1) ... Setting up m4 (1.4.18-5) ... Setting up libexception-class-perl (1.44-1) ... Setting up libdevel-callchecker-perl (0.008-1ubuntu2) ... Setting up libxml-sax-perl (1.02+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libhcrypto4-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libnl-route-3-200:amd64 (3.4.0-1) ... Setting up libbio-tools-run-alignment-clustalw-perl (1.7.4-2) ... Setting up libwind0-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libtest-exception-perl (0.43-1) ... Setting up autoconf (2.69-14) ... Setting up libxml-libxml-perl (2.0134+dfsg-2build1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up dwz (0.13+20201015-2) ... Setting up groff-base (1.22.4-5) ... 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Setting up libcgi-pm-perl (4.51-1) ... Setting up libxext6:amd64 (2:1.3.4-0ubuntu1) ... Setting up python3 (3.9.1-1) ... Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libxnvctrl0:amd64 (440.82-0ubuntu1) ... Setting up ncbi-blast+ (2.10.1+ds-1) ... Setting up python3-six (1.15.0-2) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libgd3:amd64 (2.3.0-2) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libkrb5-26-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up bioperl (1.7.7-2) ... Setting up ncbi-blast+-legacy (2.10.1+ds-1) ... Setting up librdmacm1:amd64 (33.0-1) ... Setting up libucx0:amd64 (1.9.0~rc1-2build4) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libmoo-perl (2.004004-1) ... Setting up libhwloc-plugins:amd64 (2.4.0+dfsg-3) ... Setting up libheimntlm0-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libarray-compare-perl (3.0.8-1) ... Setting up libgssapi3-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libfabric1 (1.11.0-2) ... Setting up libpmix2:amd64 (3.2.2~rc1-1ubuntu1) ... Setting up libopenmpi3:amd64 (4.0.5-7ubuntu1) ... Setting up libldap-2.4-2:amd64 (2.4.56+dfsg-1ubuntu1) ... Setting up libcurl3-gnutls:amd64 (7.72.0-1ubuntu1) ... Setting up hyphy-pt (2.5.24+dfsg-2) ... Setting up openmpi-bin (4.0.5-7ubuntu1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up phyml (3:3.3.20200621-1) ... Setting up libhts3:amd64 (1.11-4) ... Setting up python3-pysam (0.15.4+ds-3build2) ... Setting up libpq5:amd64 (13.1-1build1) ... Setting up samtools (1.11-1) ... Setting up emboss-lib (6.6.0+dfsg-7ubuntu2) ... Setting up python3-pybedtools (0.8.0-5build2) ... Setting up emboss (6.6.0+dfsg-7ubuntu2) ... Setting up libbio-asn1-entrezgene-perl (1.730-1) ... Setting up dh-autoreconf (19) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up libwww-perl (6.51-1) ... Setting up debhelper (13.3ubuntu4) ... Setting up libbio-eutilities-perl (1.77-1) ... Setting up libbio-tools-run-remoteblast-perl (1.7.3-3) ... Setting up libxml-parser-perl:amd64 (2.46-2) ... Setting up libxml-twig-perl (1:3.52-1) ... Setting up libbio-db-ncbihelper-perl (1.7.6-2) ... Setting up libxml-perl (0.08-3.1) ... Setting up libxml-dom-perl (1.46-1) ... Setting up libxml-dom-xpath-perl (0.14-3) ... Setting up libbio-variation-perl (1.7.5-1) ... Setting up libbio-featureio-perl (1.6.905-2) ... Setting up libbio-cluster-perl (1.7.3-5) ... Setting up sbuild-build-depends-bioperl-run-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.32-0ubuntu6) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-129-generic amd64 (x86_64) Toolchain package versions: binutils_2.35.50.20210106-1ubuntu2 dpkg-dev_1.20.5ubuntu3 g++-10_10.2.1-2ubuntu3 gcc-10_10.2.1-2ubuntu3 libc6-dev_2.32-0ubuntu6 libstdc++-10-dev_10.2.1-2ubuntu3 libstdc++6_10.2.1-2ubuntu3 linux-libc-dev_5.8.0-34.37+21.04.1 Package versions: adduser_3.118ubuntu4 advancecomp_2.1-2.1build1 amap-align_2.2+git20080214.600fc29+dfsg-2 apt_2.1.15 autoconf_2.69-14 automake_1:1.16.3-2ubuntu1 autopoint_0.21-3 autotools-dev_20180224.1+nmu1 base-files_11ubuntu16 base-passwd_3.5.48 bash_5.1-1ubuntu1 bedtools_2.29.2+dfsg-5 bedtools-test_2.29.2+dfsg-5 binutils_2.35.50.20210106-1ubuntu2 binutils-common_2.35.50.20210106-1ubuntu2 binutils-x86-64-linux-gnu_2.35.50.20210106-1ubuntu2 bioperl_1.7.7-2 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libunistring2_0.9.10-4 liburi-perl_5.05-1 libuuid1_2.36.1-1ubuntu2 libwebp6_0.6.1-2 libwind0-heimdal_7.7.0+dfsg-2 libwww-perl_6.51-1 libwww-robotrules-perl_6.02-1 libx11-6_2:1.7.0-1 libx11-data_2:1.7.0-1 libxau6_1:1.0.9-0ubuntu1 libxcb1_1.14-2.1 libxdmcp6_1:1.1.3-0ubuntu1 libxext6_2:1.3.4-0ubuntu1 libxml-dom-perl_1.46-1 libxml-dom-xpath-perl_0.14-3 libxml-libxml-perl_2.0134+dfsg-2build1 libxml-namespacesupport-perl_1.12-1.1 libxml-parser-perl_2.46-2 libxml-perl_0.08-3.1 libxml-regexp-perl_0.04-1.1 libxml-sax-base-perl_1.09-1.1 libxml-sax-perl_1.02+dfsg-1 libxml-simple-perl_2.25-1 libxml-twig-perl_1:3.52-1 libxml-writer-perl_0.900-1 libxml-xpathengine-perl_0.14-1 libxml2_2.9.10+dfsg-6.3build1 libxnvctrl0_440.82-0ubuntu1 libxpm4_1:3.5.12-1 libxxhash0_0.8.0-1 libzstd1_1.4.8+dfsg-1 linux-libc-dev_5.8.0-34.37+21.04.1 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu7 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-5 mafft_7.475-1 mailcap_3.68ubuntu1 make_4.3-4ubuntu1 man-db_2.9.3-2 mawk_1.3.4.20200120-2 media-types_2.0.0 mime-support_3.66 mount_2.36.1-1ubuntu2 muscle_1:3.8.1551-2build1 mysql-common_5.8+1.0.5ubuntu2 ncbi-blast+_2.10.1+ds-1 ncbi-blast+-legacy_2.10.1+ds-1 ncbi-data_6.1.20170106+dfsg1-9 ncoils_2002-8 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 netbase_6.2 ocl-icd-libopencl1_2.2.13-1 openmpi-bin_4.0.5-7ubuntu1 openmpi-common_4.0.5-7ubuntu1 openssh-client_1:8.4p1-3 openssl_1.1.1f-1ubuntu5 optipng_0.7.7-1 pal2nal_14.1-3 passwd_1:4.8.1-1ubuntu7 patch_2.7.6-6 perl_5.32.0-6 perl-base_5.32.0-6 perl-modules-5.30_5.30.3-4 perl-modules-5.32_5.32.0-6 perl-openssl-defaults_5 pftools_3.2.6-1 phyml_3:3.3.20200621-1 pinentry-curses_1.1.0-4build1 pkgbinarymangler_146 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 primer3_2.4.0-4 probcons_1.12-13 procps_2:3.3.16-5ubuntu2 python3_3.9.1-1 python3-minimal_3.9.1-1 python3-pybedtools_0.8.0-5build2 python3-pysam_0.15.4+ds-3build2 python3-six_1.15.0-2 python3.9_3.9.1-1 python3.9-minimal_3.9.1-1 raxml_8.2.12+dfsg-6 readline-common_8.1-1 rpcsvc-proto_1.4.2-0ubuntu4 samtools_1.11-1 sbuild-build-depends-bioperl-run-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1ubuntu1 sensible-utils_0.0.13 sim4_0.0.20121010-8 systemd_247.1-4ubuntu1 systemd-sysv_247.1-4ubuntu1 systemd-timesyncd_247.1-4ubuntu1 sysvinit-utils_2.96-5ubuntu1 tar_1.32+dfsg-1 tigr-glimmer_3.02b-5 tzdata_2020f-1ubuntu1 ubuntu-keyring_2020.06.17.1 ucf_3.0043 util-linux_2.36.1-1ubuntu2 wise_2.4.1-23 wise-data_2.4.1-23 xz-utils_5.2.4-1ubuntu1 zlib1g_1:1.2.11.dfsg-2ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Wed Jan 6 21:46:40 2021 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bioperl-run_1.7.3-6.dsc dpkg-source: info: extracting bioperl-run in /<> dpkg-source: info: unpacking bioperl-run_1.7.3.orig.tar.gz dpkg-source: info: unpacking bioperl-run_1.7.3-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Extract_version_from_BEDTools_properly.patch dpkg-source: info: applying skip_tests_for_RemoteBlast_rpsblast.patch dpkg-source: info: applying skip_tests_for_RemoteBlast.patch dpkg-source: info: applying kalign-input-via-piping.patch dpkg-source: info: applying kalign-version-regex.patch dpkg-source: info: applying skip_tests_for_wise.patch dpkg-source: info: applying skip_tests_for_phylip.patch dpkg-source: info: applying skip_tests_for_phyml.patch dpkg-source: info: applying skip_tests_for_infernal.patch dpkg-source: info: applying skip_tests_for_muscle.patch dpkg-source: info: applying skip_tests_for_ncbi-blast+.patch dpkg-source: info: applying hyphy.patch dpkg-source: info: applying remove_tests_for_ensembl.patch dpkg-source: info: applying skip_tests_for_soap.patch dpkg-source: info: applying get-overlap.patch dpkg-source: info: applying alternate-data.patch dpkg-source: info: applying skip-test-for-kalign.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-20778089 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-20778089 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-20778089 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package bioperl-run dpkg-buildpackage: info: source version 1.7.3-6 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- --install_scripts perl 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,-Bsymbolic-functions -Wl,-z,relro" --install_scripts Do you want to run tests that require connection to servers across the internet (likely to cause some failures)? y/n [n ]n Can't find dist packages without a MANIFEST file Run 'Build manifest' to generate one WARNING: Possible missing or corrupt 'MANIFEST' file. Nothing to enter for 'provides' field in metafile. - will not run internet-requiring tests Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'BioPerl-Run' version '1.007003' make[1]: Leaving directory '/<>' 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 RepeatMasker Phyml Hyphy MCS ; do mv t/${t}.t t.skip ; done PATH=$PATH:/usr/lib/emboss:/usr/lib/phylip/bin/:/usr/lib/tigr-glimmer:debian/test_hack_bin \ PHYLIPDIR=/usr/lib/phylip/bin HOME_4_TCOFFEE=/tmp COILSDIR=/usr/share/ncoils/ \ dh_auto_test --no-parallel perl Build test --verbose 1 AMAP version AMAP.2.2 - align multiple protein sequences and print to standard output PROBCONS Written by Chuong Do AMAP algorithm implemented by Ariel Schwartz Using parameter set: initDistrib[] = { 0.400000006 0.3000000119 0.3000000119 } gapOpen[] = { 0.01993141696 0.01993141696 } gapExtend[] = { 0.7943345308 0.7943345308 } Loading sequence file: t/data/cysprot.fa Computing posterior matrices Building DAG Starting the sequence annealing process Creating candidate edge list Adding edges to the DAG AMAP version AMAP.2.2 - align multiple protein sequences and print to standard output PROBCONS Written by Chuong Do AMAP algorithm implemented by Ariel Schwartz Using parameter set: initDistrib[] = { 0.400000006 0.3000000119 0.3000000119 } gapOpen[] = { 0.01993141696 0.01993141696 } gapExtend[] = { 0.7943345308 0.7943345308 } Loading sequence file: /tmp/NVafIOqXWN Computing posterior matrices Building DAG Starting the sequence annealing process Creating candidate edge list Adding edges to the DAG t/Amap.t ...................... 1..18 ok 1 - use Bio::Tools::Run::Alignment::Amap; ok 2 - use Bio::SeqIO; ok 3 - use File::Spec; ok 4 - Found input file ok 5 - An object of class 'Bio::Tools::Run::Alignment::Amap' isa 'Bio::Tools::Run::Alignment::Amap' ok 6 - program_dir returned correct default ok 7 - error_string returned correct default ok 8 - aformat returned correct default ok 9 - outfile_name returned correct default ok 10 - Correct exe default name ok 11 - Correct minimum program version ok 12 - No error occured ok 13 - outfile_name returned something ok 14 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 15 - Correct number of seqs returned ok 16 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 17 - Correct number of seqs returned ok 18 - Got the correct ave % identity ok t/BEDTools.t .................. 1..423 ok 1 - make a default factory ok 2 - default to command 'bam_to_bed' ok 3 - make a factory using command 'annotate' ok 4 - factory command for 'annotate' is correct ok 5 - all available options for 'annotate' ok 6 - available parameters for 'annotate' ok 7 - available switches for 'annotate' ok 8 - get version for 'annotate' ok 9 - can run command 'annotate' ok 10 - result files exists for command 'annotate' ok 11 - can return output format for command 'annotate' ok 12 - result claims to be in correct format for command 'annotate' ok 13 - can return output file for command 'annotate' ok 14 - file format of '/tmp/TmZ0TRjXXP/krre7x2Liq.bed' consistent with claim for 'annotate' ok 15 - can set want to IO object for command 'annotate' ok 16 - can get the basic object result for command 'annotate' ok 17 - 'returned object is correct for command 'annotate'' isa 'Bio::Root::IO' ok 18 - can get the specific object result for command 'annotate' ok 19 - 'returned object is correct for command 'annotate'' isa 'Bio::SeqFeature::Collection' ok 20 - correct number of features for command 'annotate' # TODO maybe adapt reference results to Debian specific dataset ok 21 - make a factory using command 'fasta_from_bed' ok 22 - factory command for 'fasta_from_bed' is correct ok 23 - all available options for 'fasta_from_bed' ok 24 - available parameters for 'fasta_from_bed' ok 25 - available switches for 'fasta_from_bed' ok 26 - get version for 'fasta_from_bed' ok 27 - can run command 'fasta_from_bed' ok 28 - result files exists for command 'fasta_from_bed' ok 29 - can return output format for command 'fasta_from_bed' ok 30 - result claims to be in correct format for command 'fasta_from_bed' ok 31 - can return output file for command 'fasta_from_bed' ok 32 - file format consistent with claim for 'fasta_from_bed' ok 33 - can set want to IO object for command 'fasta_from_bed' ok 34 - can get the basic object result for command 'fasta_from_bed' ok 35 - 'returned object is correct for command 'fasta_from_bed'' isa 'Bio::Root::IO' ok 36 - can get the specific object result for command 'fasta_from_bed' ok 37 - 'returned object is correct for command 'fasta_from_bed'' isa 'Bio::SeqIO' ok 38 - correct number of sequences for command 'fasta_from_bed' ok 39 - make a factory using command 'overlap' ok 40 - factory command for 'overlap' is correct ok 41 - all available options for 'overlap' ok 42 - available parameters for 'overlap' ok 43 - available switches for 'overlap' ok 44 - get version for 'overlap' ok 45 - can set parameter -columns => '2,3,5,6' ok 46 - can run command 'overlap' ok 47 - result files exists for command 'overlap' ok 48 - can return output format for command 'overlap' ok 49 - result claims to be in correct format for command 'overlap' ok 50 - can return output file for command 'overlap' ok 51 - file format of '/tmp/c_f5DoAhiA/8wMwKJPNXE.bed' consistent with claim for 'overlap' ok 52 - can set want to IO object for command 'overlap' ok 53 - can get the basic object result for command 'overlap' ok 54 - 'returned object is correct for command 'overlap'' isa 'Bio::Root::IO' ok 55 - can get the specific object result for command 'overlap' ok 56 - 'returned object is correct for command 'overlap'' isa 'Bio::SeqFeature::Collection' ok 57 - correct number of features for command 'overlap' # TODO maybe adapt reference results to Debian specific dataset ok 58 - make a factory using command 'bam_to_bed' ok 59 - factory command for 'bam_to_bed' is correct ok 60 - all available options for 'bam_to_bed' ok 61 - available parameters for 'bam_to_bed' ok 62 - available switches for 'bam_to_bed' ok 63 - get version for 'bam_to_bed' ok 64 - can run command 'bam_to_bed' ok 65 - result files exists for command 'bam_to_bed' ok 66 - can return output format for command 'bam_to_bed' ok 67 - result claims to be in correct format for command 'bam_to_bed' ok 68 - can return output file for command 'bam_to_bed' ok 69 - file format of '/tmp/MjQkzO78yX/RSt_ylQAbF.bed' consistent with claim for 'bam_to_bed' ok 70 - can set want to IO object for command 'bam_to_bed' ok 71 - can get the basic object result for command 'bam_to_bed' ok 72 - 'returned object is correct for command 'bam_to_bed'' isa 'Bio::Root::IO' ok 73 - can get the specific object result for command 'bam_to_bed' ok 74 - 'returned object is correct for command 'bam_to_bed'' isa 'Bio::SeqFeature::Collection' ok 75 - correct number of features for command 'bam_to_bed' # TODO maybe adapt reference results to Debian specific dataset ok 76 - make a factory using command 'genome_coverage' ok 77 - factory command for 'genome_coverage' is correct ok 78 - all available options for 'genome_coverage' ok 79 - available parameters for 'genome_coverage' ok 80 - available switches for 'genome_coverage' ok 81 - get version for 'genome_coverage' ok 82 - can run command 'genome_coverage' ok 83 - result files exists for command 'genome_coverage' ok 84 - can return output format for command 'genome_coverage' ok 85 - result claims to be in correct format for command 'genome_coverage' ok 86 - can return output file for command 'genome_coverage' ok 87 - make readable output not ok 88 - - number of lines # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test ' - number of lines' # at t/BEDTools.t line 331. # got: '87' # expected: '38' ok 89 - can set want to IO object for command 'genome_coverage' ok 90 - can get the basic object result for command 'genome_coverage' ok 91 - 'returned object is correct for command 'genome_coverage'' isa 'Bio::Root::IO' ok 92 - make a factory using command 'pair_to_pair' ok 93 - factory command for 'pair_to_pair' is correct ok 94 - all available options for 'pair_to_pair' ok 95 - available parameters for 'pair_to_pair' ok 96 - available switches for 'pair_to_pair' ok 97 - get version for 'pair_to_pair' ok 98 - can set parameter -type => 'neither' ok 99 - can run command 'pair_to_pair' ok 100 - result files exists for command 'pair_to_pair' ok 101 - can return output format for command 'pair_to_pair' ok 102 - result claims to be in correct format for command 'pair_to_pair' ok 103 - can return output file for command 'pair_to_pair' ok 104 - file format of '/tmp/bPBnR7AmXM/l77HOMLu7v.bedpe' consistent with claim for 'pair_to_pair' ok 105 - can set want to IO object for command 'pair_to_pair' ok 106 - can get the basic object result for command 'pair_to_pair' ok 107 - 'returned object is correct for command 'pair_to_pair'' isa 'Bio::Root::IO' ok 108 - can get the specific object result for command 'pair_to_pair' ok 109 - 'returned object is correct for command 'pair_to_pair'' isa 'Bio::SeqFeature::Collection' ok 110 - correct number of features for command 'pair_to_pair' # TODO maybe adapt reference results to Debian specific dataset ok 111 - make a factory using command 'bed_to_bam' ok 112 - factory command for 'bed_to_bam' is correct ok 113 - all available options for 'bed_to_bam' ok 114 - available parameters for 'bed_to_bam' ok 115 - available switches for 'bed_to_bam' ok 116 - get version for 'bed_to_bam' ok 117 - can run command 'bed_to_bam' ok 118 - result files exists for command 'bed_to_bam' ok 119 - can return output format for command 'bed_to_bam' ok 120 - result claims to be in correct format for command 'bed_to_bam' ok 121 - can return output file for command 'bed_to_bam' ok 122 - can set want to IO object for command 'bed_to_bam' ok 123 - can get the basic object result for command 'bed_to_bam' ok 124 - 'returned object is correct for command 'bed_to_bam'' isa 'Bio::Root::IO' ok 125 - make a factory using command 'graph_union' ok 126 - factory command for 'graph_union' is correct ok 127 - all available options for 'graph_union' ok 128 - available parameters for 'graph_union' ok 129 - available switches for 'graph_union' ok 130 - get version for 'graph_union' ok 131 - can run command 'graph_union' ok 132 - result files exists for command 'graph_union' ok 133 - can return output format for command 'graph_union' ok 134 - result claims to be in correct format for command 'graph_union' ok 135 - can return output file for command 'graph_union' ok 136 - can set want to IO object for command 'graph_union' ok 137 - can get the basic object result for command 'graph_union' ok 138 - 'returned object is correct for command 'graph_union'' isa 'Bio::Root::IO' ok 139 - make a factory using command 'pair_to_bed' ok 140 - factory command for 'pair_to_bed' is correct ok 141 - all available options for 'pair_to_bed' ok 142 - available parameters for 'pair_to_bed' ok 143 - available switches for 'pair_to_bed' ok 144 - get version for 'pair_to_bed' ok 145 - can run command 'pair_to_bed' ok 146 - result files exists for command 'pair_to_bed' ok 147 - can return output format for command 'pair_to_bed' ok 148 - result claims to be in correct format for command 'pair_to_bed' ok 149 - can return output file for command 'pair_to_bed' ok 150 - can set want to IO object for command 'pair_to_bed' ok 151 - can get the basic object result for command 'pair_to_bed' ok 152 - 'returned object is correct for command 'pair_to_bed'' isa 'Bio::Root::IO' ok 153 - can get the specific object result for command 'pair_to_bed' ok 154 - 'returned object is correct for command 'pair_to_bed'' isa 'Bio::SeqFeature::Collection' ok 155 - correct number of features for command 'pair_to_bed' # TODO maybe adapt reference results to Debian specific dataset ok 156 - make a factory using command 'bed_to_IGV' ok 157 - factory command for 'bed_to_IGV' is correct ok 158 - all available options for 'bed_to_IGV' ok 159 - available parameters for 'bed_to_IGV' ok 160 - available switches for 'bed_to_IGV' ok 161 - get version for 'bed_to_IGV' ok 162 - can run command 'bed_to_IGV' ok 163 - result files exists for command 'bed_to_IGV' ok 164 - can return output format for command 'bed_to_IGV' ok 165 - result claims to be in correct format for command 'bed_to_IGV' ok 166 - can return output file for command 'bed_to_IGV' ok 167 - can set want to IO object for command 'bed_to_IGV' ok 168 - can get the basic object result for command 'bed_to_IGV' ok 169 - 'returned object is correct for command 'bed_to_IGV'' isa 'Bio::Root::IO' ok 170 - make a factory using command 'group_by' ok 171 - factory command for 'group_by' is correct ok 172 - all available options for 'group_by' ok 173 - available parameters for 'group_by' ok 174 - available switches for 'group_by' ok 175 - get version for 'group_by' ok 176 - can set parameter -group => 1 ok 177 - can set parameter -columns => '2,2,3,3' ok 178 - can set parameter -operations => 'min,max,min,max' ok 179 - can run command 'group_by' ok 180 - result files exists for command 'group_by' ok 181 - can return output format for command 'group_by' ok 182 - result claims to be in correct format for command 'group_by' ok 183 - can return output file for command 'group_by' ok 184 - file format of '/tmp/6ySkU1JnQ_/x2ortuY3sZ.bed' consistent with claim for 'group_by' ok 185 - can set want to IO object for command 'group_by' ok 186 - can get the basic object result for command 'group_by' ok 187 - 'returned object is correct for command 'group_by'' isa 'Bio::Root::IO' ok 188 - can get the specific object result for command 'group_by' ok 189 - 'returned object is correct for command 'group_by'' isa 'Bio::SeqFeature::Collection' ok 190 - correct number of features for command 'group_by' # TODO maybe adapt reference results to Debian specific dataset ok 191 - make a factory using command 'shuffle' ok 192 - factory command for 'shuffle' is correct ok 193 - all available options for 'shuffle' ok 194 - available parameters for 'shuffle' ok 195 - available switches for 'shuffle' ok 196 - get version for 'shuffle' ok 197 - can run command 'shuffle' ok 198 - result files exists for command 'shuffle' ok 199 - can return output format for command 'shuffle' ok 200 - result claims to be in correct format for command 'shuffle' ok 201 - can return output file for command 'shuffle' ok 202 - file format of '/tmp/eNK_NYo7fj/eO6sGwkYvI.bed' consistent with claim for 'shuffle' ok 203 - can set want to IO object for command 'shuffle' ok 204 - can get the basic object result for command 'shuffle' ok 205 - 'returned object is correct for command 'shuffle'' isa 'Bio::Root::IO' ok 206 - can get the specific object result for command 'shuffle' ok 207 - 'returned object is correct for command 'shuffle'' isa 'Bio::SeqFeature::Collection' ok 208 - correct number of features for command 'shuffle' # TODO maybe adapt reference results to Debian specific dataset ok 209 - make a factory using command 'b12_to_b6' ok 210 - factory command for 'b12_to_b6' is correct ok 211 - all available options for 'b12_to_b6' ok 212 - available parameters for 'b12_to_b6' ok 213 - available switches for 'b12_to_b6' ok 214 - get version for 'b12_to_b6' ok 215 - can run command 'b12_to_b6' ok 216 - result files exists for command 'b12_to_b6' ok 217 - can return output format for command 'b12_to_b6' ok 218 - result claims to be in correct format for command 'b12_to_b6' ok 219 - can return output file for command 'b12_to_b6' ok 220 - file format of '/tmp/cMEy41U0MQ/CNLynTKfdt.bed' consistent with claim for 'b12_to_b6' ok 221 - can set want to IO object for command 'b12_to_b6' ok 222 - can get the basic object result for command 'b12_to_b6' ok 223 - 'returned object is correct for command 'b12_to_b6'' isa 'Bio::Root::IO' ok 224 - can get the specific object result for command 'b12_to_b6' ok 225 - 'returned object is correct for command 'b12_to_b6'' isa 'Bio::SeqFeature::Collection' ok 226 - correct number of features for command 'b12_to_b6' # TODO maybe adapt reference results to Debian specific dataset ok 227 - make a factory using command 'intersect' ok 228 - factory command for 'intersect' is correct ok 229 - all available options for 'intersect' ok 230 - available parameters for 'intersect' ok 231 - available switches for 'intersect' ok 232 - get version for 'intersect' ok 233 - can run command 'intersect' ok 234 - result files exists for command 'intersect' ok 235 - can return output format for command 'intersect' ok 236 - result claims to be in correct format for command 'intersect' ok 237 - can return output file for command 'intersect' ok 238 - can set want to IO object for command 'intersect' ok 239 - can get the basic object result for command 'intersect' ok 240 - 'returned object is correct for command 'intersect'' isa 'Bio::Root::IO' ok 241 - can get the specific object result for command 'intersect' ok 242 - 'returned object is correct for command 'intersect'' isa 'Bio::SeqFeature::Collection' not ok 243 - correct number of features for command 'intersect' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'intersect'' # at t/BEDTools.t line 364. # got: '1305' # expected: '72534' ok 244 - make a factory using command 'slop' ok 245 - factory command for 'slop' is correct ok 246 - all available options for 'slop' ok 247 - available parameters for 'slop' ok 248 - available switches for 'slop' ok 249 - get version for 'slop' ok 250 - can set parameter -add_bidirectional => 100 ok 251 - can run command 'slop' ok 252 - result files exists for command 'slop' ok 253 - can return output format for command 'slop' ok 254 - result claims to be in correct format for command 'slop' ok 255 - can return output file for command 'slop' ok 256 - file format of '/tmp/j3pDr_Y5m_/McAGuZsJuG.bed' consistent with claim for 'slop' ok 257 - can set want to IO object for command 'slop' ok 258 - can get the basic object result for command 'slop' ok 259 - 'returned object is correct for command 'slop'' isa 'Bio::Root::IO' ok 260 - can get the specific object result for command 'slop' ok 261 - 'returned object is correct for command 'slop'' isa 'Bio::SeqFeature::Collection' ok 262 - correct number of features for command 'slop' # TODO maybe adapt reference results to Debian specific dataset ok 263 - make a factory using command 'closest' ok 264 - factory command for 'closest' is correct ok 265 - all available options for 'closest' ok 266 - available parameters for 'closest' ok 267 - available switches for 'closest' ok 268 - get version for 'closest' ok 269 - can run command 'closest' ok 270 - result files exists for command 'closest' ok 271 - can return output format for command 'closest' ok 272 - result claims to be in correct format for command 'closest' ok 273 - can return output file for command 'closest' ok 274 - file format of '/tmp/_Je8NlkCNz/RARjOFa7GE.bedpe' consistent with claim for 'closest' ok 275 - can set want to IO object for command 'closest' ok 276 - can get the basic object result for command 'closest' ok 277 - 'returned object is correct for command 'closest'' isa 'Bio::Root::IO' ok 278 - can get the specific object result for command 'closest' ok 279 - 'returned object is correct for command 'closest'' isa 'Bio::SeqFeature::Collection' not ok 280 - correct number of features for command 'closest' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'closest'' # at t/BEDTools.t line 364. # got: '2121' # expected: '845' ok 281 - make a factory using command 'links' ok 282 - factory command for 'links' is correct ok 283 - all available options for 'links' ok 284 - available parameters for 'links' ok 285 - available switches for 'links' ok 286 - get version for 'links' ok 287 - can run command 'links' ok 288 - result files exists for command 'links' ok 289 - can return output format for command 'links' ok 290 - result claims to be in correct format for command 'links' ok 291 - can return output file for command 'links' ok 292 - make readable output ok 293 - - html tag line ok 294 - - number of lines ok 295 - can set want to IO object for command 'links' ok 296 - can get the basic object result for command 'links' ok 297 - 'returned object is correct for command 'links'' isa 'Bio::Root::IO' ok 298 - make a factory using command 'sort' ok 299 - factory command for 'sort' is correct ok 300 - all available options for 'sort' ok 301 - available parameters for 'sort' ok 302 - available switches for 'sort' ok 303 - get version for 'sort' ok 304 - can run command 'sort' ok 305 - result files exists for command 'sort' ok 306 - can return output format for command 'sort' ok 307 - result claims to be in correct format for command 'sort' ok 308 - can return output file for command 'sort' ok 309 - file format of '/tmp/jEPVbHa7T2/6UN82zN8_p.bed' consistent with claim for 'sort' ok 310 - can set want to IO object for command 'sort' ok 311 - can get the basic object result for command 'sort' ok 312 - 'returned object is correct for command 'sort'' isa 'Bio::Root::IO' ok 313 - can get the specific object result for command 'sort' ok 314 - 'returned object is correct for command 'sort'' isa 'Bio::SeqFeature::Collection' ok 315 - correct number of features for command 'sort' # TODO maybe adapt reference results to Debian specific dataset ok 316 - make a factory using command 'complement' ok 317 - factory command for 'complement' is correct ok 318 - all available options for 'complement' ok 319 - available parameters for 'complement' ok 320 - available switches for 'complement' ok 321 - get version for 'complement' ok 322 - can run command 'complement' ok 323 - result files exists for command 'complement' ok 324 - can return output format for command 'complement' ok 325 - result claims to be in correct format for command 'complement' ok 326 - can return output file for command 'complement' ok 327 - file format of '/tmp/FDvOk6ReMH/pa5wOoD08C.bed' consistent with claim for 'complement' ok 328 - can set want to IO object for command 'complement' ok 329 - can get the basic object result for command 'complement' ok 330 - 'returned object is correct for command 'complement'' isa 'Bio::Root::IO' ok 331 - can get the specific object result for command 'complement' ok 332 - 'returned object is correct for command 'complement'' isa 'Bio::SeqFeature::Collection' not ok 333 - correct number of features for command 'complement' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'complement'' # at t/BEDTools.t line 364. # got: '292' # expected: '291' ok 334 - make a factory using command 'mask_fasta_from_bed' ok 335 - factory command for 'mask_fasta_from_bed' is correct ok 336 - all available options for 'mask_fasta_from_bed' ok 337 - available parameters for 'mask_fasta_from_bed' ok 338 - available switches for 'mask_fasta_from_bed' ok 339 - get version for 'mask_fasta_from_bed' ok 340 - can run command 'mask_fasta_from_bed' ok 341 - result files exists for command 'mask_fasta_from_bed' ok 342 - can return output format for command 'mask_fasta_from_bed' ok 343 - result claims to be in correct format for command 'mask_fasta_from_bed' ok 344 - can return output file for command 'mask_fasta_from_bed' ok 345 - file format consistent with claim for 'mask_fasta_from_bed' ok 346 - can set want to IO object for command 'mask_fasta_from_bed' ok 347 - can get the basic object result for command 'mask_fasta_from_bed' ok 348 - 'returned object is correct for command 'mask_fasta_from_bed'' isa 'Bio::Root::IO' ok 349 - can get the specific object result for command 'mask_fasta_from_bed' ok 350 - 'returned object is correct for command 'mask_fasta_from_bed'' isa 'Bio::SeqIO' ok 351 - correct number of sequences for command 'mask_fasta_from_bed' ok 352 - make a factory using command 'subtract' ok 353 - factory command for 'subtract' is correct ok 354 - all available options for 'subtract' ok 355 - available parameters for 'subtract' ok 356 - available switches for 'subtract' ok 357 - get version for 'subtract' ok 358 - can run command 'subtract' ok 359 - result files exists for command 'subtract' ok 360 - can return output format for command 'subtract' ok 361 - result claims to be in correct format for command 'subtract' ok 362 - can return output file for command 'subtract' ok 363 - file format of '/tmp/rHsgxZViD1/gja0p839Oh.bed' consistent with claim for 'subtract' ok 364 - can set want to IO object for command 'subtract' ok 365 - can get the basic object result for command 'subtract' ok 366 - 'returned object is correct for command 'subtract'' isa 'Bio::Root::IO' ok 367 - can get the specific object result for command 'subtract' ok 368 - 'returned object is correct for command 'subtract'' isa 'Bio::SeqFeature::Collection' not ok 369 - correct number of features for command 'subtract' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'subtract'' # at t/BEDTools.t line 364. # got: '1802' # expected: '57959' ok 370 - make a factory using command 'coverage' ok 371 - factory command for 'coverage' is correct ok 372 - all available options for 'coverage' ok 373 - available parameters for 'coverage' ok 374 - available switches for 'coverage' ok 375 - get version for 'coverage' ok 376 - can run command 'coverage' ok 377 - result files exists for command 'coverage' ok 378 - can return output format for command 'coverage' ok 379 - result claims to be in correct format for command 'coverage' ok 380 - can return output file for command 'coverage' ok 381 - file format of '/tmp/skuuJYQmjf/2vc1POXbwO.bed' consistent with claim for 'coverage' ok 382 - can set want to IO object for command 'coverage' ok 383 - can get the basic object result for command 'coverage' ok 384 - 'returned object is correct for command 'coverage'' isa 'Bio::Root::IO' ok 385 - can get the specific object result for command 'coverage' ok 386 - 'returned object is correct for command 'coverage'' isa 'Bio::SeqFeature::Collection' not ok 387 - correct number of features for command 'coverage' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'coverage'' # at t/BEDTools.t line 364. # got: '828' # expected: '57261' ok 388 - make a factory using command 'merge' ok 389 - factory command for 'merge' is correct ok 390 - all available options for 'merge' ok 391 - available parameters for 'merge' ok 392 - available switches for 'merge' ok 393 - get version for 'merge' ok 394 - can run command 'merge' ok 395 - result files exists for command 'merge' ok 396 - can return output format for command 'merge' ok 397 - result claims to be in correct format for command 'merge' ok 398 - can return output file for command 'merge' ok 399 - file format of '/tmp/HpdGwRT85g/3_ld6bM3qs.bed' consistent with claim for 'merge' ok 400 - can set want to IO object for command 'merge' ok 401 - can get the basic object result for command 'merge' ok 402 - 'returned object is correct for command 'merge'' isa 'Bio::Root::IO' ok 403 - can get the specific object result for command 'merge' ok 404 - 'returned object is correct for command 'merge'' isa 'Bio::SeqFeature::Collection' ok 405 - correct number of features for command 'merge' # TODO maybe adapt reference results to Debian specific dataset ok 406 - make a factory using command 'window' ok 407 - factory command for 'window' is correct ok 408 - all available options for 'window' ok 409 - available parameters for 'window' ok 410 - available switches for 'window' ok 411 - get version for 'window' ok 412 - can run command 'window' ok 413 - result files exists for command 'window' ok 414 - can return output format for command 'window' ok 415 - result claims to be in correct format for command 'window' ok 416 - can return output file for command 'window' ok 417 - file format of '/tmp/jsh3adG7rS/z0qgZBtnpN.bedpe' consistent with claim for 'window' ok 418 - can set want to IO object for command 'window' ok 419 - can get the basic object result for command 'window' ok 420 - 'returned object is correct for command 'window'' isa 'Bio::Root::IO' ok 421 - can get the specific object result for command 'window' ok 422 - 'returned object is correct for command 'window'' isa 'Bio::SeqFeature::Collection' not ok 423 - correct number of features for command 'window' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'window'' # at t/BEDTools.t line 364. # got: '1331' # expected: '74998' ok # You named your test '71'. You shouldn't use numbers for your test names. # Very confusing. # You named your test '91'. You shouldn't use numbers for your test names. # Very confusing. t/Coil.t ...................... 1..6 ok 1 - use Bio::Tools::Run::Coil; ok 2 - use Bio::SeqIO; ok 3 ok 4 ok 5 - 71 ok 6 - 91 ok # Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present t/Consense.t .................. 1..8 ok 1 - use Bio::Tools::Run::Phylo::Phylip::Consense; ok 2 - use Bio::AlignIO; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 6%] 4000 Cells done [ 8%] 5000 Cells done [10%] 6000 Cells done [12%] 7000 Cells done [14%] 8000 Cells done [17%] 9000 Cells done [19%] 10000 Cells done [21%] 11000 Cells done [23%] 12000 Cells done [25%] 13000 Cells done [27%] 14000 Cells done [29%] 15000 Cells done [32%] 16000 Cells done [34%] 17000 Cells done [36%] 18000 Cells done [38%] 19000 Cells done [40%] 20000 Cells done [42%] 21000 Cells done [44%] 22000 Cells done [46%] 23000 Cells done [49%] 24000 Cells done [51%] 25000 Cells done [53%] 26000 Cells done [55%] 27000 Cells done [57%] 28000 Cells done [59%] 29000 Cells done [61%] 30000 Cells done [64%] 31000 Cells done [66%] 32000 Cells done [68%] 33000 Cells done [70%] 34000 Cells done [72%] 35000 Cells done [74%] 36000 Cells done [76%] 37000 Cells done [79%] 38000 Cells done [81%] 39000 Cells done [83%] 40000 Cells done [85%] 41000 Cells done [87%] 42000 Cells done [89%] 43000 Cells done [91%] 44000 Cells done [93%] 45000 Cells done [96%] 46000 Cells done [98%][0,0][0,0] Score 0 Recovering alignment: [0,0][0,0] Explicit read offWarning Error Major problem (!) - in DnaMatchBlock read off, position 0,0 state 0 no source found! Warning Error In DnaMatchBlock hidden read off, between 0:0,0:0 - at got bad read off. Problem! Warning Error In full dc, at 0:0,0:0 got a bad hidden explicit read off... Warning Error Major problem (!) - in DnaMatchBlock matrix to special read off, position 0,0 state 0 no source found! Warning Error Problem in reading off special state system, hit a non start state (or an internal error) in a single alignment mode Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 7%] 4000 Cells done [ 9%] 5000 Cells done [12%] 6000 Cells done [14%] 7000 Cells done [17%] 8000 Cells done [19%] 9000 Cells done [21%] 10000 Cells done [24%] 11000 Cells done [26%] 12000 Cells done [29%] 13000 Cells done [31%] 14000 Cells done [34%] 15000 Cells done [36%] 16000 Cells done [38%] 17000 Cells done [41%] 18000 Cells done [43%] 19000 Cells done [46%] 20000 Cells done [48%] 21000 Cells done [51%] 22000 Cells done [53%] 23000 Cells done [55%] 24000 Cells done [58%] 25000 Cells done [60%] 26000 Cells done [63%] 27000 Cells done [65%] 28000 Cells done [68%] 29000 Cells done [70%] 30000 Cells done [72%] 31000 Cells done [75%] 32000 Cells done [77%] 33000 Cells done [80%] 34000 Cells done [82%] 35000 Cells done [85%] 36000 Cells done [87%] 37000 Cells done [89%] 38000 Cells done [92%] 39000 Cells done [94%] 40000 Cells done [97%] 41000 Cells done [99%][0,0][0,0] Score 0 Recovering alignment: [0,0][0,0] Explicit read offWarning Error Major problem (!) - in DnaMatchBlock read off, position 0,0 state 0 no source found! Warning Error In DnaMatchBlock hidden read off, between 0:0,0:0 - at got bad read off. Problem! Warning Error In full dc, at 0:0,0:0 got a bad hidden explicit read off... Warning Error Major problem (!) - in DnaMatchBlock matrix to special read off, position 0,0 state 0 no source found! Warning Error Problem in reading off special state system, hit a non start state (or an internal error) in a single alignment mode Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 6%] 4000 Cells done [ 8%] 5000 Cells done [10%] 6000 Cells done [12%] 7000 Cells done [14%] 8000 Cells done [17%] 9000 Cells done [19%] 10000 Cells done [21%] 11000 Cells done [23%] 12000 Cells done [25%] 13000 Cells done [27%] 14000 Cells done [29%] 15000 Cells done [32%] 16000 Cells done [34%] 17000 Cells done [36%] 18000 Cells done [38%] 19000 Cells done [40%] 20000 Cells done [42%] 21000 Cells done [44%] 22000 Cells done [46%] 23000 Cells done [49%] 24000 Cells done [51%] 25000 Cells done [53%] 26000 Cells done [55%] 27000 Cells done [57%] 28000 Cells done [59%] 29000 Cells done [61%] 30000 Cells done [64%] 31000 Cells done [66%] 32000 Cells done [68%] 33000 Cells done [70%] 34000 Cells done [72%] 35000 Cells done [74%] 36000 Cells done [76%] 37000 Cells done [79%] 38000 Cells done [81%] 39000 Cells done [83%] 40000 Cells done [85%] 41000 Cells done [87%] 42000 Cells done [89%] 43000 Cells done [91%] 44000 Cells done [93%] 45000 Cells done [96%] 46000 Cells done [98%][0,0][0,0] Score 0 Recovering alignment: [0,0][0,0] Explicit read offWarning Error Major problem (!) - in DnaMatchBlock read off, position 0,0 state 0 no source found! Warning Error In DnaMatchBlock hidden read off, between 0:0,0:0 - at got bad read off. Problem! Warning Error In full dc, at 0:0,0:0 got a bad hidden explicit read off... Warning Error Major problem (!) - in DnaMatchBlock matrix to special read off, position 0,0 state 0 no source found! Warning Error Problem in reading off special state system, hit a non start state (or an internal error) in a single alignment mode t/DBA.t ....................... 1..5 ok 1 - use Bio::Tools::Run::Alignment::DBA; ok 2 - use Bio::SimpleAlign; ok 3 - use Bio::AlignIO; ok 4 - use Bio::SeqIO; ok 5 - An object of class 'Bio::Tools::Run::Alignment::DBA' isa 'Bio::Tools::Run::Alignment::DBA' ok # Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present t/DrawGram.t .................. 1..6 ok 1 - use Bio::Tools::Run::Phylo::Phylip::DrawGram; ok 2 - use Bio::TreeIO; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present ok # Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present t/DrawTree.t .................. 1..6 ok 1 - use Bio::Tools::Run::Phylo::Phylip::DrawTree; ok 2 - use Bio::TreeIO; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present ok -- namet is "-sequence" associated seqall qualifiers -- namet is "-outfile" associated outfile qualifiers t/EMBOSS.t .................... 1..31 ok 1 - use Bio::Root::IO; ok 2 - use Bio::SeqIO; ok 3 - use Bio::AlignIO; ok 4 - use Bio::Factory::EMBOSS; ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok t/Exonerate.t ................. 1..89 ok 1 - use Bio::Tools::Run::Alignment::Exonerate; ok 2 - An object of class 'Bio::Tools::Run::Alignment::Exonerate' isa 'Bio::Tools::Run::Alignment::Exonerate' ok 3 ok 4 - An object of class 'Bio::SearchIO::exonerate' isa 'Bio::SearchIO' ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 - An object of class 'Bio::SearchIO::exonerate' isa 'Bio::SearchIO' ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok t/FastTree.t .................. 1..9 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Phylo::FastTree; ok 3 - use Bio::AlignIO; ok 4 - Make the object ok 5 - Tree is defined ok 6 - Number of nodes is correct ok 7 - Tree is defined ok 8 - Tree is defined ok 9 - Tree is defined ok # Required executable for Bio::Tools::Run::FootPrinter is not present t/FootPrinter.t ............... 1..24 ok 1 - use Bio::Tools::Run::FootPrinter; ok 2 - use Bio::SeqIO; ok 3 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 4 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 5 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 6 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 7 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 8 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 9 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 10 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 11 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 12 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 13 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 14 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 15 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 16 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 17 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 18 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 19 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 20 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 21 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 22 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 23 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 24 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok # Required environment variable $GENEMARK_MODELS is not set t/Genemark.hmm.prokaryotic.t .. 1..99 ok 1 - use Bio::Tools::Run::Genemark; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 # skip Required environment variable $GENEMARK_MODELS is not set ok 5 # skip Required environment variable $GENEMARK_MODELS is not set ok 6 # skip Required environment variable $GENEMARK_MODELS is not set ok 7 # skip Required environment variable $GENEMARK_MODELS is not set ok 8 # skip Required environment variable $GENEMARK_MODELS is not set ok 9 # skip Required environment variable $GENEMARK_MODELS is not set ok 10 # skip Required environment variable $GENEMARK_MODELS is not set ok 11 # skip Required environment variable $GENEMARK_MODELS is not set ok 12 # skip Required environment variable $GENEMARK_MODELS is not set ok 13 # skip Required environment variable $GENEMARK_MODELS is not set ok 14 # skip Required environment variable $GENEMARK_MODELS is not set ok 15 # skip Required environment variable $GENEMARK_MODELS is not set ok 16 # skip Required environment variable $GENEMARK_MODELS is not set ok 17 # skip Required environment variable $GENEMARK_MODELS is not set ok 18 # skip Required environment variable $GENEMARK_MODELS is not set ok 19 # skip Required environment variable $GENEMARK_MODELS is not set ok 20 # skip Required environment variable $GENEMARK_MODELS is not set ok 21 # skip Required environment variable $GENEMARK_MODELS is not set ok 22 # skip Required environment variable $GENEMARK_MODELS is not set ok 23 # skip Required environment variable $GENEMARK_MODELS is not set ok 24 # skip Required environment variable $GENEMARK_MODELS is not set ok 25 # skip Required environment variable $GENEMARK_MODELS is not set ok 26 # skip Required environment variable $GENEMARK_MODELS is not set ok 27 # skip Required environment variable $GENEMARK_MODELS is not set ok 28 # skip Required environment variable $GENEMARK_MODELS is not set ok 29 # skip Required environment variable $GENEMARK_MODELS is not set ok 30 # skip Required environment variable $GENEMARK_MODELS is not set ok 31 # skip Required environment variable $GENEMARK_MODELS is not set ok 32 # skip Required environment variable $GENEMARK_MODELS is not set ok 33 # skip Required environment variable $GENEMARK_MODELS is not set ok 34 # skip Required environment variable $GENEMARK_MODELS is not set ok 35 # skip Required environment variable $GENEMARK_MODELS is not set ok 36 # skip Required environment variable $GENEMARK_MODELS is not set ok 37 # skip Required environment variable $GENEMARK_MODELS is not set ok 38 # skip Required environment variable $GENEMARK_MODELS is not set ok 39 # skip Required environment variable $GENEMARK_MODELS is not set ok 40 # skip Required environment variable $GENEMARK_MODELS is not set ok 41 # skip Required environment variable $GENEMARK_MODELS is not set ok 42 # skip Required environment variable $GENEMARK_MODELS is not set ok 43 # skip Required environment variable $GENEMARK_MODELS is not set ok 44 # skip Required environment variable $GENEMARK_MODELS is not set ok 45 # skip Required environment variable $GENEMARK_MODELS is not set ok 46 # skip Required environment variable $GENEMARK_MODELS is not set ok 47 # skip Required environment variable $GENEMARK_MODELS is not set ok 48 # skip Required environment variable $GENEMARK_MODELS is not set ok 49 # skip Required environment variable $GENEMARK_MODELS is not set ok 50 # skip Required environment variable $GENEMARK_MODELS is not set ok 51 # skip Required environment variable $GENEMARK_MODELS is not set ok 52 # skip Required environment variable $GENEMARK_MODELS is not set ok 53 # skip Required environment variable $GENEMARK_MODELS is not set ok 54 # skip Required environment variable $GENEMARK_MODELS is not set ok 55 # skip Required environment variable $GENEMARK_MODELS is not set ok 56 # skip Required environment variable $GENEMARK_MODELS is not set ok 57 # skip Required environment variable $GENEMARK_MODELS is not set ok 58 # skip Required environment variable $GENEMARK_MODELS is not set ok 59 # skip Required environment variable $GENEMARK_MODELS is not set ok 60 # skip Required environment variable $GENEMARK_MODELS is not set ok 61 # skip Required environment variable $GENEMARK_MODELS is not set ok 62 # skip Required environment variable $GENEMARK_MODELS is not set ok 63 # skip Required environment variable $GENEMARK_MODELS is not set ok 64 # skip Required environment variable $GENEMARK_MODELS is not set ok 65 # skip Required environment variable $GENEMARK_MODELS is not set ok 66 # skip Required environment variable $GENEMARK_MODELS is not set ok 67 # skip Required environment variable $GENEMARK_MODELS is not set ok 68 # skip Required environment variable $GENEMARK_MODELS is not set ok 69 # skip Required environment variable $GENEMARK_MODELS is not set ok 70 # skip Required environment variable $GENEMARK_MODELS is not set ok 71 # skip Required environment variable $GENEMARK_MODELS is not set ok 72 # skip Required environment variable $GENEMARK_MODELS is not set ok 73 # skip Required environment variable $GENEMARK_MODELS is not set ok 74 # skip Required environment variable $GENEMARK_MODELS is not set ok 75 # skip Required environment variable $GENEMARK_MODELS is not set ok 76 # skip Required environment variable $GENEMARK_MODELS is not set ok 77 # skip Required environment variable $GENEMARK_MODELS is not set ok 78 # skip Required environment variable $GENEMARK_MODELS is not set ok 79 # skip Required environment variable $GENEMARK_MODELS is not set ok 80 # skip Required environment variable $GENEMARK_MODELS is not set ok 81 # skip Required environment variable $GENEMARK_MODELS is not set ok 82 # skip Required environment variable $GENEMARK_MODELS is not set ok 83 # skip Required environment variable $GENEMARK_MODELS is not set ok 84 # skip Required environment variable $GENEMARK_MODELS is not set ok 85 # skip Required environment variable $GENEMARK_MODELS is not set ok 86 # skip Required environment variable $GENEMARK_MODELS is not set ok 87 # skip Required environment variable $GENEMARK_MODELS is not set ok 88 # skip Required environment variable $GENEMARK_MODELS is not set ok 89 # skip Required environment variable $GENEMARK_MODELS is not set ok 90 # skip Required environment variable $GENEMARK_MODELS is not set ok 91 # skip Required environment variable $GENEMARK_MODELS is not set ok 92 # skip Required environment variable $GENEMARK_MODELS is not set ok 93 # skip Required environment variable $GENEMARK_MODELS is not set ok 94 # skip Required environment variable $GENEMARK_MODELS is not set ok 95 # skip Required environment variable $GENEMARK_MODELS is not set ok 96 # skip Required environment variable $GENEMARK_MODELS is not set ok 97 # skip Required environment variable $GENEMARK_MODELS is not set ok 98 # skip Required environment variable $GENEMARK_MODELS is not set ok 99 # skip Required environment variable $GENEMARK_MODELS is not set ok These tests may fail because I'm not sure about your genewise version -- using wise 2.2.3-rc7 values t/Genewise.t .................. 1..17 ok 1 - use Bio::Tools::Run::Genewise; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Genewise' isa 'Bio::Tools::Run::Genewise' ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok # Required environment variable $GENSCANDIR is not set t/Genscan.t ................... 1..6 ok 1 - use Bio::Tools::Run::Genscan; ok 2 - use Bio::Root::IO; ok 3 # skip Required environment variable $GENSCANDIR is not set ok 4 # skip Required environment variable $GENSCANDIR is not set ok 5 # skip Required environment variable $GENSCANDIR is not set ok 6 # skip Required environment variable $GENSCANDIR is not set ok # Required executable for Bio::Tools::Run::Phylo::Gerp is not present t/Gerp.t ...................... 1..33 ok 1 - use Bio::Tools::Run::Phylo::Gerp; ok 2 - use Bio::AlignIO; ok 3 - use Bio::TreeIO; ok 4 - use Bio::Root::Utilities; ok 5 - Found input alignment file ok 6 - Found input tree file ok 7 - An object of class 'Bio::Tools::Run::Phylo::Gerp' isa 'Bio::Tools::Run::Phylo::Gerp' ok 8 - has a created method not in args supplied to new ok 9 - quiet was set ok 10 - program_dir returned correct default ok 11 - Correct exe default name ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 15 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 20 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 21 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 22 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 23 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 24 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 25 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 26 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 27 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 28 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 29 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 30 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 31 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 32 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 33 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok t/Glimmer3.t .................. 1..111 ok 1 - use Bio::Tools::Run::Glimmer; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Glimmer' isa 'Bio::Tools::Run::Glimmer' ok 5 - An object of class 'Bio::Tools::Glimmer' isa 'Bio::Tools::Glimmer' ok 6 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 7 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 8 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 9 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 10 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 11 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 12 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 13 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 14 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 15 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 16 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 17 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 18 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 19 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 20 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 21 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 22 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 23 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 24 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 25 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 26 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 27 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 28 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 29 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 30 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 31 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 32 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 33 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 34 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 35 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 36 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 37 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 38 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 39 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 40 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 41 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 42 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 43 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 44 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 45 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 46 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 47 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 48 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 49 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 50 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 51 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 52 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 53 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 54 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 55 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 56 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 57 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 58 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 59 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 60 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 61 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 62 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 63 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 64 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 65 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 66 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 67 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 68 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 69 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 70 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 71 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 72 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 73 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 74 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 75 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 76 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 77 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 78 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 79 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 80 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 81 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 82 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 83 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 84 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 85 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 86 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 87 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 88 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 89 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 90 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 91 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 92 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 93 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 94 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 95 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 96 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 97 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 98 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 99 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 100 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 101 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 102 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 103 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 104 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 105 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 106 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 107 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 108 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 109 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 110 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 111 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok # Required executable for Bio::Tools::Run::Hmmer is not present t/Hmmer.t ..................... 1..27 ok 1 - use Bio::Tools::Run::Hmmer; ok 2 - use Bio::SeqIO; ok 3 - use Bio::AlignIO; ok 4 - An object of class 'Bio::Tools::Run::Hmmer' isa 'Bio::Tools::Run::Hmmer' ok 5 ok 6 ok 7 ok 8 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 9 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 10 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 11 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 12 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 13 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 14 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 15 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 16 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 17 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 18 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 19 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 20 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 21 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 22 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 23 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 24 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 25 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 26 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 27 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok t/Infernal.t .................. 1..3 ok 1 - use Bio::Tools::Run::Infernal; ok 2 - use Bio::SeqIO; ok 3 - use Bio::AlignIO; ok t/Kalign.t .................... 1..7 ok 1 - use Bio::Tools::Run::Alignment::Kalign; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - Code tested only on kalign versions >= 2 Kalign (3.3) Copyright (C) 2006,2019,2020 Timo Lassmann This program comes with ABSOLUTELY NO WARRANTY; for details type: `kalign -showw'. This is free software, and you are welcome to redistribute it under certain conditions; consult the COPYING file for details. Please cite: Lassmann, Timo. "Kalign 3: multiple sequence alignment of large data sets." Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795 WARNING: AVX2 instruction set not found! Kalign will not run optimally. [2021-01-07 13:42:40] : LOG : Detected protein sequences. [2021-01-07 13:42:40] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2021-01-07 13:42:40] : LOG : Detected: 7 sequences. [2021-01-07 13:42:40] : LOG : Calculating pairwise distances [2021-01-07 13:42:40] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 [2021-01-07 13:42:40] : LOG : 7 anchors [2021-01-07 13:42:40] : LOG : Building guide tree. [2021-01-07 13:42:40] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2021-01-07 13:42:40] : LOG : Aligning [2021-01-07 13:42:40] : LOG : CPU Time: 0.16u 00:00:00.15 Elapsed: 00:00:00.00 ok 5 ok 6 Kalign (3.3) Copyright (C) 2006,2019,2020 Timo Lassmann This program comes with ABSOLUTELY NO WARRANTY; for details type: `kalign -showw'. This is free software, and you are welcome to redistribute it under certain conditions; consult the COPYING file for details. Please cite: Lassmann, Timo. "Kalign 3: multiple sequence alignment of large data sets." Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795 WARNING: AVX2 instruction set not found! Kalign will not run optimally. [2021-01-07 13:42:40] : LOG : Detected protein sequences. [2021-01-07 13:42:40] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2021-01-07 13:42:40] : LOG : Detected: 7 sequences. [2021-01-07 13:42:40] : LOG : Calculating pairwise distances [2021-01-07 13:42:40] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 [2021-01-07 13:42:40] : LOG : 7 anchors [2021-01-07 13:42:40] : LOG : Building guide tree. [2021-01-07 13:42:40] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2021-01-07 13:42:40] : LOG : Aligning [2021-01-07 13:42:40] : LOG : CPU Time: 0.15u 00:00:00.15 Elapsed: 00:00:00.00 ok 7 ok # Required executable for Bio::Tools::Run::Phylo::LVB is not present t/LVB.t ....................... 1..19 ok 1 - use Bio::Tools::Run::Phylo::LVB; ok 2 - use Bio::AlignIO; ok 3 - An object of class 'Bio::Tools::Run::Phylo::LVB' isa 'Bio::Tools::Run::Phylo::LVB' ok 4 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 12 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 14 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 15 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 16 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 17 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 18 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 19 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok # Required executable for Bio::Tools::Run::Alignment::Lagan is not present t/Lagan.t ..................... 1..12 ok 1 - use Bio::AlignIO; ok 2 - use Bio::Tools::Run::Alignment::Lagan; ok 3 - use Bio::Root::IO; ok 4 - use Bio::SeqIO; ok 5 - use Bio::Seq; ok 6 - use Bio::Matrix::Mlagan; ok 7 - An object of class 'Bio::Tools::Run::Alignment::Lagan' isa 'Bio::Tools::Run::Alignment::Lagan' ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present ok 9 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present ok 10 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present ok 11 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present ok 12 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present ok t/MAFFT.t ..................... 1..23 ok 1 - use Bio::Tools::Run::Alignment::MAFFT; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - An object of class 'Bio::Tools::Run::Alignment::MAFFT' isa 'Bio::Tools::Run::Alignment::MAFFT' ok 5 ok 6 ok 7 ok 8 ok 9 - 42 or 43 expected ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 # skip Tests require version 6 of MAFFT ok 19 # skip Tests require version 6 of MAFFT ok 20 # skip Tests require version 6 of MAFFT ok 21 # skip Tests require version 6 of MAFFT ok 22 # skip Tests require version 6 of MAFFT ok 23 # skip Tests require version 6 of MAFFT ok # Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present t/MSAProbs.t .................. 1..19 ok 1 - use Bio::Tools::Run::Alignment::MSAProbs; ok 2 - use Bio::Tools::GuessSeqFormat; ok 3 - use Bio::AlignIO; ok 4 - use Bio::SeqIO; ok 5 - use Bio::Root::IO; ok 6 - use POSIX; ok 7 ok 8 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 9 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 10 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 11 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 12 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 13 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 14 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 15 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 16 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 17 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 18 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 19 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok # Required executable for Bio::Tools::Run::Match is not present t/Match.t ..................... 1..7 ok 1 - use Bio::Tools::Run::Match; ok 2 - An object of class 'Bio::Tools::Run::Match' isa 'Bio::Tools::Run::Match' ok 3 - mxlib parameter was set ok 4 - program_dir returned correct default ok 5 - Correct exe default name ok 6 # skip Required executable for Bio::Tools::Run::Match is not present ok 7 # skip Required executable for Bio::Tools::Run::Match is not present ok # Required executable for Bio::Tools::Run::Mdust is not present t/Mdust.t ..................... 1..5 ok 1 - use Bio::Tools::Run::Mdust; ok 2 - use Bio::SeqIO; ok 3 - An object of class 'Bio::Tools::Run::Mdust' isa 'Bio::Tools::Run::Mdust' ok 4 # skip Required executable for Bio::Tools::Run::Mdust is not present ok 5 # skip Required executable for Bio::Tools::Run::Mdust is not present ok # Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present t/Molphy.t .................... 1..10 ok 1 - use Bio::Tools::Phylo::Molphy; ok 2 - use Bio::Tools::Run::Phylo::Molphy::ProtML; ok 3 - use Bio::AlignIO; ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok t/Muscle.t .................... 1..8 ok 1 - use Bio::Tools::Run::Alignment::Muscle; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - use Bio::Root::IO; ok 5 - use POSIX; ok 6 ok 7 - Code tested only on muscle versions > 3.6 ok 8 - log file ok # Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present t/Neighbor.t .................. 1..19 ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtDist; ok 2 - use Bio::Tools::Run::Phylo::Phylip::Neighbor; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 15 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok # Required executable for Bio::Tools::Run::Phylo::Njtree::Best is not present t/Njtree.t .................... 1..6 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Phylo::Njtree::Best; ok 3 - use Bio::AlignIO; ok 4 - use Bio::TreeIO; ok 5 ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Njtree::Best is not present ok --------------------- WARNING --------------------- MSG: In sequence pseudogene residue count gives end value 183. Overriding value [178] with value 183 for Bio::LocatableSeq::end(). ----LNCIVNDSQKMGIIRNGDLP*PQLKNKF2-FQRMTTPSSAEGKENLVFLIRKNWFSITEKNQPLKYIINLVVSRESKEPPQRPPFLD*SLGDALKRIEQLKLANKQDVFFTVGGSSVYKESMN*-DHFKLFVTWIMQDFQSDTFFS4EGDLEKYKLLPEYPQGVVSDVEEEKGIKYKFEVYEKND --------------------------------------------------- --------------------- WARNING --------------------- MSG: In sequence pseudogene residue count gives end value 183. Overriding value [178] with value 183 for Bio::LocatableSeq::end(). ----LNCIVNDSQKMGIIRNGDLP*PQLKNKF2-FQRMTTPSSAEGKENLVFLIRKNWFSITEKNQPLKYIINLVVSRESKEPPQRPPFLD*SLGDALKRIEQLKLANKQDVFFTVGGSSVYKESMN*-DHFKLFVTWIMQDFQSDTFFS4EGDLEKYKLLPEYPQGVVSDVEEEKGIKYKFEVYEKND --------------------------------------------------- t/Pal2Nal.t ................... 1..9 ok 1 - use Bio::Tools::Run::Alignment::Pal2Nal; ok 2 - An object of class 'Bio::Tools::Run::Alignment::Pal2Nal' isa 'Bio::Tools::Run::Alignment::Pal2Nal' ok 3 - program_dir returned correct default ok 4 - Correct exe default name ok 5 ok 6 - use Bio::AlignIO; ok 7 - use Bio::SeqIO; ok 8 ok 9 ok t/PhastCons.t ................. skipped: The optional module Clone (or dependencies thereof) was not installed # Required executable for Bio::Tools::Run::Primate is not present t/Primate.t ................... 1..8 ok 1 - use Bio::Tools::Run::Primate; ok 2 - use Bio::SeqIO; ok 3 # skip Required executable for Bio::Tools::Run::Primate is not present ok 4 # skip Required executable for Bio::Tools::Run::Primate is not present ok 5 # skip Required executable for Bio::Tools::Run::Primate is not present ok 6 # skip Required executable for Bio::Tools::Run::Primate is not present ok 7 # skip Required executable for Bio::Tools::Run::Primate is not present ok 8 # skip Required executable for Bio::Tools::Run::Primate is not present ok t/Primer3.t ................... skipped: The optional module Clone (or dependencies thereof) was not installed # Required executable for Bio::Tools::Run::Prints is not present t/Prints.t .................... 1..7 ok 1 - use Bio::Tools::Run::Prints; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Prints' isa 'Bio::Tools::Run::Prints' ok 5 # skip Required executable for Bio::Tools::Run::Prints is not present ok 6 # skip Required executable for Bio::Tools::Run::Prints is not present ok 7 # skip Required executable for Bio::Tools::Run::Prints is not present ok # Required executable for Bio::Tools::Run::Alignment::Probalign is not present t/Probalign.t ................. 1..13 ok 1 - use Bio::Tools::Run::Alignment::Probalign; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - use Cwd; ok 5 - use POSIX; ok 6 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 7 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 9 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 10 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 11 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 12 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 13 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok PROBCONS version 1.12 - align multiple protein sequences and print to standard output Written by Chuong Do Using parameter set: initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } Loading sequence file: t/data/cysprot.fa Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) PROBCONS version 1.12 - align multiple protein sequences and print to standard output Written by Chuong Do Using parameter set: initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } Loading sequence file: /tmp/N3NmnS6R1i 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/YaJZ0bzB6f 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/TtGOBR7JKM Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) t/Probcons.t .................. 1..11 ok 1 - use Bio::Tools::Run::Alignment::Probcons; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - Code tested only on probcons versions > 1.09 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok # You named your test '15'. You shouldn't use numbers for your test names. # Very confusing. # You named your test '340'. You shouldn't use numbers for your test names. # Very confusing. t/Profile.t ................... 1..7 ok 1 - use Bio::Tools::Run::Profile; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Profile' isa 'Bio::Tools::Run::Profile' ok 5 - An object of class 'Bio::SeqFeature::FeaturePair' isa 'Bio::SeqFeatureI' ok 6 - 15 ok 7 - 340 ok t/Promoterwise.t .............. 1..9 ok 1 - use Bio::Tools::Run::Promoterwise; ok 2 - use Bio::Seq; ok 3 - An object of class 'Bio::Tools::Run::Promoterwise' isa 'Bio::Tools::Run::Promoterwise' ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok # Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present t/ProtDist.t .................. 1..14 ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtDist; ok 2 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok # Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present t/ProtPars.t .................. 1..11 ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtPars; ok 2 - An object of class 'Bio::Tools::Run::Phylo::Phylip::ProtPars' isa 'Bio::Tools::Run::Phylo::Phylip::ProtPars' ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok # Required executable for Bio::Tools::Run::Pseudowise is not present t/Pseudowise.t ................ 1..18 ok 1 - use Bio::Tools::Run::Pseudowise; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 ok 5 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 6 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 7 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 8 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 9 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 10 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 11 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 12 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 13 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 14 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 15 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 16 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 17 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 18 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok # Required executable for Bio::Tools::Run::Phylo::QuickTree is not present t/QuickTree.t ................. 1..13 ok 1 - use Bio::Tools::Run::Phylo::QuickTree; ok 2 - use Bio::AlignIO; ok 3 - Found input file ok 4 - An object of class 'Bio::Tools::Run::Phylo::QuickTree' isa 'Bio::Tools::Run::Phylo::QuickTree' ok 5 - program_dir returned correct default ok 6 - Correct exe default name ok 7 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 12 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok t/Raxml.t ..................... 1..12 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Phylo::Raxml; ok 3 - use Bio::AlignIO; ok 4 - Make the object ok 5 - An object of class 'Bio::Tools::Run::Phylo::Raxml' isa 'Bio::Tools::Run::Phylo::Raxml' ok 6 - Tree is defined ok 7 - Tree is defined ok 8 - File containing best tree exists in tempdir ok 9 - Tree is defined ok 10 - Tree is defined ok 11 - Number of nodes is correct ok 12 - Tree is defined ok # DB and mask make tests # run BLAST methods t/SABlastPlus.t ............... 1..71 ok 1 - use Bio::Tools::Run::StandAloneBlastPlus; ok 2 - use Bio::Tools::Run::WrapperBase; ok 3 - use Bio::Tools::Run::WrapperBase::CommandExts; ok 4 - BlastPlus factory ok 5 - make factory ok 6 - test db made with fasta ok 7 - temp db ok 8 - right type ok 9 ok 10 - named db made ok 11 - check_db ok 12 - correct name ok 13 - dbinfo hash returned ok 14 - correct type ok 15 - windowmasker mask made ok 16 - dustmasker mask made ok 17 - check_db with arg ok 18 - db_info with arg ok 19 - protein db made ok 20 - correct type ok 21 - segmasker mask made ok 22 - segmasker mask made; blastdb as data ok 23 ok 24 - protein db made with pre-built mask ok 25 - db_info records mask info ok 26 ok 27 - mask built and db made on construction (windowmasker) ok 28 ok 29 - mask built and db made on construction (segmasker) ok 30 ok 31 - mask built and db made on construction (dustmasker) ok 32 ok 33 ok 34 ok 35 - make db from Bio::SeqIO ok 36 ok 37 - make db from Bio::AlignIO ok 38 ok 39 - make db from \@seqs ok 40 - dbdir : ./a/b; dbname : test; create ok 41 - make db ok 42 ok 43 ok 44 ok 45 ok 46 - run blastn ok 47 - default hit limit ok 48 - return more alignments (arg spec) ok 49 - got more hits ok 50 - run blastn with Bio::Seq query ok 51 - run tblastn ok 52 - tblastn hits ok 53 - run tblastx ok 54 - tblastx hits ok 55 ok 56 - run blastp ok 57 - blastp hits ok 58 - bl2seq (blastn) ok 59 - got hit ok 60 - bl2seq (tblastx) ok 61 - got hit ok 62 - bl2seq (blastx) ok 63 - got hit ok 64 - bl2seq (blastp) ok 65 - no hit ok 66 - bl2seq (blastp) ok 67 - got hit ok 68 - bl2seq (tblastx) - multiple outfmt options ok 69 - bl2seq (tblastx) - multiple outfmt options (use method arg) ok 70 - bl2seq (tblastx) - multiple outfmt options (no explict quotes should also work) ok 71 - bl2seq (tblastx) - multiple outfmt options (a single format number in quotes ok # Required executable for Bio::Tools::Run::Phylo::SLR is not present t/SLR.t ....................... 1..7 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Phylo::SLR; ok 3 - use Bio::AlignIO; ok 4 - use Bio::TreeIO; ok 5 ok 6 # skip Required executable for Bio::Tools::Run::Phylo::SLR is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::SLR is not present ok t/Samtools.t .................. 1..41 ok 1 - make a factory using command 'pileup' ok 2 - parameters changed on construction ok 3 - access parameter ok 4 - parameters_changed cleared on read ok 5 - set a param not set in constructor ok 6 - parameters_changed set ok 7 - parameter really set ok 8 - original parameter unchanged ok 9 - parameters_changed cleared on read ok 10 - change an original parameter ok 11 - parameter really changed ok 12 - reset parameters with arg ok 13 - original parameters undefined ok 14 - parameter really reset via arg ok 15 - parameters changed ok 16 - all available options ok 17 - available parameters ok 18 - available switches ok 19 - get_parameters correct ok 20 - command attribute set ok 21 - internal command array set ok 22 - internal prefix hash set ok 23 - commands filtered by prefix ok 24 - translate_params: command correct ok 25 - translate_params: options correct ok 26 - merge bam factory instantiated ok 27 - merged bam file created ok 28 - fasta index factory ok 29 - make fasta index ok 30 - fai file present ok 31 - bam -> sam cvt factory ok 32 - convert bam -> sam ok 33 - sam file present and text ok 34 - sam -> bam cvt factory ok 35 - convert sam -> bam ok 36 - bam file present and binary ok 37 - bam sort factory ok 38 - sort bam file ok 39 - bam index factory ok 40 - make bam index ok 41 - bai file present and binary ok # Required executable for Bio::Tools::Run::Seg is not present t/Seg.t ....................... 1..8 ok 1 - use Bio::Tools::Run::Seg; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Seg' isa 'Bio::Tools::Run::Seg' ok 5 # skip Required executable for Bio::Tools::Run::Seg is not present ok 6 # skip Required executable for Bio::Tools::Run::Seg is not present ok 7 # skip Required executable for Bio::Tools::Run::Seg is not present ok 8 # skip Required executable for Bio::Tools::Run::Seg is not present ok # Required executable for Bio::Tools::Run::Phylo::Semphy is not present t/Semphy.t .................... 1..19 ok 1 - use Bio::Tools::Run::Phylo::Semphy; ok 2 - An object of class 'Bio::Tools::Run::Phylo::Semphy' isa 'Bio::Tools::Run::Phylo::Semphy' ok 3 - has a created method not in args ok 4 - ratio param was set via -z ok 5 - jtt switch was set ok 6 - program_dir returned correct default ok 7 - Correct exe default name ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 15 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok # Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present t/SeqBoot.t ................... 1..9 ok 1 - use Bio::Tools::Run::Phylo::Phylip::SeqBoot; ok 2 - use Bio::AlignIO; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok # Required executable for Bio::Tools::Run::Signalp is not present t/Signalp.t ................... 1..7 ok 1 - use Bio::Tools::Run::Signalp; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Signalp' isa 'Bio::Tools::Run::Signalp' ok 5 # skip Required executable for Bio::Tools::Run::Signalp is not present ok 6 # skip Required executable for Bio::Tools::Run::Signalp is not present ok 7 # skip Required executable for Bio::Tools::Run::Signalp is not present ok t/Sim4.t ...................... 1..23 ok 1 - use Bio::Tools::Run::Alignment::Sim4; ok 2 - use Bio::SimpleAlign; ok 3 - use Bio::AlignIO; ok 4 - use Bio::SeqIO; ok 5 - An object of class 'Bio::Tools::Run::Alignment::Sim4' isa 'Bio::Tools::Run::Alignment::Sim4' ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok # Required executable for Bio::Tools::Run::Simprot is not present t/Simprot.t ................... 1..6 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Simprot; ok 3 - use Bio::AlignIO; ok 4 - use Bio::TreeIO; ok 5 ok 6 # skip Required executable for Bio::Tools::Run::Simprot is not present ok t/SoapEU-function.t ........... skipped: The optional module Bio::DB::ESoap (or dependencies thereof) was not installed t/SoapEU-unit.t ............... skipped: The optional module Bio::DB::ESoap (or dependencies thereof) was not installed # Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present t/StandAloneFasta.t ........... 1..15 ok 1 - use Bio::Tools::Run::Alignment::StandAloneFasta; ok 2 - use Bio::SeqIO; ok 3 ok 4 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 5 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 6 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 7 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 8 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 9 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 10 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 11 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 12 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 13 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 14 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 15 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok # Required executable for Bio::Tools::Run::Tmhmm is not present t/Tmhmm.t ..................... 1..9 ok 1 - use Bio::Tools::Run::Tmhmm; ok 2 - use Bio::SeqIO; ok 3 - An object of class 'Bio::Tools::Run::Tmhmm' isa 'Bio::Tools::Run::Tmhmm' ok 4 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 5 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 6 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 7 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 8 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 9 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok t/TribeMCL.t .................. 1..24 ok 1 - use Bio::Tools::Run::TribeMCL; ok 2 - use Bio::SearchIO; ok 3 - An object of class 'Bio::Tools::Run::TribeMCL' isa 'Bio::Tools::Run::TribeMCL' ok 4 # skip Tribe Matrix program not found. Skipping tests... ok 5 # skip Tribe Matrix program not found. Skipping tests... ok 6 # skip Tribe Matrix program not found. Skipping tests... ok 7 # skip Tribe Matrix program not found. Skipping tests... ok 8 # skip Tribe Matrix program not found. Skipping tests... ok 9 # skip Tribe Matrix program not found. Skipping tests... ok 10 # skip Tribe Matrix program not found. Skipping tests... ok 11 # skip Tribe Matrix program not found. Skipping tests... ok 12 # skip Tribe Matrix program not found. Skipping tests... ok 13 # skip Tribe Matrix program not found. Skipping tests... ok 14 # skip Tribe Matrix program not found. Skipping tests... ok 15 # skip Tribe Matrix program not found. Skipping tests... ok 16 # skip Tribe Matrix program not found. Skipping tests... ok 17 # skip Tribe Matrix program not found. Skipping tests... ok 18 # skip Tribe Matrix program not found. Skipping tests... ok 19 # skip Tribe Matrix program not found. Skipping tests... ok 20 # skip Tribe Matrix program not found. Skipping tests... ok 21 # skip Tribe Matrix program not found. Skipping tests... ok 22 # skip Tribe Matrix program not found. Skipping tests... ok 23 # skip Tribe Matrix program not found. Skipping tests... ok 24 # skip Tribe Matrix program not found. Skipping tests... ok t/Vista.t ..................... 1..7 ok 1 - use Bio::Tools::Run::Vista; ok 2 - use Bio::AlignIO; ok 3 # skip Skipping due to old java version ok 4 # skip Skipping due to old java version ok 5 # skip Skipping due to old java version ok 6 # skip Skipping due to old java version ok 7 # skip Skipping due to old java version ok # Required executable for Bio::Tools::Run::Alignment::Gmap is not present t/gmap-run.t .................. 1..8 ok 1 - use Bio::Tools::Run::Alignment::Gmap; ok 2 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 3 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 4 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 5 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 6 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 7 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok # Required executable for Bio::Tools::Run::tRNAscanSE is not present t/tRNAscanSE.t ................ 1..12 ok 1 - use Bio::Tools::Run::tRNAscanSE; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::tRNAscanSE' isa 'Bio::Tools::Run::tRNAscanSE' ok 5 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 6 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 7 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 8 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 9 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 10 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 11 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 12 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok All tests successful. Test Summary Report ------------------- t/BEDTools.t (Wstat: 0 Tests: 423 Failed: 0) TODO passed: 20, 57, 75, 110, 155, 190, 208, 226, 262 315, 405 Files=60, Tests=1454, 198 wallclock secs ( 0.35 usr 0.59 sys + 181.63 cusr 17.99 csys = 200.56 CPU) Result: PASS mv t.skip/* t rm -rf t.skip make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install perl Build install --destdir /<>/debian/tmp --create_packlist 0 Building BioPerl-Run Installing /<>/debian/tmp/usr/share/man/man1/bp_papplmaker.pl.1p Installing /<>/debian/tmp/usr/share/man/man1/bp_run_protdist.pl.1p Installing /<>/debian/tmp/usr/share/man/man1/bp_multi_hmmsearch.pl.1p Installing /<>/debian/tmp/usr/share/man/man1/bp_panalysis.pl.1p Installing /<>/debian/tmp/usr/share/man/man1/bp_run_neighbor.pl.1p Installing /<>/debian/tmp/usr/share/perl5/Bio/Factory/EMBOSS.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Simprot.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Tmhmm.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Mdust.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/MCS.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/RNAMotif.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/tRNAscanSE.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genemark.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Seg.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Pseudowise.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genewise.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primate.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Infernal.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/TribeMCL.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Match.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Coil.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/RepeatMasker.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Hmmer.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Ensembl.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Vista.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSApplication.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Prints.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneWUBlast.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Signalp.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genscan.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/FootPrinter.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primer3.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Profile.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Eponine.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Promoterwise.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSacd.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/ERPIN.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Glimmer.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneNCBIBlast.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools/Config.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools/Config.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Analysis/soap.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/StandAloneFasta.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Muscle.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Blat.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Amap.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Pal2Nal.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Proda.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Exonerate.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/DBA.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probalign.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MAFFT.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Kalign.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probcons.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Lagan.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Sim4.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Gmap.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MSAProbs.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus/Config.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Raxml.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Gerp.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Semphy.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/QuickTree.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phyml.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/SLR.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/FastTree.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/LVB.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Base.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/REL.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/FEL.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhastCons.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Molphy/ProtML.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Base.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Consense.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Njtree/Best.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/Tools/Run/AnalysisFactory/soap.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/DB/ESoap.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/GQueryAdaptor.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/LinkAdaptor.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/Result.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/DocSumAdaptor.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm Installing /<>/debian/tmp/usr/share/perl5/Bio/DB/ESoap/WSDL.pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Eponine.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genscan.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::DBA.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::SLR.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Proda.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Infernal.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::DB::ESoap::WSDL.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Mdust.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Hmmer.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::SLAC.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Promoterwise.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Lagan.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Seg.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Gmap.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::GQueryAdaptor.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::RNAMotif.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phyml.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Primer3.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::Base.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BEDTools::Config.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Consense.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genewise.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneNCBIBlast.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Base.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::StandAloneFasta.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::DocSumAdaptor.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Pseudowise.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawTree.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Probalign.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Tmhmm.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::FootPrinter.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Samtools::Config.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Semphy.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor::species.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtPars.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Njtree::Best.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Exonerate.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::LinkAdaptor.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Molphy::ProtML.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Kalign.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Factory::EMBOSS.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::TribeMCL.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Simprot.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phast::PhyloFit.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::AnalysisFactory::soap.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus::BlastMethods.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::Modeltest.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Primate.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Pal2Nal.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::BatchFile.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Amap.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::MAFFT.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Sim4.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::QuickTree.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Blat.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Prints.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::RepeatMasker.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtDist.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phast::PhastCons.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BlastPlus.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::EMBOSSacd.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Glimmer.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::SeqBoot.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::MCS.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Match.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::ERPIN.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor::seq.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Neighbor.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::REL.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::Result.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlast.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::PhylipConf.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Signalp.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Profile.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genemark.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Probcons.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Raxml.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Samtools.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Vista.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawGram.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BEDTools.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneWUBlast.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::DB::ESoap.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::MSAProbs.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::tRNAscanSE.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::FastTree.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Gerp.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Muscle.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Analysis::soap.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::EMBOSSApplication.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::LVB.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Coil.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::FEL.3pm Installing /<>/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Ensembl.3pm Installing /<>/debian/tmp/usr/bin/bp_papplmaker.pl Installing /<>/debian/tmp/usr/bin/bp_multi_hmmsearch.pl Installing /<>/debian/tmp/usr/bin/bp_run_protdist.pl Installing /<>/debian/tmp/usr/bin/bp_panalysis.pl Installing /<>/debian/tmp/usr/bin/bp_run_neighbor.pl dh_install dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb INFO: pkgstriptranslations version 146 INFO: pkgstriptranslations version 146 pkgstriptranslations: processing libbio-perl-run-perl (in debian/libbio-perl-run-perl); do_strip: , oemstrip: pkgstriptranslations: processing bioperl-run (in debian/bioperl-run); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libbio-perl-run-perl/DEBIAN/control, package libbio-perl-run-perl, directory debian/libbio-perl-run-perl INFO: pkgstripfiles: waiting for lock (libbio-perl-run-perl) ... INFO: pkgstripfiles: waiting for lock (libbio-perl-run-perl) ... INFO: pkgstripfiles: waiting for lock (libbio-perl-run-perl) ... INFO: pkgstripfiles: waiting for lock (libbio-perl-run-perl) ... INFO: pkgstripfiles: waiting for lock (libbio-perl-run-perl) ... pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/bioperl-run/DEBIAN/control, package bioperl-run, directory debian/bioperl-run Searching for duplicated docs in dependency libbio-perl-run-perl... symlinking changelog.Debian.gz in bioperl-run to file in libbio-perl-run-perl pkgstripfiles: Running PNG optimization (using 4 cpus) for package bioperl-run ... pkgstripfiles: No PNG files. dpkg-deb: building package 'bioperl-run' in '../bioperl-run_1.7.3-6_all.deb'. pkgstripfiles: Truncating usr/share/doc/libbio-perl-run-perl/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package libbio-perl-run-perl ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libbio-perl-run-perl' in '../libbio-perl-run-perl_1.7.3-6_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../bioperl-run_1.7.3-6_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2021-01-07T13:43:13Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ bioperl-run_1.7.3-6_amd64.changes: ---------------------------------- Format: 1.8 Date: Wed, 06 Jan 2021 22:38:23 +0100 Source: bioperl-run Binary: bioperl-run libbio-perl-run-perl Architecture: all Version: 1.7.3-6 Distribution: hirsute-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Étienne Mollier Description: bioperl-run - BioPerl wrappers: scripts libbio-perl-run-perl - BioPerl wrappers: modules Changes: bioperl-run (1.7.3-6) unstable; urgency=medium . * Team upload. * d/control: restrict build-dependencies to their supported architectures. * added skip-test-for-kalign.patch Checksums-Sha1: 6fb56cbeff2966069f2b700fa180424a79a4d37f 35312 bioperl-run_1.7.3-6_all.deb ac0c2146a24a540f13d139c0d4866e5804e732a8 13042 bioperl-run_1.7.3-6_amd64.buildinfo e61a3f219492dbe6614650b3251b1725cdbc8d86 601604 libbio-perl-run-perl_1.7.3-6_all.deb Checksums-Sha256: 0835ca0ef69568c319332c80d66b6ff1b0db0e59feb0277f2977b89ca0b712a0 35312 bioperl-run_1.7.3-6_all.deb 7dbcd0d8b1301aec87de9992c66ac286907b8ce24a9e3f2ba8c48b9475565b71 13042 bioperl-run_1.7.3-6_amd64.buildinfo 81c2b0b34726253d50d06b125cb513a475f2a246356fb7e206f10f1e2b7222c2 601604 libbio-perl-run-perl_1.7.3-6_all.deb Files: 7582e7fba0376a37ffc4a50b9c70969a 35312 science optional bioperl-run_1.7.3-6_all.deb 9f96f5bcebcf3bd0c05a38d884ae39e7 13042 science optional bioperl-run_1.7.3-6_amd64.buildinfo d8fac53c4efa7936f898a7d66b23f856 601604 perl optional libbio-perl-run-perl_1.7.3-6_all.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: bioperl-run Binary: bioperl-run libbio-perl-run-perl Architecture: all Version: 1.7.3-6 Checksums-Md5: 7582e7fba0376a37ffc4a50b9c70969a 35312 bioperl-run_1.7.3-6_all.deb d8fac53c4efa7936f898a7d66b23f856 601604 libbio-perl-run-perl_1.7.3-6_all.deb Checksums-Sha1: 6fb56cbeff2966069f2b700fa180424a79a4d37f 35312 bioperl-run_1.7.3-6_all.deb e61a3f219492dbe6614650b3251b1725cdbc8d86 601604 libbio-perl-run-perl_1.7.3-6_all.deb Checksums-Sha256: 0835ca0ef69568c319332c80d66b6ff1b0db0e59feb0277f2977b89ca0b712a0 35312 bioperl-run_1.7.3-6_all.deb 81c2b0b34726253d50d06b125cb513a475f2a246356fb7e206f10f1e2b7222c2 601604 libbio-perl-run-perl_1.7.3-6_all.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Thu, 07 Jan 2021 13:43:13 +0000 Build-Path: /<> Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: adduser (= 3.118ubuntu4), amap-align (= 2.2+git20080214.600fc29+dfsg-2), autoconf (= 2.69-14), automake (= 1:1.16.3-2ubuntu1), autopoint (= 0.21-3), autotools-dev (= 20180224.1+nmu1), base-files (= 11ubuntu16), base-passwd (= 3.5.48), bash (= 5.1-1ubuntu1), bedtools (= 2.29.2+dfsg-5), bedtools-test (= 2.29.2+dfsg-5), binutils (= 2.35.50.20210106-1ubuntu2), binutils-common (= 2.35.50.20210106-1ubuntu2), binutils-x86-64-linux-gnu (= 2.35.50.20210106-1ubuntu2), bioperl (= 1.7.7-2), bsdextrautils (= 2.36.1-1ubuntu2), bsdutils (= 1:2.36.1-1ubuntu2), build-essential (= 12.8ubuntu3), bzip2 (= 1.0.8-4ubuntu2), ca-certificates (= 20200601), clustalw (= 2.1+lgpl-7), coreutils (= 8.32-4ubuntu2), cpp (= 4:10.2.0-1ubuntu1), cpp-10 (= 10.2.1-2ubuntu3), dash (= 0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1), debconf (= 1.5.74), debhelper (= 13.3ubuntu4), debianutils (= 4.11.2), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.9.0-1), diffutils (= 1:3.7-3ubuntu1), dpkg (= 1.20.5ubuntu3), dpkg-dev (= 1.20.5ubuntu3), dwz (= 0.13+20201015-2), emboss (= 6.6.0+dfsg-7ubuntu2), emboss-data (= 6.6.0+dfsg-7ubuntu2), emboss-lib (= 6.6.0+dfsg-7ubuntu2), exonerate (= 2.4.0-5), fasttree (= 2.1.11-2), file (= 1:5.39-3), findutils (= 4.7.0-1ubuntu2), fontconfig-config (= 2.13.1-4.2ubuntu2), fonts-dejavu-core (= 2.37-2), g++ (= 4:10.2.0-1ubuntu1), g++-10 (= 10.2.1-2ubuntu3), gcc (= 4:10.2.0-1ubuntu1), gcc-10 (= 10.2.1-2ubuntu3), gcc-10-base (= 10.2.1-2ubuntu3), gettext (= 0.21-3), gettext-base (= 0.21-3), grep (= 3.6-1), groff-base (= 1.22.4-5), gzip (= 1.10-2ubuntu1), hmmer (= 3.3.2+dfsg-1), hostname (= 3.23), hyphy-common (= 2.5.24+dfsg-2), hyphy-pt (= 2.5.24+dfsg-2), ibverbs-providers (= 33.0-1), infernal (= 1.1.4-1), init-system-helpers (= 1.60), intltool-debian (= 0.35.0+20060710.5), kalign (= 1:3.3-1), lagan (= 2.0-6), libacl1 (= 2.2.53-9), libalgorithm-diff-perl (= 1.201-1), libarchive-zip-perl (= 1.68-1), libarray-compare-perl (= 3.0.8-1), libasan6 (= 10.2.1-2ubuntu3), libasn1-8-heimdal (= 7.7.0+dfsg-2), libatomic1 (= 10.2.1-2ubuntu3), libattr1 (= 1:2.4.48-6), libaudit-common (= 1:2.8.5-3ubuntu3), libaudit1 (= 1:2.8.5-3ubuntu3), libb-hooks-op-check-perl (= 0.22-1build3), libbinutils (= 2.35.50.20210106-1ubuntu2), libbio-asn1-entrezgene-perl (= 1.730-1), libbio-cluster-perl (= 1.7.3-5), libbio-db-ncbihelper-perl (= 1.7.6-2), libbio-eutilities-perl (= 1.77-1), libbio-featureio-perl (= 1.6.905-2), libbio-perl-perl (= 1.7.7-2), libbio-perl-run-perl (= 1.7.3-5), libbio-tools-run-alignment-clustalw-perl (= 1.7.4-2), libbio-tools-run-remoteblast-perl (= 1.7.3-3), libbio-variation-perl (= 1.7.5-1), libblkid1 (= 2.36.1-1ubuntu2), libbrotli1 (= 1.0.9-2build2), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-4ubuntu2), libc-bin (= 2.32-0ubuntu6), libc-dev-bin (= 2.32-0ubuntu6), libc6 (= 2.32-0ubuntu6), libc6-dev (= 2.32-0ubuntu6), libcache-cache-perl (= 1.08-2), libcap-ng0 (= 0.7.9-2.2build1), libcap2 (= 1:2.44-1), libcapture-tiny-perl (= 0.48-1), libcbor0.6 (= 0.6.0-0ubuntu3), libcc1-0 (= 10.2.1-2ubuntu3), libcgi-pm-perl (= 4.51-1), libclass-data-inheritable-perl (= 0.08-3), libclass-method-modifiers-perl (= 2.13-1), libcom-err2 (= 1.45.6-1ubuntu1), libconfig-any-perl (= 0.32-1), libcrypt-dev (= 1:4.4.17-1ubuntu1), libcrypt1 (= 1:4.4.17-1ubuntu1), libctf-nobfd0 (= 2.35.50.20210106-1ubuntu2), libctf0 (= 2.35.50.20210106-1ubuntu2), libcurl3-gnutls (= 7.72.0-1ubuntu1), libdata-stag-perl (= 0.14-2), libdb5.3 (= 5.3.28+dfsg1-0.6ubuntu3), libdebconfclient0 (= 0.256ubuntu1), libdebhelper-perl (= 13.3ubuntu4), libdeflate0 (= 1.7-1), libdevel-callchecker-perl (= 0.008-1ubuntu2), libdevel-stacktrace-perl (= 2.0400-1), libdivsufsort3 (= 2.0.1-5), libdpkg-perl (= 1.20.5ubuntu3), libdynaloader-functions-perl (= 0.003-1.1), libedit2 (= 3.1-20191231-2), libelf1 (= 0.182-3), libencode-locale-perl (= 1.05-1.1), liberror-perl (= 0.17029-1), libevent-core-2.1-7 (= 2.1.12-stable-1), libevent-pthreads-2.1-7 (= 2.1.12-stable-1), libexception-class-perl (= 1.44-1), libexpat1 (= 2.2.10-1), libexporter-tiny-perl (= 1.002002-1), libfabric1 (= 1.11.0-2), libffi8ubuntu1 (= 3.4~20200819gead65ca871-0ubuntu3), libfido2-1 (= 1.5.0-2), libfile-listing-perl (= 6.14-1), libfile-slurp-perl (= 9999.32-1), libfile-slurp-tiny-perl (= 0.004-1), libfile-sort-perl (= 1.01-2), libfile-stripnondeterminism-perl (= 1.9.0-1), libfontconfig1 (= 2.13.1-4.2ubuntu2), libfreetype6 (= 2.10.4+dfsg-1), libgcc-10-dev (= 10.2.1-2ubuntu3), libgcc-s1 (= 10.2.1-2ubuntu3), libgcrypt20 (= 1.8.7-2ubuntu1), libgd3 (= 2.3.0-2), libgdbm-compat4 (= 1.18.1-5.1), libgdbm6 (= 1.18.1-5.1), libgfortran5 (= 10.2.1-2ubuntu3), libglib2.0-0 (= 2.66.4-1), libgmp10 (= 2:6.2.0+dfsg-6ubuntu1), libgnutls30 (= 3.6.15-4ubuntu2), libgomp1 (= 10.2.1-2ubuntu3), libgpg-error0 (= 1.38-2), libgssapi-krb5-2 (= 1.17-10ubuntu1), libgssapi3-heimdal (= 7.7.0+dfsg-2), libhcrypto4-heimdal (= 7.7.0+dfsg-2), libheimbase1-heimdal (= 7.7.0+dfsg-2), libheimntlm0-heimdal (= 7.7.0+dfsg-2), libhogweed6 (= 3.6-2), libhpdf-2.3.0 (= 2.3.0+dfsg-1build1), libhtml-parser-perl (= 3.75-1build1), libhtml-tagset-perl (= 3.20-4), libhtml-tree-perl (= 5.07-2), libhts3 (= 1.11-4), libhttp-cookies-perl (= 6.10-1), libhttp-date-perl (= 6.05-1), libhttp-message-perl (= 6.27-1), libhttp-negotiate-perl (= 6.01-1), libhwloc-plugins (= 2.4.0+dfsg-3), libhwloc15 (= 2.4.0+dfsg-3), libhx509-5-heimdal (= 7.7.0+dfsg-2), libibverbs1 (= 33.0-1), libicu67 (= 67.1-5), libidn2-0 (= 2.3.0-4), libimport-into-perl (= 1.002005-1), libio-html-perl (= 1.001-1.1), libio-pty-perl (= 1:1.15-2), libio-socket-ssl-perl (= 2.068-1), libio-string-perl (= 1.08-3.1), libipc-run-perl (= 20200505.0-1), libipc-sharelite-perl (= 0.17-4build4), libisl23 (= 0.23-1), libitm1 (= 10.2.1-2ubuntu3), libjbig0 (= 2.1-3.1build1), libjpeg-turbo8 (= 2.0.3-0ubuntu2), libjpeg8 (= 8c-2ubuntu8), libk5crypto3 (= 1.17-10ubuntu1), libkeyutils1 (= 1.6.1-2ubuntu1), libkrb5-26-heimdal (= 7.7.0+dfsg-2), libkrb5-3 (= 1.17-10ubuntu1), libkrb5support0 (= 1.17-10ubuntu1), libldap-2.4-2 (= 2.4.56+dfsg-1ubuntu1), liblmdb0 (= 0.9.24-1), liblsan0 (= 10.2.1-2ubuntu3), liblwp-mediatypes-perl (= 6.04-1), liblwp-protocol-https-perl (= 6.10-1), liblz4-1 (= 1.9.3-0ubuntu1), liblzma5 (= 5.2.4-1ubuntu1), libmagic-mgc (= 1:5.39-3), libmagic1 (= 1:5.39-3), libmbedcrypto3 (= 2.16.9-0.1ubuntu1), libmbedtls12 (= 2.16.9-0.1ubuntu1), libmbedx509-0 (= 2.16.9-0.1ubuntu1), libmodule-build-perl (= 0.423100-1), libmodule-pluggable-perl (= 5.2-1), libmodule-runtime-perl (= 0.016-1), libmoo-perl (= 2.004004-1), libmount1 (= 2.36.1-1ubuntu2), libmpc3 (= 1.2.0-1), libmpfr6 (= 4.1.0-3), libmysqlclient21 (= 8.0.22-0ubuntu0.20.10.2), libncurses6 (= 6.2+20201114-2), libncursesw6 (= 6.2+20201114-2), libnet-http-perl (= 6.19-1), libnet-ssleay-perl (= 1.88-2ubuntu2), libnettle8 (= 3.6-2), libnghttp2-14 (= 1.42.0-1), libnl-3-200 (= 3.4.0-1), libnl-route-3-200 (= 3.4.0-1), libnsl-dev (= 1.3.0-0ubuntu3), libnsl2 (= 1.3.0-0ubuntu3), libnuma1 (= 2.0.12-1build1), libopenmpi3 (= 4.0.5-7ubuntu1), libp11-kit0 (= 0.23.22-1), libpam-modules (= 1.3.1-5ubuntu6), libpam-modules-bin (= 1.3.1-5ubuntu6), libpam-runtime (= 1.3.1-5ubuntu6), libpam0g (= 1.3.1-5ubuntu6), libparams-classify-perl (= 0.015-1build3), libpciaccess0 (= 0.16-1), libpcre2-8-0 (= 10.35-2ubuntu1), libpcre3 (= 2:8.39-13), libperl5.32 (= 5.32.0-6), libpipeline1 (= 1.5.3-1), libpmix2 (= 3.2.2~rc1-1ubuntu1), libpng16-16 (= 1.6.37-3), libpq5 (= 13.1-1build1), libpsl5 (= 0.21.0-1.1ubuntu1), libpsm-infinipath1 (= 3.3+20.604758e7-6.1), libpsm2-2 (= 11.2.185-1), libpython3-stdlib (= 3.9.1-1), libpython3.9-minimal (= 3.9.1-1), libpython3.9-stdlib (= 3.9.1-1), libquadmath0 (= 10.2.1-2ubuntu3), librdmacm1 (= 33.0-1), libreadline8 (= 8.1-1), libroken18-heimdal (= 7.7.0+dfsg-2), librole-tiny-perl (= 2.001004-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build2), libsasl2-2 (= 2.1.27+dfsg-2ubuntu1), libsasl2-modules-db (= 2.1.27+dfsg-2ubuntu1), libseccomp2 (= 2.4.3-1ubuntu6), libselinux1 (= 3.1-2build2), libsemanage-common (= 3.1-1build2), libsemanage1 (= 3.1-1build2), libsepol1 (= 3.1-1), libsigsegv2 (= 2.12-3), libsmartcols1 (= 2.36.1-1ubuntu2), libsqlite3-0 (= 3.34.0-1), libssh-4 (= 0.9.5-1), libssl1.1 (= 1.1.1f-1ubuntu5), libstdc++-10-dev (= 10.2.1-2ubuntu3), libstdc++6 (= 10.2.1-2ubuntu3), libstrictures-perl (= 2.000006-1), libsub-override-perl (= 0.09-2), libsub-quote-perl (= 2.006006-1), libsub-uplevel-perl (= 0.2800-1.1), libsystemd0 (= 247.1-4ubuntu1), libtasn1-6 (= 4.16.0-2), libtest-deep-perl (= 1.130-1), libtest-differences-perl (= 0.67-1), libtest-exception-perl (= 0.43-1), libtest-most-perl (= 0.37-1), libtest-warn-perl (= 0.36-1), libtext-csv-perl (= 2.00-1), libtext-diff-perl (= 1.45-1), libtiff5 (= 4.2.0-1), libtimedate-perl (= 2.3300-1), libtinfo6 (= 6.2+20201114-2), libtirpc-common (= 1.3.1-1), libtirpc-dev (= 1.3.1-1), libtirpc3 (= 1.3.1-1), libtool (= 2.4.6-14), libtree-dagnode-perl (= 1.31-1), libtry-tiny-perl (= 0.30-1), libtsan0 (= 10.2.1-2ubuntu3), libtype-tiny-perl (= 1.012000-1), libubsan1 (= 10.2.1-2ubuntu3), libuchardet0 (= 0.0.7-1), libucx0 (= 1.9.0~rc1-2build4), libudev1 (= 247.1-4ubuntu1), libunistring2 (= 0.9.10-4), liburi-perl (= 5.05-1), libuuid1 (= 2.36.1-1ubuntu2), libwebp6 (= 0.6.1-2), libwind0-heimdal (= 7.7.0+dfsg-2), libwww-perl (= 6.51-1), libwww-robotrules-perl (= 6.02-1), libx11-6 (= 2:1.7.0-1), libx11-data (= 2:1.7.0-1), libxau6 (= 1:1.0.9-0ubuntu1), libxcb1 (= 1.14-2.1), libxdmcp6 (= 1:1.1.3-0ubuntu1), libxext6 (= 2:1.3.4-0ubuntu1), libxml-dom-perl (= 1.46-1), libxml-dom-xpath-perl (= 0.14-3), libxml-libxml-perl (= 2.0134+dfsg-2build1), libxml-namespacesupport-perl (= 1.12-1.1), libxml-parser-perl (= 2.46-2), libxml-perl (= 0.08-3.1), libxml-regexp-perl (= 0.04-1.1), libxml-sax-base-perl (= 1.09-1.1), libxml-sax-perl (= 1.02+dfsg-1), libxml-simple-perl (= 2.25-1), libxml-twig-perl (= 1:3.52-1), libxml-writer-perl (= 0.900-1), libxml-xpathengine-perl (= 0.14-1), libxml2 (= 2.9.10+dfsg-6.3build1), libxnvctrl0 (= 440.82-0ubuntu1), libxpm4 (= 1:3.5.12-1), libzstd1 (= 1.4.8+dfsg-1), linux-libc-dev (= 5.8.0-34.37+21.04.1), login (= 1:4.8.1-1ubuntu7), lsb-base (= 11.1.0ubuntu2), m4 (= 1.4.18-5), mafft (= 7.475-1), mailcap (= 3.68ubuntu1), make (= 4.3-4ubuntu1), man-db (= 2.9.3-2), mawk (= 1.3.4.20200120-2), media-types (= 2.0.0), mime-support (= 3.66), muscle (= 1:3.8.1551-2build1), mysql-common (= 5.8+1.0.5ubuntu2), ncbi-blast+ (= 2.10.1+ds-1), ncbi-blast+-legacy (= 2.10.1+ds-1), ncbi-data (= 6.1.20170106+dfsg1-9), ncoils (= 2002-8), ncurses-base (= 6.2+20201114-2), ncurses-bin (= 6.2+20201114-2), netbase (= 6.2), ocl-icd-libopencl1 (= 2.2.13-1), openmpi-bin (= 4.0.5-7ubuntu1), openmpi-common (= 4.0.5-7ubuntu1), openssh-client (= 1:8.4p1-3), openssl (= 1.1.1f-1ubuntu5), pal2nal (= 14.1-3), passwd (= 1:4.8.1-1ubuntu7), patch (= 2.7.6-6), perl (= 5.32.0-6), perl-base (= 5.32.0-6), perl-modules-5.32 (= 5.32.0-6), perl-openssl-defaults (= 5), pftools (= 3.2.6-1), phyml (= 3:3.3.20200621-1), po-debconf (= 1.0.21+nmu1), primer3 (= 2.4.0-4), probcons (= 1.12-13), python3 (= 3.9.1-1), python3-minimal (= 3.9.1-1), python3-pybedtools (= 0.8.0-5build2), python3-pysam (= 0.15.4+ds-3build2), python3-six (= 1.15.0-2), python3.9 (= 3.9.1-1), python3.9-minimal (= 3.9.1-1), raxml (= 8.2.12+dfsg-6), readline-common (= 8.1-1), rpcsvc-proto (= 1.4.2-0ubuntu4), samtools (= 1.11-1), sed (= 4.7-1ubuntu1), sensible-utils (= 0.0.13), sim4 (= 0.0.20121010-8), sysvinit-utils (= 2.96-5ubuntu1), tar (= 1.32+dfsg-1), tigr-glimmer (= 3.02b-5), tzdata (= 2020f-1ubuntu1), ucf (= 3.0043), util-linux (= 2.36.1-1ubuntu2), wise (= 2.4.1-23), wise-data (= 2.4.1-23), xz-utils (= 5.2.4-1ubuntu1), zlib1g (= 1:1.2.11.dfsg-2ubuntu4) Environment: DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1609969103" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ bioperl-run_1.7.3-6_all.deb --------------------------- new Debian package, version 2.0. size 35312 bytes: control archive=1328 bytes. 1152 bytes, 16 lines control 909 bytes, 13 lines md5sums Package: bioperl-run Version: 1.7.3-6 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 90 Depends: perl:any, bioperl (>= 1.7.4), libbio-perl-run-perl (= 1.7.3-6), libbio-tools-run-alignment-clustalw-perl, libbio-featureio-perl, libbio-cluster-perl, libtest-requiresinternet-perl, libbio-eutilities-perl, libbio-tools-run-remoteblast-perl, default-jdk-headless, hyphy-pt | hyphy-mpi Recommends: amap-align, bedtools, ncbi-blast+-legacy, bowtie, bwa, clustalw, emboss, exonerate, hmmer, infernal, kalign, maq, mafft, muscle, ncoils, phylip, phyml, primer3, probalign, probcons, raxml, samtools, sim4, t-coffee, tigr-glimmer, wise, lagan, pal2nal, pftools Suggests: gmap, fasta3, trnascan-se Section: science Priority: optional Homepage: https://metacpan.org/release/BioPerl-Run Description: BioPerl wrappers: scripts Contains scripts from the BioPerl-Run package. This package will also install all wrappable applications packaged in Debian. The ones that are not Free are "Suggested" by this package. drwxr-xr-x root/root 0 2021-01-06 21:38 ./ drwxr-xr-x root/root 0 2021-01-06 21:38 ./usr/ drwxr-xr-x root/root 0 2021-01-06 21:38 ./usr/bin/ -rwxr-xr-x root/root 3552 2021-01-06 21:38 ./usr/bin/bp_multi_hmmsearch.pl -rwxr-xr-x root/root 23728 2021-01-06 21:38 ./usr/bin/bp_panalysis.pl -rwxr-xr-x root/root 15037 2021-01-06 21:38 ./usr/bin/bp_papplmaker.pl -rwxr-xr-x root/root 1324 2021-01-06 21:38 ./usr/bin/bp_run_neighbor.pl -rwxr-xr-x root/root 2111 2021-01-06 21:38 ./usr/bin/bp_run_protdist.pl drwxr-xr-x root/root 0 2021-01-06 21:38 ./usr/share/ drwxr-xr-x root/root 0 2021-01-06 21:38 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-01-06 21:38 ./usr/share/doc/bioperl-run/ -rw-r--r-- root/root 1418 2020-11-10 22:31 ./usr/share/doc/bioperl-run/README.Debian lrwxrwxrwx root/root 0 2021-01-06 21:38 ./usr/share/doc/bioperl-run/changelog.Debian.gz -> ../libbio-perl-run-perl/changelog.Debian.gz -rw-r--r-- root/root 3304 2021-01-06 21:38 ./usr/share/doc/bioperl-run/copyright drwxr-xr-x root/root 0 2021-01-06 21:38 ./usr/share/lintian/ drwxr-xr-x root/root 0 2021-01-06 21:38 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 505 2020-11-10 22:31 ./usr/share/lintian/overrides/bioperl-run drwxr-xr-x root/root 0 2021-01-06 21:38 ./usr/share/man/ drwxr-xr-x root/root 0 2021-01-06 21:38 ./usr/share/man/man1/ -rw-r--r-- root/root 2509 2021-01-06 21:38 ./usr/share/man/man1/bp_multi_hmmsearch.pl.1p.gz -rw-r--r-- root/root 6900 2021-01-06 21:38 ./usr/share/man/man1/bp_panalysis.pl.1p.gz -rw-r--r-- root/root 4096 2021-01-06 21:38 ./usr/share/man/man1/bp_papplmaker.pl.1p.gz -rw-r--r-- root/root 2080 2021-01-06 21:38 ./usr/share/man/man1/bp_run_neighbor.pl.1p.gz -rw-r--r-- root/root 2318 2021-01-06 21:38 ./usr/share/man/man1/bp_run_protdist.pl.1p.gz libbio-perl-run-perl_1.7.3-6_all.deb ------------------------------------ new Debian package, version 2.0. size 601604 bytes: control archive=5676 bytes. 783 bytes, 17 lines control 17078 bytes, 197 lines md5sums Package: libbio-perl-run-perl Source: bioperl-run Version: 1.7.3-6 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1808 Depends: perl:any, libbio-perl-perl (>= 1.7.1-1), libipc-run-perl, libfile-sort-perl Recommends: libalgorithm-diff-perl, libio-string-perl, libxml-twig-perl, libwww-perl Breaks: libbio-perl-perl (<< 1.7.1-1) Replaces: libbio-perl-perl (<< 1.7.1-1) Section: perl Priority: optional Homepage: https://metacpan.org/release/BioPerl-Run Description: BioPerl wrappers: modules Contains modules that provide a Perl interface to various bioinformatics applications to allow them to be used with common BioPerl objects. drwxr-xr-x root/root 0 2021-01-06 21:38 ./ drwxr-xr-x root/root 0 2021-01-06 21:38 ./usr/ drwxr-xr-x root/root 0 2021-01-06 21:38 ./usr/share/ drwxr-xr-x root/root 0 2021-01-06 21:38 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-01-06 21:38 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Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: n/a Build-Time: 210 Distribution: hirsute-proposed Host Architecture: amd64 Install-Time: 95 Job: bioperl-run_1.7.3-6.dsc Machine Architecture: amd64 Package: bioperl-run Package-Time: 307 Source-Version: 1.7.3-6 Space: n/a Status: successful Version: 1.7.3-6 -------------------------------------------------------------------------------- Finished at 2021-01-07T13:43:13Z Build needed 00:05:07, no disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20778089 Scanning for processes to kill in build PACKAGEBUILD-20778089