Diff of the two buildlogs: -- --- b1/build.log 2023-04-29 11:22:16.014455724 +0000 +++ b2/build.log 2023-04-29 11:28:00.303366112 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 28 23:18:31 -12 2023 -I: pbuilder-time-stamp: 1682767111 +I: Current time: Sat Jun 1 07:45:19 +14 2024 +I: pbuilder-time-stamp: 1717177519 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: copying [./bioperl_1.7.8.orig.tar.gz] I: copying [./bioperl_1.7.8-1.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Aug 15 01:02:07 2021 -12 +gpgv: Signature made Mon Aug 16 03:02:07 2021 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key @@ -27,137 +27,169 @@ dpkg-source: info: unpacking bioperl_1.7.8-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/18702/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/104887/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 1 07:45 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/104887/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/104887/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='cb613bd66c3244e9971c33b5a52f5a9b' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='18702' - PS1='# ' - PS2='> ' + INVOCATION_ID=a02411759c554b1686579a8f6ad5cba3 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=104887 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.TaOkdPBE/pbuilderrc_3S4N --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.TaOkdPBE/b1 --logfile b1/build.log bioperl_1.7.8-1.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.TaOkdPBE/pbuilderrc_NRtg --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.TaOkdPBE/b2 --logfile b2/build.log --extrapackages usrmerge bioperl_1.7.8-1.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos12-i386 5.10.0-21-686-pae #1 SMP Debian 5.10.162-1 (2023-01-21) i686 GNU/Linux + Linux i-capture-the-hostname 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 6036 - -rwxr-xr-x 1 root root 1408088 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown - -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp - -rwxr-xr-x 1 root root 136916 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 137160 Sep 20 2022 date - -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd - -rwxr-xr-x 1 root root 108940 Sep 20 2022 df - -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir - -rwxr-xr-x 1 root root 87760 Mar 22 22:20 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 34664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 84272 Mar 22 22:20 findmnt - -rwsr-xr-x 1 root root 30240 Mar 22 20:38 fusermount - -rwxr-xr-x 1 root root 218680 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 21916 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln - -rwxr-xr-x 1 root root 55600 Mar 22 23:43 login - -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls - -rwxr-xr-x 1 root root 214568 Mar 22 22:20 lsblk - -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 63016 Mar 22 22:20 more - -rwsr-xr-x 1 root root 58912 Mar 22 22:20 mount - -rwxr-xr-x 1 root root 13856 Mar 22 22:20 mountpoint - -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm - -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 22308 Nov 2 04:31 run-parts - -rwxr-xr-x 1 root root 133224 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty - -rwsr-xr-x 1 root root 83492 Mar 22 22:20 su - -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync - -rwxr-xr-x 1 root root 598456 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 13860 Nov 2 04:31 tempfile - -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch - -rwxr-xr-x 1 root root 34664 Sep 20 2022 true - -rwxr-xr-x 1 root root 17892 Mar 22 20:38 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Mar 22 22:20 umount - -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 71216 Mar 22 22:20 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/18702/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1408088 Apr 24 2023 bash + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 42920 Sep 21 2022 cat + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown + -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp + -rwxr-xr-x 1 root root 136916 Jan 6 2023 dash + -rwxr-xr-x 1 root root 137160 Sep 21 2022 date + -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd + -rwxr-xr-x 1 root root 108940 Sep 21 2022 df + -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir + -rwxr-xr-x 1 root root 87760 Mar 24 2023 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 34664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 84272 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 218680 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 21916 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln + -rwxr-xr-x 1 root root 55600 Mar 24 2023 login + -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls + -rwxr-xr-x 1 root root 214568 Mar 24 2023 lsblk + -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 63016 Mar 24 2023 more + -rwsr-xr-x 1 root root 58912 Mar 24 2023 mount + -rwxr-xr-x 1 root root 13856 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash + -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm + -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133224 Jan 6 2023 sed + lrwxrwxrwx 1 root root 9 Jun 1 07:45 sh -> /bin/bash + -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty + -rwsr-xr-x 1 root root 83492 Mar 24 2023 su + -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync + -rwxr-xr-x 1 root root 598456 Apr 7 2023 tar + -rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch + -rwxr-xr-x 1 root root 34664 Sep 21 2022 true + -rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Mar 24 2023 umount + -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 71216 Mar 24 2023 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/104887/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -532,7 +564,7 @@ Get: 239 http://deb.debian.org/debian bookworm/main i386 libxml-simple-perl all 2.25-2 [69.8 kB] Get: 240 http://deb.debian.org/debian bookworm/main i386 libyaml-perl all 1.30-2 [63.4 kB] Get: 241 http://deb.debian.org/debian bookworm/main i386 rename all 2.01-1 [21.0 kB] -Fetched 53.8 MB in 4s (14.2 MB/s) +Fetched 53.8 MB in 1s (36.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package netbase. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19604 files and directories currently installed.) @@ -1538,8 +1570,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/bioperl-1.7.8/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bioperl_1.7.8-1_source.changes +I: user script /srv/workspace/pbuilder/104887/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/104887/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/bioperl-1.7.8/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../bioperl_1.7.8-1_source.changes dpkg-buildpackage: info: source package bioperl dpkg-buildpackage: info: source version 1.7.8-1 dpkg-buildpackage: info: source distribution unstable @@ -1568,508 +1611,508 @@ Writing MYMETA.yml and MYMETA.json make[1]: Leaving directory '/build/bioperl-1.7.8' dh_auto_build - make -j8 + make -j15 make[1]: Entering directory '/build/bioperl-1.7.8' -cp lib/Bio/AlignIO/fasta.pm blib/lib/Bio/AlignIO/fasta.pm -cp lib/Bio/AlignIO/phylip.pm blib/lib/Bio/AlignIO/phylip.pm -cp lib/Bio/AlignIO/po.pm blib/lib/Bio/AlignIO/po.pm -cp lib/Bio/AnalysisParserI.pm blib/lib/Bio/AnalysisParserI.pm +cp lib/Bio/Annotation/Relation.pm blib/lib/Bio/Annotation/Relation.pm +cp lib/Bio/AlignIO/mega.pm blib/lib/Bio/AlignIO/mega.pm cp lib/Bio/AlignIO/psi.pm blib/lib/Bio/AlignIO/psi.pm -cp lib/Bio/Align/PairwiseStatistics.pm blib/lib/Bio/Align/PairwiseStatistics.pm -cp lib/Bio/Align/DNAStatistics.pm blib/lib/Bio/Align/DNAStatistics.pm -cp lib/Bio/AlignIO/proda.pm blib/lib/Bio/AlignIO/proda.pm +cp lib/Bio/Align/Utilities.pm blib/lib/Bio/Align/Utilities.pm +cp lib/Bio/Align/StatisticsI.pm blib/lib/Bio/Align/StatisticsI.pm +cp lib/Bio/AlignIO/meme.pm blib/lib/Bio/AlignIO/meme.pm cp lib/Bio/AlignIO/metafasta.pm blib/lib/Bio/AlignIO/metafasta.pm -cp lib/Bio/AlignIO/emboss.pm blib/lib/Bio/AlignIO/emboss.pm -cp lib/Bio/Annotation/Reference.pm blib/lib/Bio/Annotation/Reference.pm -cp lib/Bio/AlignIO/maf.pm blib/lib/Bio/AlignIO/maf.pm -cp lib/Bio/Annotation/OntologyTerm.pm blib/lib/Bio/Annotation/OntologyTerm.pm -cp lib/Bio/Annotation/Comment.pm blib/lib/Bio/Annotation/Comment.pm -cp lib/Bio/Annotation/DBLink.pm blib/lib/Bio/Annotation/DBLink.pm cp lib/Bio/AnalysisI.pm blib/lib/Bio/AnalysisI.pm -cp lib/Bio/AlignIO/mase.pm blib/lib/Bio/AlignIO/mase.pm -cp lib/Bio/AlignIO/prodom.pm blib/lib/Bio/AlignIO/prodom.pm -cp lib/Bio/Align/StatisticsI.pm blib/lib/Bio/Align/StatisticsI.pm -cp lib/Bio/AlignIO/largemultifasta.pm blib/lib/Bio/AlignIO/largemultifasta.pm -cp lib/Bio/Annotation/Collection.pm blib/lib/Bio/Annotation/Collection.pm -cp lib/Bio/Align/AlignI.pm blib/lib/Bio/Align/AlignI.pm -cp lib/Bio/Annotation/Relation.pm blib/lib/Bio/Annotation/Relation.pm -cp lib/Bio/AlignIO/selex.pm blib/lib/Bio/AlignIO/selex.pm -cp lib/Bio/AnalysisResultI.pm blib/lib/Bio/AnalysisResultI.pm -cp lib/Bio/AlignIO/msf.pm blib/lib/Bio/AlignIO/msf.pm +cp lib/Bio/Align/ProteinStatistics.pm blib/lib/Bio/Align/ProteinStatistics.pm cp lib/Bio/AlignIO/nexus.pm blib/lib/Bio/AlignIO/nexus.pm -cp lib/Bio/AnnotatableI.pm blib/lib/Bio/AnnotatableI.pm -cp lib/Bio/AlignIO/meme.pm blib/lib/Bio/AlignIO/meme.pm -cp lib/Bio/AlignIO/pfam.pm blib/lib/Bio/AlignIO/pfam.pm +cp lib/Bio/Annotation/AnnotationFactory.pm blib/lib/Bio/Annotation/AnnotationFactory.pm +cp lib/Bio/AlignIO/fasta.pm blib/lib/Bio/AlignIO/fasta.pm +cp lib/Bio/Annotation/Comment.pm blib/lib/Bio/Annotation/Comment.pm +cp lib/Bio/Align/DNAStatistics.pm blib/lib/Bio/Align/DNAStatistics.pm cp lib/Bio/AlignIO/Handler/GenericAlignHandler.pm blib/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm -cp lib/Bio/AlignIO/bl2seq.pm blib/lib/Bio/AlignIO/bl2seq.pm +cp lib/Bio/AlignIO.pm blib/lib/Bio/AlignIO.pm +cp lib/Bio/AlignIO/pfam.pm blib/lib/Bio/AlignIO/pfam.pm +cp lib/Bio/AnnotatableI.pm blib/lib/Bio/AnnotatableI.pm +cp lib/Bio/AlignIO/proda.pm blib/lib/Bio/AlignIO/proda.pm +cp lib/Bio/AnalysisResultI.pm blib/lib/Bio/AnalysisResultI.pm +cp lib/Bio/AlignIO/phylip.pm blib/lib/Bio/AlignIO/phylip.pm cp lib/Bio/AlignIO/xmfa.pm blib/lib/Bio/AlignIO/xmfa.pm -cp lib/Bio/Annotation/AnnotationFactory.pm blib/lib/Bio/Annotation/AnnotationFactory.pm +cp lib/Bio/Annotation/OntologyTerm.pm blib/lib/Bio/Annotation/OntologyTerm.pm +cp lib/Bio/AnalysisParserI.pm blib/lib/Bio/AnalysisParserI.pm +cp lib/Bio/AlignIO/maf.pm blib/lib/Bio/AlignIO/maf.pm +cp lib/Bio/AlignIO/prodom.pm blib/lib/Bio/AlignIO/prodom.pm cp lib/Bio/AlignIO/arp.pm blib/lib/Bio/AlignIO/arp.pm +cp lib/Bio/AlignIO/selex.pm blib/lib/Bio/AlignIO/selex.pm +cp lib/Bio/AlignIO/po.pm blib/lib/Bio/AlignIO/po.pm +cp lib/Bio/AlignIO/bl2seq.pm blib/lib/Bio/AlignIO/bl2seq.pm +cp lib/Bio/AlignIO/msf.pm blib/lib/Bio/AlignIO/msf.pm +cp lib/Bio/Annotation/Collection.pm blib/lib/Bio/Annotation/Collection.pm +cp lib/Bio/AlignIO/mase.pm blib/lib/Bio/AlignIO/mase.pm +cp lib/Bio/AlignIO/emboss.pm blib/lib/Bio/AlignIO/emboss.pm cp lib/Bio/AlignIO/clustalw.pm blib/lib/Bio/AlignIO/clustalw.pm -cp lib/Bio/Align/Utilities.pm blib/lib/Bio/Align/Utilities.pm -cp lib/Bio/AlignIO.pm blib/lib/Bio/AlignIO.pm -cp lib/Bio/Align/ProteinStatistics.pm blib/lib/Bio/Align/ProteinStatistics.pm -cp lib/Bio/AlignIO/mega.pm blib/lib/Bio/AlignIO/mega.pm -cp lib/Bio/CodonUsage/IO.pm blib/lib/Bio/CodonUsage/IO.pm -cp lib/Bio/Annotation/Target.pm blib/lib/Bio/Annotation/Target.pm -cp lib/Bio/DB/GenericWebAgent.pm blib/lib/Bio/DB/GenericWebAgent.pm -cp lib/Bio/DB/IndexedBase.pm blib/lib/Bio/DB/IndexedBase.pm +cp lib/Bio/AlignIO/largemultifasta.pm blib/lib/Bio/AlignIO/largemultifasta.pm +cp lib/Bio/Annotation/Reference.pm blib/lib/Bio/Annotation/Reference.pm +cp lib/Bio/Align/PairwiseStatistics.pm blib/lib/Bio/Align/PairwiseStatistics.pm +cp lib/Bio/Align/AlignI.pm blib/lib/Bio/Align/AlignI.pm +cp lib/Bio/Annotation/DBLink.pm blib/lib/Bio/Annotation/DBLink.pm +cp lib/Bio/DB/Flat/BinarySearch.pm blib/lib/Bio/DB/Flat/BinarySearch.pm +cp lib/Bio/DB/DBFetch.pm blib/lib/Bio/DB/DBFetch.pm cp lib/Bio/DB/Taxonomy/greengenes.pm blib/lib/Bio/DB/Taxonomy/greengenes.pm -cp lib/Bio/DB/UpdateableSeqI.pm blib/lib/Bio/DB/UpdateableSeqI.pm -cp lib/Bio/DB/Qual.pm blib/lib/Bio/DB/Qual.pm -cp lib/Bio/DB/SeqI.pm blib/lib/Bio/DB/SeqI.pm -cp lib/Bio/Annotation/TypeManager.pm blib/lib/Bio/Annotation/TypeManager.pm -cp lib/Bio/DB/Flat/BDB/embl.pm blib/lib/Bio/DB/Flat/BDB/embl.pm -cp lib/Bio/DB/ReferenceI.pm blib/lib/Bio/DB/ReferenceI.pm -cp lib/Bio/DB/Failover.pm blib/lib/Bio/DB/Failover.pm -cp lib/Bio/Annotation/TagTree.pm blib/lib/Bio/Annotation/TagTree.pm -cp lib/Bio/DB/QueryI.pm blib/lib/Bio/DB/QueryI.pm -cp lib/Bio/DB/LocationI.pm blib/lib/Bio/DB/LocationI.pm +cp lib/Bio/DB/Flat/BDB.pm blib/lib/Bio/DB/Flat/BDB.pm +cp lib/Bio/DB/Flat/BDB/swiss.pm blib/lib/Bio/DB/Flat/BDB/swiss.pm +cp lib/Bio/DB/RandomAccessI.pm blib/lib/Bio/DB/RandomAccessI.pm cp lib/Bio/Annotation/StructuredValue.pm blib/lib/Bio/Annotation/StructuredValue.pm cp lib/Bio/DB/Query/WebQuery.pm blib/lib/Bio/DB/Query/WebQuery.pm cp lib/Bio/DB/InMemoryCache.pm blib/lib/Bio/DB/InMemoryCache.pm -cp lib/Bio/DB/Taxonomy/list.pm blib/lib/Bio/DB/Taxonomy/list.pm -cp lib/Bio/DB/Flat/BDB/genbank.pm blib/lib/Bio/DB/Flat/BDB/genbank.pm -cp lib/Bio/DB/DBFetch.pm blib/lib/Bio/DB/DBFetch.pm -cp lib/Bio/DB/Flat.pm blib/lib/Bio/DB/Flat.pm -cp lib/Bio/DB/GFF/Util/Binning.pm blib/lib/Bio/DB/GFF/Util/Binning.pm -cp lib/Bio/DB/FileCache.pm blib/lib/Bio/DB/FileCache.pm -cp lib/Bio/DB/RandomAccessI.pm blib/lib/Bio/DB/RandomAccessI.pm -cp lib/Bio/DB/Taxonomy/silva.pm blib/lib/Bio/DB/Taxonomy/silva.pm -cp lib/Bio/AnnotationCollectionI.pm blib/lib/Bio/AnnotationCollectionI.pm +cp lib/Bio/Annotation/TagTree.pm blib/lib/Bio/Annotation/TagTree.pm +cp lib/Bio/DB/ReferenceI.pm blib/lib/Bio/DB/ReferenceI.pm cp lib/Bio/DB/Registry.pm blib/lib/Bio/DB/Registry.pm +cp lib/Bio/DB/Flat/BDB/embl.pm blib/lib/Bio/DB/Flat/BDB/embl.pm cp lib/Bio/DB/GFF/Util/Rearrange.pm blib/lib/Bio/DB/GFF/Util/Rearrange.pm +cp lib/Bio/DB/SeqI.pm blib/lib/Bio/DB/SeqI.pm +cp lib/Bio/DB/GenericWebAgent.pm blib/lib/Bio/DB/GenericWebAgent.pm +cp lib/Bio/DB/LocationI.pm blib/lib/Bio/DB/LocationI.pm cp lib/Bio/CodonUsage/Table.pm blib/lib/Bio/CodonUsage/Table.pm -cp lib/Bio/Annotation/Tree.pm blib/lib/Bio/Annotation/Tree.pm -cp lib/Bio/DB/Taxonomy.pm blib/lib/Bio/DB/Taxonomy.pm -cp lib/Bio/DB/Flat/BinarySearch.pm blib/lib/Bio/DB/Flat/BinarySearch.pm -cp lib/Bio/DB/Flat/BDB.pm blib/lib/Bio/DB/Flat/BDB.pm -cp lib/Bio/DB/Taxonomy/flatfile.pm blib/lib/Bio/DB/Taxonomy/flatfile.pm -cp lib/Bio/DB/Flat/BDB/swiss.pm blib/lib/Bio/DB/Flat/BDB/swiss.pm -cp lib/Bio/Annotation/SimpleValue.pm blib/lib/Bio/Annotation/SimpleValue.pm cp lib/Bio/DB/Flat/BDB/fasta.pm blib/lib/Bio/DB/Flat/BDB/fasta.pm +cp lib/Bio/DB/FileCache.pm blib/lib/Bio/DB/FileCache.pm +cp lib/Bio/DB/Taxonomy/list.pm blib/lib/Bio/DB/Taxonomy/list.pm cp lib/Bio/AnnotationI.pm blib/lib/Bio/AnnotationI.pm +cp lib/Bio/DB/Flat.pm blib/lib/Bio/DB/Flat.pm +cp lib/Bio/Annotation/TypeManager.pm blib/lib/Bio/Annotation/TypeManager.pm +cp lib/Bio/DB/Qual.pm blib/lib/Bio/DB/Qual.pm +cp lib/Bio/DB/Taxonomy.pm blib/lib/Bio/DB/Taxonomy.pm +cp lib/Bio/DB/QueryI.pm blib/lib/Bio/DB/QueryI.pm +cp lib/Bio/DB/IndexedBase.pm blib/lib/Bio/DB/IndexedBase.pm +cp lib/Bio/Annotation/Tree.pm blib/lib/Bio/Annotation/Tree.pm cp lib/Bio/DB/Fasta.pm blib/lib/Bio/DB/Fasta.pm -cp lib/Bio/Index/SwissPfam.pm blib/lib/Bio/Index/SwissPfam.pm -cp lib/Bio/Factory/ObjectFactoryI.pm blib/lib/Bio/Factory/ObjectFactoryI.pm +cp lib/Bio/AnnotationCollectionI.pm blib/lib/Bio/AnnotationCollectionI.pm +cp lib/Bio/DB/Taxonomy/silva.pm blib/lib/Bio/DB/Taxonomy/silva.pm +cp lib/Bio/CodonUsage/IO.pm blib/lib/Bio/CodonUsage/IO.pm +cp lib/Bio/DB/Failover.pm blib/lib/Bio/DB/Failover.pm +cp lib/Bio/Annotation/SimpleValue.pm blib/lib/Bio/Annotation/SimpleValue.pm +cp lib/Bio/DB/Flat/BDB/genbank.pm blib/lib/Bio/DB/Flat/BDB/genbank.pm +cp lib/Bio/DB/Taxonomy/flatfile.pm blib/lib/Bio/DB/Taxonomy/flatfile.pm +cp lib/Bio/Annotation/Target.pm blib/lib/Bio/Annotation/Target.pm +cp lib/Bio/DB/UpdateableSeqI.pm blib/lib/Bio/DB/UpdateableSeqI.pm +cp lib/Bio/DB/GFF/Util/Binning.pm blib/lib/Bio/DB/GFF/Util/Binning.pm +cp lib/Bio/Index/GenBank.pm blib/lib/Bio/Index/GenBank.pm +cp lib/Bio/Event/EventGeneratorI.pm blib/lib/Bio/Event/EventGeneratorI.pm cp lib/Bio/Index/Fasta.pm blib/lib/Bio/Index/Fasta.pm -cp lib/Bio/Index/EMBL.pm blib/lib/Bio/Index/EMBL.pm -cp lib/Bio/LocatableSeq.pm blib/lib/Bio/LocatableSeq.pm -cp lib/Bio/IdentifiableI.pm blib/lib/Bio/IdentifiableI.pm cp lib/Bio/Index/Qual.pm blib/lib/Bio/Index/Qual.pm cp lib/Bio/Factory/SequenceProcessorI.pm blib/lib/Bio/Factory/SequenceProcessorI.pm -cp lib/Bio/Factory/TreeFactoryI.pm blib/lib/Bio/Factory/TreeFactoryI.pm -cp lib/Bio/Factory/FTLocationFactory.pm blib/lib/Bio/Factory/FTLocationFactory.pm -cp lib/Bio/IdCollectionI.pm blib/lib/Bio/IdCollectionI.pm -cp lib/Bio/DescribableI.pm blib/lib/Bio/DescribableI.pm -cp lib/Bio/DasI.pm blib/lib/Bio/DasI.pm -cp lib/Bio/Index/GenBank.pm blib/lib/Bio/Index/GenBank.pm -cp lib/Bio/Event/EventGeneratorI.pm blib/lib/Bio/Event/EventGeneratorI.pm cp lib/Bio/Index/Swissprot.pm blib/lib/Bio/Index/Swissprot.pm -cp lib/Bio/Index/Fastq.pm blib/lib/Bio/Index/Fastq.pm -cp lib/Bio/Event/EventHandlerI.pm blib/lib/Bio/Event/EventHandlerI.pm -cp lib/Bio/Das/FeatureTypeI.pm blib/lib/Bio/Das/FeatureTypeI.pm -cp lib/Bio/Factory/SequenceStreamI.pm blib/lib/Bio/Factory/SequenceStreamI.pm -cp lib/Bio/FeatureHolderI.pm blib/lib/Bio/FeatureHolderI.pm -cp lib/Bio/Factory/LocationFactoryI.pm blib/lib/Bio/Factory/LocationFactoryI.pm -cp lib/Bio/Factory/DriverFactory.pm blib/lib/Bio/Factory/DriverFactory.pm -cp lib/Bio/DB/WebDBSeqI.pm blib/lib/Bio/DB/WebDBSeqI.pm -cp lib/Bio/DBLinkContainerI.pm blib/lib/Bio/DBLinkContainerI.pm +cp lib/Bio/Factory/FTLocationFactory.pm blib/lib/Bio/Factory/FTLocationFactory.pm cp lib/Bio/Das/SegmentI.pm blib/lib/Bio/Das/SegmentI.pm +cp lib/Bio/Index/EMBL.pm blib/lib/Bio/Index/EMBL.pm cp lib/Bio/Factory/ObjectFactory.pm blib/lib/Bio/Factory/ObjectFactory.pm -cp lib/Bio/Index/AbstractSeq.pm blib/lib/Bio/Index/AbstractSeq.pm +cp lib/Bio/Factory/LocationFactoryI.pm blib/lib/Bio/Factory/LocationFactoryI.pm +cp lib/Bio/Factory/TreeFactoryI.pm blib/lib/Bio/Factory/TreeFactoryI.pm +cp lib/Bio/Factory/AnalysisI.pm blib/lib/Bio/Factory/AnalysisI.pm +cp lib/Bio/DasI.pm blib/lib/Bio/DasI.pm +cp lib/Bio/Index/SwissPfam.pm blib/lib/Bio/Index/SwissPfam.pm +cp lib/Bio/Factory/SequenceStreamI.pm blib/lib/Bio/Factory/SequenceStreamI.pm +cp lib/Bio/Das/FeatureTypeI.pm blib/lib/Bio/Das/FeatureTypeI.pm +cp lib/Bio/Index/Fastq.pm blib/lib/Bio/Index/Fastq.pm cp lib/Bio/Factory/SeqAnalysisParserFactory.pm blib/lib/Bio/Factory/SeqAnalysisParserFactory.pm -cp lib/Bio/Index/Blast.pm blib/lib/Bio/Index/Blast.pm -cp lib/Bio/Factory/SeqAnalysisParserFactoryI.pm blib/lib/Bio/Factory/SeqAnalysisParserFactoryI.pm -cp lib/Bio/Factory/ApplicationFactoryI.pm blib/lib/Bio/Factory/ApplicationFactoryI.pm -cp lib/Bio/Index/Abstract.pm blib/lib/Bio/Index/Abstract.pm cp lib/Bio/Factory/SequenceFactoryI.pm blib/lib/Bio/Factory/SequenceFactoryI.pm +cp lib/Bio/Factory/ObjectFactoryI.pm blib/lib/Bio/Factory/ObjectFactoryI.pm +cp lib/Bio/IdentifiableI.pm blib/lib/Bio/IdentifiableI.pm +cp lib/Bio/Index/Blast.pm blib/lib/Bio/Index/Blast.pm cp lib/Bio/HandlerBaseI.pm blib/lib/Bio/HandlerBaseI.pm -cp lib/Bio/Factory/AnalysisI.pm blib/lib/Bio/Factory/AnalysisI.pm cp lib/Bio/Factory/ObjectBuilderI.pm blib/lib/Bio/Factory/ObjectBuilderI.pm +cp lib/Bio/Factory/SeqAnalysisParserFactoryI.pm blib/lib/Bio/Factory/SeqAnalysisParserFactoryI.pm +cp lib/Bio/DB/WebDBSeqI.pm blib/lib/Bio/DB/WebDBSeqI.pm +cp lib/Bio/DescribableI.pm blib/lib/Bio/DescribableI.pm +cp lib/Bio/Event/EventHandlerI.pm blib/lib/Bio/Event/EventHandlerI.pm +cp lib/Bio/FeatureHolderI.pm blib/lib/Bio/FeatureHolderI.pm +cp lib/Bio/Index/Abstract.pm blib/lib/Bio/Index/Abstract.pm +cp lib/Bio/IdCollectionI.pm blib/lib/Bio/IdCollectionI.pm +cp lib/Bio/Index/AbstractSeq.pm blib/lib/Bio/Index/AbstractSeq.pm cp lib/Bio/Index/BlastTable.pm blib/lib/Bio/Index/BlastTable.pm -cp lib/Bio/Matrix/Generic.pm blib/lib/Bio/Matrix/Generic.pm -cp lib/Bio/Location/Simple.pm blib/lib/Bio/Location/Simple.pm -cp lib/Bio/Location/SplitLocationI.pm blib/lib/Bio/Location/SplitLocationI.pm -cp lib/Bio/Matrix/PSM/ProtMatrix.pm blib/lib/Bio/Matrix/PSM/ProtMatrix.pm -cp lib/Bio/Matrix/PSM/IO/masta.pm blib/lib/Bio/Matrix/PSM/IO/masta.pm -cp lib/Bio/Location/NarrowestCoordPolicy.pm blib/lib/Bio/Location/NarrowestCoordPolicy.pm -cp lib/Bio/Matrix/IO/scoring.pm blib/lib/Bio/Matrix/IO/scoring.pm -cp lib/Bio/Matrix/PSM/ProtPsm.pm blib/lib/Bio/Matrix/PSM/ProtPsm.pm -cp lib/Bio/Matrix/PSM/InstanceSite.pm blib/lib/Bio/Matrix/PSM/InstanceSite.pm -cp lib/Bio/Matrix/IO/phylip.pm blib/lib/Bio/Matrix/IO/phylip.pm -cp lib/Bio/Matrix/MatrixI.pm blib/lib/Bio/Matrix/MatrixI.pm -cp lib/Bio/Matrix/PSM/IO.pm blib/lib/Bio/Matrix/PSM/IO.pm -cp lib/Bio/Matrix/PSM/IO/meme.pm blib/lib/Bio/Matrix/PSM/IO/meme.pm -cp lib/Bio/Ontology/DocumentRegistry.pm blib/lib/Bio/Ontology/DocumentRegistry.pm -cp lib/Bio/Location/Fuzzy.pm blib/lib/Bio/Location/Fuzzy.pm -cp lib/Bio/Matrix/PSM/IO/psiblast.pm blib/lib/Bio/Matrix/PSM/IO/psiblast.pm -cp lib/Bio/Matrix/PhylipDist.pm blib/lib/Bio/Matrix/PhylipDist.pm -cp lib/Bio/Matrix/Mlagan.pm blib/lib/Bio/Matrix/Mlagan.pm -cp lib/Bio/Matrix/PSM/SiteMatrixI.pm blib/lib/Bio/Matrix/PSM/SiteMatrixI.pm -cp lib/Bio/Matrix/PSM/IO/transfac.pm blib/lib/Bio/Matrix/PSM/IO/transfac.pm -cp lib/Bio/Location/Atomic.pm blib/lib/Bio/Location/Atomic.pm +cp lib/Bio/Factory/ApplicationFactoryI.pm blib/lib/Bio/Factory/ApplicationFactoryI.pm +cp lib/Bio/Factory/DriverFactory.pm blib/lib/Bio/Factory/DriverFactory.pm +cp lib/Bio/LocatableSeq.pm blib/lib/Bio/LocatableSeq.pm +cp lib/Bio/DBLinkContainerI.pm blib/lib/Bio/DBLinkContainerI.pm +cp lib/Bio/Location/AvWithinCoordPolicy.pm blib/lib/Bio/Location/AvWithinCoordPolicy.pm cp lib/Bio/Matrix/PSM/PsmHeader.pm blib/lib/Bio/Matrix/PSM/PsmHeader.pm -cp lib/Bio/Location/CoordinatePolicyI.pm blib/lib/Bio/Location/CoordinatePolicyI.pm -cp lib/Bio/Matrix/PSM/Psm.pm blib/lib/Bio/Matrix/PSM/Psm.pm -cp lib/Bio/Location/WidestCoordPolicy.pm blib/lib/Bio/Location/WidestCoordPolicy.pm cp lib/Bio/Matrix/IO.pm blib/lib/Bio/Matrix/IO.pm -cp lib/Bio/Location/FuzzyLocationI.pm blib/lib/Bio/Location/FuzzyLocationI.pm -cp lib/Bio/Matrix/PSM/PsmI.pm blib/lib/Bio/Matrix/PSM/PsmI.pm -cp lib/Bio/Matrix/PSM/IO/mast.pm blib/lib/Bio/Matrix/PSM/IO/mast.pm cp lib/Bio/Location/Split.pm blib/lib/Bio/Location/Split.pm -cp lib/Bio/Location/AvWithinCoordPolicy.pm blib/lib/Bio/Location/AvWithinCoordPolicy.pm cp lib/Bio/Matrix/PSM/SiteMatrix.pm blib/lib/Bio/Matrix/PSM/SiteMatrix.pm +cp lib/Bio/Location/Fuzzy.pm blib/lib/Bio/Location/Fuzzy.pm +cp lib/Bio/Location/NarrowestCoordPolicy.pm blib/lib/Bio/Location/NarrowestCoordPolicy.pm +cp lib/Bio/Location/SplitLocationI.pm blib/lib/Bio/Location/SplitLocationI.pm +cp lib/Bio/Matrix/PSM/SiteMatrixI.pm blib/lib/Bio/Matrix/PSM/SiteMatrixI.pm +cp lib/Bio/Ontology/DocumentRegistry.pm blib/lib/Bio/Ontology/DocumentRegistry.pm +cp lib/Bio/Location/WidestCoordPolicy.pm blib/lib/Bio/Location/WidestCoordPolicy.pm +cp lib/Bio/Matrix/PSM/IO/meme.pm blib/lib/Bio/Matrix/PSM/IO/meme.pm +cp lib/Bio/Location/CoordinatePolicyI.pm blib/lib/Bio/Location/CoordinatePolicyI.pm +cp lib/Bio/Matrix/PSM/IO/mast.pm blib/lib/Bio/Matrix/PSM/IO/mast.pm cp lib/Bio/Matrix/IO/mlagan.pm blib/lib/Bio/Matrix/IO/mlagan.pm -cp lib/Bio/Matrix/PSM/PsmHeaderI.pm blib/lib/Bio/Matrix/PSM/PsmHeaderI.pm +cp lib/Bio/Matrix/PSM/IO.pm blib/lib/Bio/Matrix/PSM/IO.pm +cp lib/Bio/Matrix/PSM/InstanceSite.pm blib/lib/Bio/Matrix/PSM/InstanceSite.pm cp lib/Bio/LocationI.pm blib/lib/Bio/LocationI.pm +cp lib/Bio/Matrix/PSM/ProtPsm.pm blib/lib/Bio/Matrix/PSM/ProtPsm.pm +cp lib/Bio/Location/Atomic.pm blib/lib/Bio/Location/Atomic.pm +cp lib/Bio/Matrix/PSM/IO/transfac.pm blib/lib/Bio/Matrix/PSM/IO/transfac.pm +cp lib/Bio/Matrix/PSM/IO/psiblast.pm blib/lib/Bio/Matrix/PSM/IO/psiblast.pm +cp lib/Bio/Matrix/PSM/ProtMatrix.pm blib/lib/Bio/Matrix/PSM/ProtMatrix.pm +cp lib/Bio/Matrix/Generic.pm blib/lib/Bio/Matrix/Generic.pm cp lib/Bio/Matrix/PSM/InstanceSiteI.pm blib/lib/Bio/Matrix/PSM/InstanceSiteI.pm +cp lib/Bio/Location/FuzzyLocationI.pm blib/lib/Bio/Location/FuzzyLocationI.pm +cp lib/Bio/Matrix/IO/phylip.pm blib/lib/Bio/Matrix/IO/phylip.pm +cp lib/Bio/Matrix/PhylipDist.pm blib/lib/Bio/Matrix/PhylipDist.pm cp lib/Bio/Matrix/Scoring.pm blib/lib/Bio/Matrix/Scoring.pm -cp lib/Bio/Ontology/TermFactory.pm blib/lib/Bio/Ontology/TermFactory.pm -cp lib/Bio/Ontology/Path.pm blib/lib/Bio/Ontology/Path.pm -cp lib/Bio/ParameterBaseI.pm blib/lib/Bio/ParameterBaseI.pm +cp lib/Bio/Matrix/IO/scoring.pm blib/lib/Bio/Matrix/IO/scoring.pm +cp lib/Bio/Matrix/Mlagan.pm blib/lib/Bio/Matrix/Mlagan.pm +cp lib/Bio/Location/Simple.pm blib/lib/Bio/Location/Simple.pm +cp lib/Bio/Matrix/PSM/Psm.pm blib/lib/Bio/Matrix/PSM/Psm.pm +cp lib/Bio/Matrix/MatrixI.pm blib/lib/Bio/Matrix/MatrixI.pm +cp lib/Bio/Matrix/PSM/PsmHeaderI.pm blib/lib/Bio/Matrix/PSM/PsmHeaderI.pm +cp lib/Bio/Matrix/PSM/PsmI.pm blib/lib/Bio/Matrix/PSM/PsmI.pm +cp lib/Bio/Matrix/PSM/IO/masta.pm blib/lib/Bio/Matrix/PSM/IO/masta.pm +cp lib/Bio/Ontology/OntologyEngineI.pm blib/lib/Bio/Ontology/OntologyEngineI.pm cp lib/Bio/Ontology/OBOterm.pm blib/lib/Bio/Ontology/OBOterm.pm +cp lib/Bio/OntologyIO/dagflat.pm blib/lib/Bio/OntologyIO/dagflat.pm cp lib/Bio/PrimarySeq.pm blib/lib/Bio/PrimarySeq.pm -cp lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm blib/lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm -cp lib/Bio/Ontology/Relationship.pm blib/lib/Bio/Ontology/Relationship.pm -cp lib/Bio/Ontology/RelationshipI.pm blib/lib/Bio/Ontology/RelationshipI.pm +cp lib/Bio/Ontology/InterProTerm.pm blib/lib/Bio/Ontology/InterProTerm.pm +cp lib/Bio/Ontology/OntologyStore.pm blib/lib/Bio/Ontology/OntologyStore.pm cp lib/Bio/OntologyIO/Handlers/InterProHandler.pm blib/lib/Bio/OntologyIO/Handlers/InterProHandler.pm -cp lib/Bio/OntologyIO/goflat.pm blib/lib/Bio/OntologyIO/goflat.pm -cp lib/Bio/Ontology/PathI.pm blib/lib/Bio/Ontology/PathI.pm -cp lib/Bio/Ontology/RelationshipType.pm blib/lib/Bio/Ontology/RelationshipType.pm -cp lib/Bio/Ontology/TermI.pm blib/lib/Bio/Ontology/TermI.pm -cp lib/Bio/PullParserI.pm blib/lib/Bio/PullParserI.pm -cp lib/Bio/OntologyIO/soflat.pm blib/lib/Bio/OntologyIO/soflat.pm -cp lib/Bio/Ontology/OntologyEngineI.pm blib/lib/Bio/Ontology/OntologyEngineI.pm +cp lib/Bio/Ontology/Ontology.pm blib/lib/Bio/Ontology/Ontology.pm cp lib/Bio/Root/Exception.pm blib/lib/Bio/Root/Exception.pm cp lib/Bio/Ontology/OBOEngine.pm blib/lib/Bio/Ontology/OBOEngine.pm -cp lib/Bio/OntologyIO/InterProParser.pm blib/lib/Bio/OntologyIO/InterProParser.pm -cp lib/Bio/Ontology/OntologyI.pm blib/lib/Bio/Ontology/OntologyI.pm -cp lib/Bio/RangeI.pm blib/lib/Bio/RangeI.pm -cp lib/Bio/Ontology/OntologyStore.pm blib/lib/Bio/Ontology/OntologyStore.pm +cp lib/Bio/Ontology/TermFactory.pm blib/lib/Bio/Ontology/TermFactory.pm cp lib/Bio/OntologyIO/obo.pm blib/lib/Bio/OntologyIO/obo.pm +cp lib/Bio/OntologyIO/soflat.pm blib/lib/Bio/OntologyIO/soflat.pm +cp lib/Bio/RangeI.pm blib/lib/Bio/RangeI.pm +cp lib/Bio/Ontology/Relationship.pm blib/lib/Bio/Ontology/Relationship.pm +cp lib/Bio/Ontology/TermI.pm blib/lib/Bio/Ontology/TermI.pm cp lib/Bio/PrimarySeqI.pm blib/lib/Bio/PrimarySeqI.pm -cp lib/Bio/Ontology/RelationshipFactory.pm blib/lib/Bio/Ontology/RelationshipFactory.pm -cp lib/Bio/OntologyIO.pm blib/lib/Bio/OntologyIO.pm +cp lib/Bio/Ontology/OntologyI.pm blib/lib/Bio/Ontology/OntologyI.pm cp lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm +cp lib/Bio/Ontology/GOterm.pm blib/lib/Bio/Ontology/GOterm.pm +cp lib/Bio/Ontology/PathI.pm blib/lib/Bio/Ontology/PathI.pm +cp lib/Bio/OntologyIO/simplehierarchy.pm blib/lib/Bio/OntologyIO/simplehierarchy.pm +cp lib/Bio/OntologyIO/InterProParser.pm blib/lib/Bio/OntologyIO/InterProParser.pm +cp lib/Bio/Ontology/RelationshipType.pm blib/lib/Bio/Ontology/RelationshipType.pm +cp lib/Bio/Ontology/RelationshipFactory.pm blib/lib/Bio/Ontology/RelationshipFactory.pm +cp lib/Bio/Ontology/SimpleOntologyEngine.pm blib/lib/Bio/Ontology/SimpleOntologyEngine.pm cp lib/Bio/Range.pm blib/lib/Bio/Range.pm +cp lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm blib/lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm +cp lib/Bio/Ontology/RelationshipI.pm blib/lib/Bio/Ontology/RelationshipI.pm +cp lib/Bio/ParameterBaseI.pm blib/lib/Bio/ParameterBaseI.pm +cp lib/Bio/OntologyIO.pm blib/lib/Bio/OntologyIO.pm +cp lib/Bio/Ontology/Path.pm blib/lib/Bio/Ontology/Path.pm +cp lib/Bio/OntologyIO/goflat.pm blib/lib/Bio/OntologyIO/goflat.pm +cp lib/Bio/PullParserI.pm blib/lib/Bio/PullParserI.pm cp lib/Bio/Ontology/Term.pm blib/lib/Bio/Ontology/Term.pm -cp lib/Bio/Ontology/InterProTerm.pm blib/lib/Bio/Ontology/InterProTerm.pm -cp lib/Bio/OntologyIO/dagflat.pm blib/lib/Bio/OntologyIO/dagflat.pm -cp lib/Bio/OntologyIO/simplehierarchy.pm blib/lib/Bio/OntologyIO/simplehierarchy.pm -cp lib/Bio/Ontology/Ontology.pm blib/lib/Bio/Ontology/Ontology.pm cp lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm blib/lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm -cp lib/Bio/Ontology/SimpleOntologyEngine.pm blib/lib/Bio/Ontology/SimpleOntologyEngine.pm -cp lib/Bio/Ontology/GOterm.pm blib/lib/Bio/Ontology/GOterm.pm -cp lib/Bio/Search/HSP/ModelHSP.pm blib/lib/Bio/Search/HSP/ModelHSP.pm -cp lib/Bio/Root/HTTPget.pm blib/lib/Bio/Root/HTTPget.pm -cp lib/Bio/Search/BlastUtils.pm blib/lib/Bio/Search/BlastUtils.pm -cp lib/Bio/Search/Iteration/IterationI.pm blib/lib/Bio/Search/Iteration/IterationI.pm -cp lib/Bio/Root/RootI.pm blib/lib/Bio/Root/RootI.pm -cp lib/Bio/Search/HSP/PullHSPI.pm blib/lib/Bio/Search/HSP/PullHSPI.pm -cp lib/Bio/Root/Version.pm blib/lib/Bio/Root/Version.pm cp lib/Bio/Search/Iteration/GenericIteration.pm blib/lib/Bio/Search/Iteration/GenericIteration.pm -cp lib/Bio/Root/TestObject.pm blib/lib/Bio/Root/TestObject.pm -cp lib/Bio/Search/HSP/FastaHSP.pm blib/lib/Bio/Search/HSP/FastaHSP.pm -cp lib/Bio/Search/Hit/HitI.pm blib/lib/Bio/Search/Hit/HitI.pm -cp lib/Bio/Search/HSP/PsiBlastHSP.pm blib/lib/Bio/Search/HSP/PsiBlastHSP.pm -cp lib/Bio/Search/Hit/BlastPullHit.pm blib/lib/Bio/Search/Hit/BlastPullHit.pm -cp lib/Bio/Root/Storable.pm blib/lib/Bio/Root/Storable.pm +cp lib/Bio/Search/HSP/HSPFactory.pm blib/lib/Bio/Search/HSP/HSPFactory.pm +cp lib/Bio/Root/Utilities.pm blib/lib/Bio/Root/Utilities.pm +cp lib/Bio/Root/Test.pm blib/lib/Bio/Root/Test.pm cp lib/Bio/Search/HSP/GenericHSP.pm blib/lib/Bio/Search/HSP/GenericHSP.pm cp lib/Bio/Search/DatabaseI.pm blib/lib/Bio/Search/DatabaseI.pm -cp lib/Bio/Search/Hit/GenericHit.pm blib/lib/Bio/Search/Hit/GenericHit.pm -cp lib/Bio/Search/HSP/HSPI.pm blib/lib/Bio/Search/HSP/HSPI.pm -cp lib/Bio/Search/Hit/PullHitI.pm blib/lib/Bio/Search/Hit/PullHitI.pm +cp lib/Bio/Search/Hit/Fasta.pm blib/lib/Bio/Search/Hit/Fasta.pm +cp lib/Bio/Search/HSP/BlastHSP.pm blib/lib/Bio/Search/HSP/BlastHSP.pm +cp lib/Bio/Search/BlastStatistics.pm blib/lib/Bio/Search/BlastStatistics.pm +cp lib/Bio/Search/GenericDatabase.pm blib/lib/Bio/Search/GenericDatabase.pm cp lib/Bio/Search/Hit/BlastHit.pm blib/lib/Bio/Search/Hit/BlastHit.pm -cp lib/Bio/Search/GenericStatistics.pm blib/lib/Bio/Search/GenericStatistics.pm +cp lib/Bio/Root/HTTPget.pm blib/lib/Bio/Root/HTTPget.pm +cp lib/Bio/Search/HSP/PSLHSP.pm blib/lib/Bio/Search/HSP/PSLHSP.pm +cp lib/Bio/Search/Hit/ModelHit.pm blib/lib/Bio/Search/Hit/ModelHit.pm +cp lib/Bio/Search/HSP/PsiBlastHSP.pm blib/lib/Bio/Search/HSP/PsiBlastHSP.pm +cp lib/Bio/Search/Hit/PullHitI.pm blib/lib/Bio/Search/Hit/PullHitI.pm +cp lib/Bio/Search/HSP/ModelHSP.pm blib/lib/Bio/Search/HSP/ModelHSP.pm +cp lib/Bio/Search/HSP/FastaHSP.pm blib/lib/Bio/Search/HSP/FastaHSP.pm +cp lib/Bio/Search/BlastUtils.pm blib/lib/Bio/Search/BlastUtils.pm cp lib/Bio/Search/HSP/BlastPullHSP.pm blib/lib/Bio/Search/HSP/BlastPullHSP.pm -cp lib/Bio/Search/BlastStatistics.pm blib/lib/Bio/Search/BlastStatistics.pm +cp lib/Bio/Search/Hit/HitFactory.pm blib/lib/Bio/Search/Hit/HitFactory.pm cp lib/Bio/Search/Hit/PsiBlastHit.pm blib/lib/Bio/Search/Hit/PsiBlastHit.pm +cp lib/Bio/Search/GenericStatistics.pm blib/lib/Bio/Search/GenericStatistics.pm cp lib/Bio/Search/HSP/WABAHSP.pm blib/lib/Bio/Search/HSP/WABAHSP.pm -cp lib/Bio/Search/Hit/HitFactory.pm blib/lib/Bio/Search/Hit/HitFactory.pm -cp lib/Bio/Root/Utilities.pm blib/lib/Bio/Root/Utilities.pm -cp lib/Bio/Search/Hit/Fasta.pm blib/lib/Bio/Search/Hit/Fasta.pm -cp lib/Bio/Search/HSP/PSLHSP.pm blib/lib/Bio/Search/HSP/PSLHSP.pm -cp lib/Bio/Search/HSP/BlastHSP.pm blib/lib/Bio/Search/HSP/BlastHSP.pm -cp lib/Bio/Root/Test.pm blib/lib/Bio/Root/Test.pm -cp lib/Bio/Search/GenericDatabase.pm blib/lib/Bio/Search/GenericDatabase.pm +cp lib/Bio/Root/Version.pm blib/lib/Bio/Root/Version.pm +cp lib/Bio/Root/RootI.pm blib/lib/Bio/Root/RootI.pm +cp lib/Bio/Search/HSP/HSPI.pm blib/lib/Bio/Search/HSP/HSPI.pm +cp lib/Bio/Root/Storable.pm blib/lib/Bio/Root/Storable.pm +cp lib/Bio/Search/Hit/GenericHit.pm blib/lib/Bio/Search/Hit/GenericHit.pm +cp lib/Bio/Search/Iteration/IterationI.pm blib/lib/Bio/Search/Iteration/IterationI.pm cp lib/Bio/Root/Root.pm blib/lib/Bio/Root/Root.pm -cp lib/Bio/Search/HSP/HSPFactory.pm blib/lib/Bio/Search/HSP/HSPFactory.pm -cp lib/Bio/Search/Hit/ModelHit.pm blib/lib/Bio/Search/Hit/ModelHit.pm -cp lib/Bio/Search/Processor.pm blib/lib/Bio/Search/Processor.pm +cp lib/Bio/Root/TestObject.pm blib/lib/Bio/Root/TestObject.pm +cp lib/Bio/Search/Hit/BlastPullHit.pm blib/lib/Bio/Search/Hit/BlastPullHit.pm +cp lib/Bio/Search/Hit/HitI.pm blib/lib/Bio/Search/Hit/HitI.pm +cp lib/Bio/Search/HSP/PullHSPI.pm blib/lib/Bio/Search/HSP/PullHSPI.pm cp lib/Bio/Root/IO.pm blib/lib/Bio/Root/IO.pm -cp lib/Bio/Search/Result/CrossMatchResult.pm blib/lib/Bio/Search/Result/CrossMatchResult.pm -cp lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm blib/lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm -cp lib/Bio/Search/Result/BlastResult.pm blib/lib/Bio/Search/Result/BlastResult.pm -cp lib/Bio/SearchIO/Writer/GbrowseGFF.pm blib/lib/Bio/SearchIO/Writer/GbrowseGFF.pm -cp lib/Bio/SearchIO/erpin.pm blib/lib/Bio/SearchIO/erpin.pm -cp lib/Bio/SearchIO/Writer/HTMLResultWriter.pm blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm -cp lib/Bio/Search/Result/BlastPullResult.pm blib/lib/Bio/Search/Result/BlastPullResult.pm +cp lib/Bio/Search/Processor.pm blib/lib/Bio/Search/Processor.pm cp lib/Bio/SearchIO/FastHitEventBuilder.pm blib/lib/Bio/SearchIO/FastHitEventBuilder.pm -cp lib/Bio/Search/StatisticsI.pm blib/lib/Bio/Search/StatisticsI.pm -cp lib/Bio/Search/Tiling/MapTiling.pm blib/lib/Bio/Search/Tiling/MapTiling.pm cp lib/Bio/SearchIO/SearchWriterI.pm blib/lib/Bio/SearchIO/SearchWriterI.pm -cp lib/Bio/Search/Tiling/TilingI.pm blib/lib/Bio/Search/Tiling/TilingI.pm -cp lib/Bio/SearchIO/blast.pm blib/lib/Bio/SearchIO/blast.pm -cp lib/Bio/SearchIO/SearchResultEventBuilder.pm blib/lib/Bio/SearchIO/SearchResultEventBuilder.pm -cp lib/Bio/SearchIO/blasttable.pm blib/lib/Bio/SearchIO/blasttable.pm +cp lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm blib/lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm +cp lib/Bio/Search/Result/BlastPullResult.pm blib/lib/Bio/Search/Result/BlastPullResult.pm cp lib/Bio/SearchIO/axt.pm blib/lib/Bio/SearchIO/axt.pm cp lib/Bio/SearchIO/EventHandlerI.pm blib/lib/Bio/SearchIO/EventHandlerI.pm -cp lib/Bio/Search/Result/ResultFactory.pm blib/lib/Bio/Search/Result/ResultFactory.pm -cp lib/Bio/Search/Result/PullResultI.pm blib/lib/Bio/Search/Result/PullResultI.pm -cp lib/Bio/Search/Result/WABAResult.pm blib/lib/Bio/Search/Result/WABAResult.pm -cp lib/Bio/Search/Result/INFERNALResult.pm blib/lib/Bio/Search/Result/INFERNALResult.pm -cp lib/Bio/SearchIO/blast_pull.pm blib/lib/Bio/SearchIO/blast_pull.pm cp lib/Bio/SearchIO/Writer/TextResultWriter.pm blib/lib/Bio/SearchIO/Writer/TextResultWriter.pm -cp lib/Bio/SearchIO/Writer/HitTableWriter.pm blib/lib/Bio/SearchIO/Writer/HitTableWriter.pm cp lib/Bio/Search/Result/GenericResult.pm blib/lib/Bio/Search/Result/GenericResult.pm -cp lib/Bio/Search/Tiling/MapTileUtils.pm blib/lib/Bio/Search/Tiling/MapTileUtils.pm +cp lib/Bio/SearchIO/blast_pull.pm blib/lib/Bio/SearchIO/blast_pull.pm +cp lib/Bio/SearchIO/Writer/GbrowseGFF.pm blib/lib/Bio/SearchIO/Writer/GbrowseGFF.pm cp lib/Bio/Search/Result/ResultI.pm blib/lib/Bio/Search/Result/ResultI.pm -cp lib/Bio/SearchIO/cross_match.pm blib/lib/Bio/SearchIO/cross_match.pm +cp lib/Bio/Search/Result/WABAResult.pm blib/lib/Bio/Search/Result/WABAResult.pm cp lib/Bio/SearchIO/Writer/HSPTableWriter.pm blib/lib/Bio/SearchIO/Writer/HSPTableWriter.pm -cp lib/Bio/SearchIO.pm blib/lib/Bio/SearchIO.pm +cp lib/Bio/SearchIO/cross_match.pm blib/lib/Bio/SearchIO/cross_match.pm +cp lib/Bio/Search/StatisticsI.pm blib/lib/Bio/Search/StatisticsI.pm +cp lib/Bio/Search/Tiling/TilingI.pm blib/lib/Bio/Search/Tiling/TilingI.pm +cp lib/Bio/Search/Result/PullResultI.pm blib/lib/Bio/Search/Result/PullResultI.pm +cp lib/Bio/SearchIO/Writer/HTMLResultWriter.pm blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm +cp lib/Bio/SearchIO/Writer/HitTableWriter.pm blib/lib/Bio/SearchIO/Writer/HitTableWriter.pm cp lib/Bio/Search/SearchUtils.pm blib/lib/Bio/Search/SearchUtils.pm +cp lib/Bio/SearchIO/erpin.pm blib/lib/Bio/SearchIO/erpin.pm +cp lib/Bio/Search/Tiling/MapTileUtils.pm blib/lib/Bio/Search/Tiling/MapTileUtils.pm +cp lib/Bio/Search/Tiling/MapTiling.pm blib/lib/Bio/Search/Tiling/MapTiling.pm +cp lib/Bio/SearchIO.pm blib/lib/Bio/SearchIO.pm +cp lib/Bio/Search/Result/BlastResult.pm blib/lib/Bio/Search/Result/BlastResult.pm cp lib/Bio/SearchIO/Writer/ResultTableWriter.pm blib/lib/Bio/SearchIO/Writer/ResultTableWriter.pm -cp lib/Bio/Seq/LargeSeq.pm blib/lib/Bio/Seq/LargeSeq.pm -cp lib/Bio/Seq/LargePrimarySeq.pm blib/lib/Bio/Seq/LargePrimarySeq.pm -cp lib/Bio/Seq/LargeSeqI.pm blib/lib/Bio/Seq/LargeSeqI.pm +cp lib/Bio/Search/Result/INFERNALResult.pm blib/lib/Bio/Search/Result/INFERNALResult.pm +cp lib/Bio/SearchIO/blast.pm blib/lib/Bio/SearchIO/blast.pm +cp lib/Bio/SearchIO/blasttable.pm blib/lib/Bio/SearchIO/blasttable.pm +cp lib/Bio/SearchIO/SearchResultEventBuilder.pm blib/lib/Bio/SearchIO/SearchResultEventBuilder.pm +cp lib/Bio/Search/Result/CrossMatchResult.pm blib/lib/Bio/Search/Result/CrossMatchResult.pm +cp lib/Bio/Search/Result/ResultFactory.pm blib/lib/Bio/Search/Result/ResultFactory.pm cp lib/Bio/SearchIO/rnamotif.pm blib/lib/Bio/SearchIO/rnamotif.pm -cp lib/Bio/Seq/RichSeqI.pm blib/lib/Bio/Seq/RichSeqI.pm +cp lib/Bio/Seq/PrimedSeq.pm blib/lib/Bio/Seq/PrimedSeq.pm cp lib/Bio/SeqFeature/Computation.pm blib/lib/Bio/SeqFeature/Computation.pm -cp lib/Bio/Seq/Meta.pm blib/lib/Bio/Seq/Meta.pm cp lib/Bio/Seq/SeqFastaSpeedFactory.pm blib/lib/Bio/Seq/SeqFastaSpeedFactory.pm -cp lib/Bio/SearchIO/sim4.pm blib/lib/Bio/SearchIO/sim4.pm -cp lib/Bio/Seq/SeqBuilder.pm blib/lib/Bio/Seq/SeqBuilder.pm -cp lib/Bio/SearchIO/psl.pm blib/lib/Bio/SearchIO/psl.pm -cp lib/Bio/SearchIO/gmap_f9.pm blib/lib/Bio/SearchIO/gmap_f9.pm +cp lib/Bio/SearchIO/waba.pm blib/lib/Bio/SearchIO/waba.pm +cp lib/Bio/SeqFeature/CollectionI.pm blib/lib/Bio/SeqFeature/CollectionI.pm +cp lib/Bio/SeqFeature/Gene/Exon.pm blib/lib/Bio/SeqFeature/Gene/Exon.pm +cp lib/Bio/SearchIO/exonerate.pm blib/lib/Bio/SearchIO/exonerate.pm +cp lib/Bio/Seq/LargeSeq.pm blib/lib/Bio/Seq/LargeSeq.pm +cp lib/Bio/SearchIO/fasta.pm blib/lib/Bio/SearchIO/fasta.pm cp lib/Bio/SeqFeature/AnnotationAdaptor.pm blib/lib/Bio/SeqFeature/AnnotationAdaptor.pm -cp lib/Bio/Seq/PrimedSeq.pm blib/lib/Bio/Seq/PrimedSeq.pm -cp lib/Bio/Seq.pm blib/lib/Bio/Seq.pm -cp lib/Bio/SearchIO/wise.pm blib/lib/Bio/SearchIO/wise.pm +cp lib/Bio/SearchIO/megablast.pm blib/lib/Bio/SearchIO/megablast.pm +cp lib/Bio/Seq/Meta.pm blib/lib/Bio/Seq/Meta.pm cp lib/Bio/Seq/SimulatedRead.pm blib/lib/Bio/Seq/SimulatedRead.pm -cp lib/Bio/Seq/TraceI.pm blib/lib/Bio/Seq/TraceI.pm -cp lib/Bio/SeqAnalysisParserI.pm blib/lib/Bio/SeqAnalysisParserI.pm cp lib/Bio/Seq/SeqFactory.pm blib/lib/Bio/Seq/SeqFactory.pm -cp lib/Bio/Seq/MetaI.pm blib/lib/Bio/Seq/MetaI.pm -cp lib/Bio/SeqFeature/Amplicon.pm blib/lib/Bio/SeqFeature/Amplicon.pm -cp lib/Bio/SearchIO/infernal.pm blib/lib/Bio/SearchIO/infernal.pm -cp lib/Bio/SearchIO/fasta.pm blib/lib/Bio/SearchIO/fasta.pm -cp lib/Bio/Seq/Quality.pm blib/lib/Bio/Seq/Quality.pm -cp lib/Bio/Seq/SequenceTrace.pm blib/lib/Bio/Seq/SequenceTrace.pm -cp lib/Bio/Seq/PrimaryQual.pm blib/lib/Bio/Seq/PrimaryQual.pm -cp lib/Bio/SeqFeature/Gene/Exon.pm blib/lib/Bio/SeqFeature/Gene/Exon.pm -cp lib/Bio/SeqFeature/CollectionI.pm blib/lib/Bio/SeqFeature/CollectionI.pm cp lib/Bio/Seq/QualI.pm blib/lib/Bio/Seq/QualI.pm -cp lib/Bio/Seq/EncodedSeq.pm blib/lib/Bio/Seq/EncodedSeq.pm +cp lib/Bio/Seq/PrimaryQual.pm blib/lib/Bio/Seq/PrimaryQual.pm +cp lib/Bio/Seq/SequenceTrace.pm blib/lib/Bio/Seq/SequenceTrace.pm cp lib/Bio/Seq/BaseSeqProcessor.pm blib/lib/Bio/Seq/BaseSeqProcessor.pm +cp lib/Bio/SeqAnalysisParserI.pm blib/lib/Bio/SeqAnalysisParserI.pm +cp lib/Bio/Seq/MetaI.pm blib/lib/Bio/Seq/MetaI.pm +cp lib/Bio/Seq/TraceI.pm blib/lib/Bio/Seq/TraceI.pm +cp lib/Bio/SearchIO/gmap_f9.pm blib/lib/Bio/SearchIO/gmap_f9.pm +cp lib/Bio/SearchIO/wise.pm blib/lib/Bio/SearchIO/wise.pm +cp lib/Bio/Seq/LargePrimarySeq.pm blib/lib/Bio/Seq/LargePrimarySeq.pm +cp lib/Bio/SeqFeature/Amplicon.pm blib/lib/Bio/SeqFeature/Amplicon.pm cp lib/Bio/SeqFeature/FeaturePair.pm blib/lib/Bio/SeqFeature/FeaturePair.pm -cp lib/Bio/SearchIO/exonerate.pm blib/lib/Bio/SearchIO/exonerate.pm -cp lib/Bio/SearchIO/megablast.pm blib/lib/Bio/SearchIO/megablast.pm cp lib/Bio/Seq/RichSeq.pm blib/lib/Bio/Seq/RichSeq.pm +cp lib/Bio/Seq/LargeSeqI.pm blib/lib/Bio/Seq/LargeSeqI.pm +cp lib/Bio/SearchIO/psl.pm blib/lib/Bio/SearchIO/psl.pm +cp lib/Bio/Seq/RichSeqI.pm blib/lib/Bio/Seq/RichSeqI.pm +cp lib/Bio/Seq/EncodedSeq.pm blib/lib/Bio/Seq/EncodedSeq.pm cp lib/Bio/Seq/LargeLocatableSeq.pm blib/lib/Bio/Seq/LargeLocatableSeq.pm +cp lib/Bio/SearchIO/infernal.pm blib/lib/Bio/SearchIO/infernal.pm cp lib/Bio/SeqFeature/Collection.pm blib/lib/Bio/SeqFeature/Collection.pm -cp lib/Bio/SearchIO/waba.pm blib/lib/Bio/SearchIO/waba.pm cp lib/Bio/Seq/Meta/Array.pm blib/lib/Bio/Seq/Meta/Array.pm -cp lib/Bio/SeqFeature/PositionProxy.pm blib/lib/Bio/SeqFeature/PositionProxy.pm -cp lib/Bio/SeqIO/embl.pm blib/lib/Bio/SeqIO/embl.pm +cp lib/Bio/Seq.pm blib/lib/Bio/Seq.pm +cp lib/Bio/Seq/SeqBuilder.pm blib/lib/Bio/Seq/SeqBuilder.pm +cp lib/Bio/Seq/Quality.pm blib/lib/Bio/Seq/Quality.pm +cp lib/Bio/SearchIO/sim4.pm blib/lib/Bio/SearchIO/sim4.pm +cp lib/Bio/SeqFeature/Tools/FeatureNamer.pm blib/lib/Bio/SeqFeature/Tools/FeatureNamer.pm +cp lib/Bio/SeqFeature/Gene/Transcript.pm blib/lib/Bio/SeqFeature/Gene/Transcript.pm +cp lib/Bio/SeqIO.pm blib/lib/Bio/SeqIO.pm cp lib/Bio/SeqFeature/Tools/TypeMapper.pm blib/lib/Bio/SeqFeature/Tools/TypeMapper.pm -cp lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm blib/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm -cp lib/Bio/SeqFeature/Similarity.pm blib/lib/Bio/SeqFeature/Similarity.pm -cp lib/Bio/SeqFeature/Primer.pm blib/lib/Bio/SeqFeature/Primer.pm -cp lib/Bio/SeqFeature/SubSeq.pm blib/lib/Bio/SeqFeature/SubSeq.pm -cp lib/Bio/SeqFeature/Gene/TranscriptI.pm blib/lib/Bio/SeqFeature/Gene/TranscriptI.pm cp lib/Bio/SeqIO/bsml_sax.pm blib/lib/Bio/SeqIO/bsml_sax.pm -cp lib/Bio/SeqIO/fastq.pm blib/lib/Bio/SeqIO/fastq.pm -cp lib/Bio/SeqIO/asciitree.pm blib/lib/Bio/SeqIO/asciitree.pm -cp lib/Bio/SeqFeature/SimilarityPair.pm blib/lib/Bio/SeqFeature/SimilarityPair.pm -cp lib/Bio/SeqFeature/Generic.pm blib/lib/Bio/SeqFeature/Generic.pm -cp lib/Bio/SeqIO.pm blib/lib/Bio/SeqIO.pm -cp lib/Bio/SeqIO/bsml.pm blib/lib/Bio/SeqIO/bsml.pm -cp lib/Bio/SeqFeature/Tools/Unflattener.pm blib/lib/Bio/SeqFeature/Tools/Unflattener.pm -cp lib/Bio/SeqFeature/Tools/FeatureNamer.pm blib/lib/Bio/SeqFeature/Tools/FeatureNamer.pm -cp lib/Bio/SeqFeature/TypedSeqFeatureI.pm blib/lib/Bio/SeqFeature/TypedSeqFeatureI.pm -cp lib/Bio/SeqIO/FTHelper.pm blib/lib/Bio/SeqIO/FTHelper.pm +cp lib/Bio/SeqFeature/Gene/ExonI.pm blib/lib/Bio/SeqFeature/Gene/ExonI.pm +cp lib/Bio/SeqFeature/Gene/Promoter.pm blib/lib/Bio/SeqFeature/Gene/Promoter.pm +cp lib/Bio/SeqIO/embl.pm blib/lib/Bio/SeqIO/embl.pm cp lib/Bio/SeqFeature/Lite.pm blib/lib/Bio/SeqFeature/Lite.pm -cp lib/Bio/SeqFeature/Gene/Poly_A_site.pm blib/lib/Bio/SeqFeature/Gene/Poly_A_site.pm +cp lib/Bio/SeqFeature/Gene/TranscriptI.pm blib/lib/Bio/SeqFeature/Gene/TranscriptI.pm +cp lib/Bio/SeqIO/FTHelper.pm blib/lib/Bio/SeqIO/FTHelper.pm +cp lib/Bio/SeqIO/bsml.pm blib/lib/Bio/SeqIO/bsml.pm +cp lib/Bio/SeqIO/MultiFile.pm blib/lib/Bio/SeqIO/MultiFile.pm +cp lib/Bio/SeqIO/fastq.pm blib/lib/Bio/SeqIO/fastq.pm +cp lib/Bio/SeqFeature/Primer.pm blib/lib/Bio/SeqFeature/Primer.pm cp lib/Bio/SeqFeature/Gene/GeneStructureI.pm blib/lib/Bio/SeqFeature/Gene/GeneStructureI.pm +cp lib/Bio/SeqFeature/PositionProxy.pm blib/lib/Bio/SeqFeature/PositionProxy.pm +cp lib/Bio/SeqI.pm blib/lib/Bio/SeqI.pm +cp lib/Bio/SeqFeature/Generic.pm blib/lib/Bio/SeqFeature/Generic.pm cp lib/Bio/SeqFeatureI.pm blib/lib/Bio/SeqFeatureI.pm +cp lib/Bio/SeqFeature/Gene/NC_Feature.pm blib/lib/Bio/SeqFeature/Gene/NC_Feature.pm +cp lib/Bio/SeqFeature/SimilarityPair.pm blib/lib/Bio/SeqFeature/SimilarityPair.pm +cp lib/Bio/SeqFeature/Similarity.pm blib/lib/Bio/SeqFeature/Similarity.pm +cp lib/Bio/SeqFeature/SubSeq.pm blib/lib/Bio/SeqFeature/SubSeq.pm cp lib/Bio/SeqIO/fasta.pm blib/lib/Bio/SeqIO/fasta.pm -cp lib/Bio/SeqFeature/Gene/Promoter.pm blib/lib/Bio/SeqFeature/Gene/Promoter.pm -cp lib/Bio/SeqFeature/Tools/IDHandler.pm blib/lib/Bio/SeqFeature/Tools/IDHandler.pm -cp lib/Bio/SeqIO/ace.pm blib/lib/Bio/SeqIO/ace.pm +cp lib/Bio/SeqFeature/TypedSeqFeatureI.pm blib/lib/Bio/SeqFeature/TypedSeqFeatureI.pm +cp lib/Bio/SeqIO/embldriver.pm blib/lib/Bio/SeqIO/embldriver.pm cp lib/Bio/SeqFeature/Gene/Intron.pm blib/lib/Bio/SeqFeature/Gene/Intron.pm -cp lib/Bio/SeqFeature/Gene/UTR.pm blib/lib/Bio/SeqFeature/Gene/UTR.pm -cp lib/Bio/SeqIO/MultiFile.pm blib/lib/Bio/SeqIO/MultiFile.pm +cp lib/Bio/SeqIO/asciitree.pm blib/lib/Bio/SeqIO/asciitree.pm +cp lib/Bio/SeqFeature/Tools/Unflattener.pm blib/lib/Bio/SeqFeature/Tools/Unflattener.pm +cp lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm blib/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm +cp lib/Bio/SeqIO/ace.pm blib/lib/Bio/SeqIO/ace.pm cp lib/Bio/SeqFeature/Gene/GeneStructure.pm blib/lib/Bio/SeqFeature/Gene/GeneStructure.pm -cp lib/Bio/SeqI.pm blib/lib/Bio/SeqI.pm -cp lib/Bio/SeqFeature/Gene/NC_Feature.pm blib/lib/Bio/SeqFeature/Gene/NC_Feature.pm -cp lib/Bio/SeqIO/embldriver.pm blib/lib/Bio/SeqIO/embldriver.pm -cp lib/Bio/SeqFeature/Gene/ExonI.pm blib/lib/Bio/SeqFeature/Gene/ExonI.pm -cp lib/Bio/SeqFeature/Gene/Transcript.pm blib/lib/Bio/SeqFeature/Gene/Transcript.pm +cp lib/Bio/SeqFeature/Tools/IDHandler.pm blib/lib/Bio/SeqFeature/Tools/IDHandler.pm +cp lib/Bio/SeqFeature/Gene/UTR.pm blib/lib/Bio/SeqFeature/Gene/UTR.pm +cp lib/Bio/SeqFeature/Gene/Poly_A_site.pm blib/lib/Bio/SeqFeature/Gene/Poly_A_site.pm cp lib/Bio/SeqIO/raw.pm blib/lib/Bio/SeqIO/raw.pm +cp lib/Bio/SimpleAnalysisI.pm blib/lib/Bio/SimpleAnalysisI.pm +cp lib/Bio/SeqIO/seqxml.pm blib/lib/Bio/SeqIO/seqxml.pm +cp lib/Bio/SeqIO/game/featHandler.pm blib/lib/Bio/SeqIO/game/featHandler.pm cp lib/Bio/SeqUtils.pm blib/lib/Bio/SeqUtils.pm cp lib/Bio/SeqIO/gbdriver.pm blib/lib/Bio/SeqIO/gbdriver.pm -cp lib/Bio/SeqIO/game/seqHandler.pm blib/lib/Bio/SeqIO/game/seqHandler.pm -cp lib/Bio/SeqIO/game.pm blib/lib/Bio/SeqIO/game.pm -cp lib/Bio/Tools/Blat.pm blib/lib/Bio/Tools/Blat.pm +cp lib/Bio/SeqIO/metafasta.pm blib/lib/Bio/SeqIO/metafasta.pm +cp lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm blib/lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm +cp lib/Bio/SeqIO/game/gameSubs.pm blib/lib/Bio/SeqIO/game/gameSubs.pm cp lib/Bio/SeqIO/table.pm blib/lib/Bio/SeqIO/table.pm -cp lib/Bio/SeqIO/game/featHandler.pm blib/lib/Bio/SeqIO/game/featHandler.pm +cp lib/Bio/SeqIO/msout.pm blib/lib/Bio/SeqIO/msout.pm +cp lib/Bio/SeqIO/game.pm blib/lib/Bio/SeqIO/game.pm +cp lib/Bio/Tools/AmpliconSearch.pm blib/lib/Bio/Tools/AmpliconSearch.pm +cp lib/Bio/SeqIO/kegg.pm blib/lib/Bio/SeqIO/kegg.pm +cp lib/Bio/SeqIO/tigrxml.pm blib/lib/Bio/SeqIO/tigrxml.pm +cp lib/Bio/SimpleAlign.pm blib/lib/Bio/SimpleAlign.pm +cp lib/Bio/SeqIO/tigr.pm blib/lib/Bio/SeqIO/tigr.pm cp lib/Bio/Tools/AnalysisResult.pm blib/lib/Bio/Tools/AnalysisResult.pm -cp lib/Bio/SeqIO/swiss.pm blib/lib/Bio/SeqIO/swiss.pm -cp lib/Bio/Tools/Alignment/Trim.pm blib/lib/Bio/Tools/Alignment/Trim.pm -cp lib/Bio/SeqIO/game/gameWriter.pm blib/lib/Bio/SeqIO/game/gameWriter.pm -cp lib/Bio/SeqIO/game/gameSubs.pm blib/lib/Bio/SeqIO/game/gameSubs.pm -cp lib/Bio/SimpleAnalysisI.pm blib/lib/Bio/SimpleAnalysisI.pm +cp lib/Bio/SeqIO/phd.pm blib/lib/Bio/SeqIO/phd.pm cp lib/Bio/SeqIO/mbsout.pm blib/lib/Bio/SeqIO/mbsout.pm +cp lib/Bio/Tools/Alignment/Trim.pm blib/lib/Bio/Tools/Alignment/Trim.pm +cp lib/Bio/Tools/Blat.pm blib/lib/Bio/Tools/Blat.pm +cp lib/Bio/SeqIO/game/gameHandler.pm blib/lib/Bio/SeqIO/game/gameHandler.pm +cp lib/Bio/SeqIO/swiss.pm blib/lib/Bio/SeqIO/swiss.pm +cp lib/Bio/SeqIO/scf.pm blib/lib/Bio/SeqIO/scf.pm cp lib/Bio/Tools/Alignment/Consed.pm blib/lib/Bio/Tools/Alignment/Consed.pm cp lib/Bio/SeqIO/pir.pm blib/lib/Bio/SeqIO/pir.pm -cp lib/Bio/SeqIO/locuslink.pm blib/lib/Bio/SeqIO/locuslink.pm -cp lib/Bio/SeqIO/tinyseq.pm blib/lib/Bio/SeqIO/tinyseq.pm -cp lib/Bio/SeqIO/scf.pm blib/lib/Bio/SeqIO/scf.pm -cp lib/Bio/SeqIO/metafasta.pm blib/lib/Bio/SeqIO/metafasta.pm -cp lib/Bio/SeqIO/genbank.pm blib/lib/Bio/SeqIO/genbank.pm -cp lib/Bio/SimpleAlign.pm blib/lib/Bio/SimpleAlign.pm -cp lib/Bio/SeqIO/tab.pm blib/lib/Bio/SeqIO/tab.pm -cp lib/Bio/Tools/AmpliconSearch.pm blib/lib/Bio/Tools/AmpliconSearch.pm -cp lib/Bio/SeqIO/kegg.pm blib/lib/Bio/SeqIO/kegg.pm -cp lib/Bio/SeqIO/largefasta.pm blib/lib/Bio/SeqIO/largefasta.pm -cp lib/Bio/SeqIO/seqxml.pm blib/lib/Bio/SeqIO/seqxml.pm -cp lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm blib/lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm -cp lib/Bio/SeqIO/tigrxml.pm blib/lib/Bio/SeqIO/tigrxml.pm -cp lib/Bio/SeqIO/qual.pm blib/lib/Bio/SeqIO/qual.pm +cp lib/Bio/SeqIO/game/gameWriter.pm blib/lib/Bio/SeqIO/game/gameWriter.pm cp lib/Bio/SeqIO/gcg.pm blib/lib/Bio/SeqIO/gcg.pm -cp lib/Bio/SeqIO/msout.pm blib/lib/Bio/SeqIO/msout.pm -cp lib/Bio/SeqIO/game/gameHandler.pm blib/lib/Bio/SeqIO/game/gameHandler.pm -cp lib/Bio/SeqIO/tigr.pm blib/lib/Bio/SeqIO/tigr.pm +cp lib/Bio/SeqIO/qual.pm blib/lib/Bio/SeqIO/qual.pm cp lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm blib/lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm -cp lib/Bio/Species.pm blib/lib/Bio/Species.pm +cp lib/Bio/SeqIO/tinyseq.pm blib/lib/Bio/SeqIO/tinyseq.pm +cp lib/Bio/Taxon.pm blib/lib/Bio/Taxon.pm +cp lib/Bio/SeqIO/game/seqHandler.pm blib/lib/Bio/SeqIO/game/seqHandler.pm cp lib/Bio/SeqIO/swissdriver.pm blib/lib/Bio/SeqIO/swissdriver.pm +cp lib/Bio/Species.pm blib/lib/Bio/Species.pm +cp lib/Bio/SeqIO/locuslink.pm blib/lib/Bio/SeqIO/locuslink.pm +cp lib/Bio/SeqIO/genbank.pm blib/lib/Bio/SeqIO/genbank.pm cp lib/Bio/SeqIO/gbxml.pm blib/lib/Bio/SeqIO/gbxml.pm -cp lib/Bio/Taxon.pm blib/lib/Bio/Taxon.pm -cp lib/Bio/SeqIO/phd.pm blib/lib/Bio/SeqIO/phd.pm -cp lib/Bio/Tools/Phylo/Gerp.pm blib/lib/Bio/Tools/Phylo/Gerp.pm -cp lib/Bio/Tools/Grail.pm blib/lib/Bio/Tools/Grail.pm -cp lib/Bio/Tools/Phylo/Molphy.pm blib/lib/Bio/Tools/Phylo/Molphy.pm -cp lib/Bio/Tools/Primer/Feature.pm blib/lib/Bio/Tools/Primer/Feature.pm -cp lib/Bio/Tools/Primer/Assessor/Base.pm blib/lib/Bio/Tools/Primer/Assessor/Base.pm -cp lib/Bio/Tools/Genomewise.pm blib/lib/Bio/Tools/Genomewise.pm -cp lib/Bio/Tools/Glimmer.pm blib/lib/Bio/Tools/Glimmer.pm -cp lib/Bio/Tools/Genscan.pm blib/lib/Bio/Tools/Genscan.pm -cp lib/Bio/Tools/IUPAC.pm blib/lib/Bio/Tools/IUPAC.pm -cp lib/Bio/Tools/ESTScan.pm blib/lib/Bio/Tools/ESTScan.pm -cp lib/Bio/Tools/Promoterwise.pm blib/lib/Bio/Tools/Promoterwise.pm -cp lib/Bio/Tools/Phylo/Phylip/ProtDist.pm blib/lib/Bio/Tools/Phylo/Phylip/ProtDist.pm +cp lib/Bio/SeqIO/largefasta.pm blib/lib/Bio/SeqIO/largefasta.pm +cp lib/Bio/SeqIO/tab.pm blib/lib/Bio/SeqIO/tab.pm cp lib/Bio/Tools/Lucy.pm blib/lib/Bio/Tools/Lucy.pm -cp lib/Bio/Tools/Est2Genome.pm blib/lib/Bio/Tools/Est2Genome.pm -cp lib/Bio/Tools/Genewise.pm blib/lib/Bio/Tools/Genewise.pm cp lib/Bio/Tools/Primer3.pm blib/lib/Bio/Tools/Primer3.pm -cp lib/Bio/Tools/Fgenesh.pm blib/lib/Bio/Tools/Fgenesh.pm -cp lib/Bio/Tools/Primer/AssessorI.pm blib/lib/Bio/Tools/Primer/AssessorI.pm +cp lib/Bio/Tools/Phylo/Gerp.pm blib/lib/Bio/Tools/Phylo/Gerp.pm +cp lib/Bio/Tools/Coil.pm blib/lib/Bio/Tools/Coil.pm +cp lib/Bio/Tools/EPCR.pm blib/lib/Bio/Tools/EPCR.pm cp lib/Bio/Tools/Profile.pm blib/lib/Bio/Tools/Profile.pm -cp lib/Bio/Tools/Prints.pm blib/lib/Bio/Tools/Prints.pm +cp lib/Bio/Tools/EMBOSS/Palindrome.pm blib/lib/Bio/Tools/EMBOSS/Palindrome.pm cp lib/Bio/Tools/Prediction/Exon.pm blib/lib/Bio/Tools/Prediction/Exon.pm +cp lib/Bio/Tools/OddCodes.pm blib/lib/Bio/Tools/OddCodes.pm +cp lib/Bio/Tools/ECnumber.pm blib/lib/Bio/Tools/ECnumber.pm +cp lib/Bio/Tools/Prints.pm blib/lib/Bio/Tools/Prints.pm +cp lib/Bio/Tools/GFF.pm blib/lib/Bio/Tools/GFF.pm +cp lib/Bio/Tools/PrositeScan.pm blib/lib/Bio/Tools/PrositeScan.pm cp lib/Bio/Tools/CodonTable.pm blib/lib/Bio/Tools/CodonTable.pm -cp lib/Bio/Tools/Primer/Pair.pm blib/lib/Bio/Tools/Primer/Pair.pm -cp lib/Bio/Tools/Phylo/Molphy/Result.pm blib/lib/Bio/Tools/Phylo/Molphy/Result.pm -cp lib/Bio/Tools/MZEF.pm blib/lib/Bio/Tools/MZEF.pm +cp lib/Bio/Tools/Glimmer.pm blib/lib/Bio/Tools/Glimmer.pm +cp lib/Bio/Tools/Phylo/Phylip/ProtDist.pm blib/lib/Bio/Tools/Phylo/Phylip/ProtDist.pm cp lib/Bio/Tools/Match.pm blib/lib/Bio/Tools/Match.pm -cp lib/Bio/Tools/EMBOSS/Palindrome.pm blib/lib/Bio/Tools/EMBOSS/Palindrome.pm -cp lib/Bio/Tools/ECnumber.pm blib/lib/Bio/Tools/ECnumber.pm +cp lib/Bio/Tools/Phylo/Molphy.pm blib/lib/Bio/Tools/Phylo/Molphy.pm +cp lib/Bio/Tools/FootPrinter.pm blib/lib/Bio/Tools/FootPrinter.pm +cp lib/Bio/Tools/ESTScan.pm blib/lib/Bio/Tools/ESTScan.pm +cp lib/Bio/Tools/Genemark.pm blib/lib/Bio/Tools/Genemark.pm +cp lib/Bio/Tools/Fgenesh.pm blib/lib/Bio/Tools/Fgenesh.pm +cp lib/Bio/Tools/IUPAC.pm blib/lib/Bio/Tools/IUPAC.pm +cp lib/Bio/Tools/Grail.pm blib/lib/Bio/Tools/Grail.pm +cp lib/Bio/Tools/Promoterwise.pm blib/lib/Bio/Tools/Promoterwise.pm +cp lib/Bio/Tools/Geneid.pm blib/lib/Bio/Tools/Geneid.pm +cp lib/Bio/Tools/Phylo/Molphy/Result.pm blib/lib/Bio/Tools/Phylo/Molphy/Result.pm +cp lib/Bio/Tools/Primer/Pair.pm blib/lib/Bio/Tools/Primer/Pair.pm +cp lib/Bio/Tools/Genscan.pm blib/lib/Bio/Tools/Genscan.pm cp lib/Bio/Tools/Eponine.pm blib/lib/Bio/Tools/Eponine.pm +cp lib/Bio/Tools/Primer/AssessorI.pm blib/lib/Bio/Tools/Primer/AssessorI.pm cp lib/Bio/Tools/Prediction/Gene.pm blib/lib/Bio/Tools/Prediction/Gene.pm -cp lib/Bio/Tools/EPCR.pm blib/lib/Bio/Tools/EPCR.pm -cp lib/Bio/Tools/OddCodes.pm blib/lib/Bio/Tools/OddCodes.pm -cp lib/Bio/Tools/Coil.pm blib/lib/Bio/Tools/Coil.pm -cp lib/Bio/Tools/PrositeScan.pm blib/lib/Bio/Tools/PrositeScan.pm +cp lib/Bio/Tools/MZEF.pm blib/lib/Bio/Tools/MZEF.pm cp lib/Bio/Tools/Pseudowise.pm blib/lib/Bio/Tools/Pseudowise.pm +cp lib/Bio/Tools/Primer/Feature.pm blib/lib/Bio/Tools/Primer/Feature.pm +cp lib/Bio/Tools/Genewise.pm blib/lib/Bio/Tools/Genewise.pm cp lib/Bio/Tools/GuessSeqFormat.pm blib/lib/Bio/Tools/GuessSeqFormat.pm -cp lib/Bio/Tools/Genemark.pm blib/lib/Bio/Tools/Genemark.pm -cp lib/Bio/Tools/FootPrinter.pm blib/lib/Bio/Tools/FootPrinter.pm -cp lib/Bio/Tools/Geneid.pm blib/lib/Bio/Tools/Geneid.pm -cp lib/Bio/Tools/GFF.pm blib/lib/Bio/Tools/GFF.pm -cp lib/Bio/Tools/Sim4/Exon.pm blib/lib/Bio/Tools/Sim4/Exon.pm -cp lib/Bio/Tools/TandemRepeatsFinder.pm blib/lib/Bio/Tools/TandemRepeatsFinder.pm +cp lib/Bio/Tools/Genomewise.pm blib/lib/Bio/Tools/Genomewise.pm +cp lib/Bio/Tools/Est2Genome.pm blib/lib/Bio/Tools/Est2Genome.pm +cp lib/Bio/Tools/Primer/Assessor/Base.pm blib/lib/Bio/Tools/Primer/Assessor/Base.pm +cp lib/Bio/Tools/SeqPattern/Backtranslate.pm blib/lib/Bio/Tools/SeqPattern/Backtranslate.pm +cp lib/Bio/Tree/DistanceFactory.pm blib/lib/Bio/Tree/DistanceFactory.pm +cp lib/Bio/Tree/Node.pm blib/lib/Bio/Tree/Node.pm +cp lib/Bio/Tools/Run/Phylo/PhyloBase.pm blib/lib/Bio/Tools/Run/Phylo/PhyloBase.pm +cp lib/Bio/Tools/Spidey/Exon.pm blib/lib/Bio/Tools/Spidey/Exon.pm +cp lib/Bio/Tools/Tmhmm.pm blib/lib/Bio/Tools/Tmhmm.pm cp lib/Bio/Tree/RandomFactory.pm blib/lib/Bio/Tree/RandomFactory.pm -cp lib/Bio/Tools/isPcr.pm blib/lib/Bio/Tools/isPcr.pm -cp lib/Bio/Tools/Run/GenericParameters.pm blib/lib/Bio/Tools/Run/GenericParameters.pm +cp lib/Bio/Tools/RepeatMasker.pm blib/lib/Bio/Tools/RepeatMasker.pm +cp lib/Bio/Tools/Signalp/ExtendedSignalp.pm blib/lib/Bio/Tools/Signalp/ExtendedSignalp.pm +cp lib/Bio/Tools/TargetP.pm blib/lib/Bio/Tools/TargetP.pm +cp lib/Bio/Tools/Sim4/Exon.pm blib/lib/Bio/Tools/Sim4/Exon.pm cp lib/Bio/Tree/Compatible.pm blib/lib/Bio/Tree/Compatible.pm -cp lib/Bio/Tools/Tmhmm.pm blib/lib/Bio/Tools/Tmhmm.pm -cp lib/Bio/Tools/SeqWords.pm blib/lib/Bio/Tools/SeqWords.pm -cp lib/Bio/Tree/Statistics.pm blib/lib/Bio/Tree/Statistics.pm -cp lib/Bio/Tools/Run/ParametersI.pm blib/lib/Bio/Tools/Run/ParametersI.pm -cp lib/Bio/Tools/SeqPattern.pm blib/lib/Bio/Tools/SeqPattern.pm -cp lib/Bio/Tools/SeqStats.pm blib/lib/Bio/Tools/SeqStats.pm -cp lib/Bio/Tools/Run/Phylo/PhyloBase.pm blib/lib/Bio/Tools/Run/Phylo/PhyloBase.pm +cp lib/Bio/Tools/ipcress.pm blib/lib/Bio/Tools/ipcress.pm +cp lib/Bio/Tools/RandomDistFunctions.pm blib/lib/Bio/Tools/RandomDistFunctions.pm cp lib/Bio/Tools/Run/WrapperBase.pm blib/lib/Bio/Tools/Run/WrapperBase.pm -cp lib/Bio/Tools/Run/AnalysisFactory.pm blib/lib/Bio/Tools/Run/AnalysisFactory.pm -cp lib/Bio/Tools/TargetP.pm blib/lib/Bio/Tools/TargetP.pm -cp lib/Bio/Tree/AnnotatableNode.pm blib/lib/Bio/Tree/AnnotatableNode.pm +cp lib/Bio/Tools/Sigcleave.pm blib/lib/Bio/Tools/Sigcleave.pm +cp lib/Bio/Tree/Statistics.pm blib/lib/Bio/Tree/Statistics.pm cp lib/Bio/Tools/Seg.pm blib/lib/Bio/Tools/Seg.pm +cp lib/Bio/Tools/SeqWords.pm blib/lib/Bio/Tools/SeqWords.pm cp lib/Bio/Tree/NodeI.pm blib/lib/Bio/Tree/NodeI.pm -cp lib/Bio/Tree/Tree.pm blib/lib/Bio/Tree/Tree.pm -cp lib/Bio/Tree/Node.pm blib/lib/Bio/Tree/Node.pm -cp lib/Bio/Tools/Signalp.pm blib/lib/Bio/Tools/Signalp.pm -cp lib/Bio/Tools/Run/WrapperBase/CommandExts.pm blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm -cp lib/Bio/Tools/ipcress.pm blib/lib/Bio/Tools/ipcress.pm +cp lib/Bio/Tools/isPcr.pm blib/lib/Bio/Tools/isPcr.pm +cp lib/Bio/Tools/Spidey/Results.pm blib/lib/Bio/Tools/Spidey/Results.pm +cp lib/Bio/Tools/QRNA.pm blib/lib/Bio/Tools/QRNA.pm +cp lib/Bio/Tools/SeqStats.pm blib/lib/Bio/Tools/SeqStats.pm +cp lib/Bio/Tools/Sim4/Results.pm blib/lib/Bio/Tools/Sim4/Results.pm +cp lib/Bio/Tools/pICalculator.pm blib/lib/Bio/Tools/pICalculator.pm +cp lib/Bio/Tools/SeqPattern.pm blib/lib/Bio/Tools/SeqPattern.pm +cp lib/Bio/Tree/AnnotatableNode.pm blib/lib/Bio/Tree/AnnotatableNode.pm +cp lib/Bio/Tools/TandemRepeatsFinder.pm blib/lib/Bio/Tools/TandemRepeatsFinder.pm cp lib/Bio/Tools/Run/Analysis.pm blib/lib/Bio/Tools/Run/Analysis.pm +cp lib/Bio/Tools/Run/ParametersI.pm blib/lib/Bio/Tools/Run/ParametersI.pm +cp lib/Bio/Tools/Signalp.pm blib/lib/Bio/Tools/Signalp.pm +cp lib/Bio/Tools/Run/AnalysisFactory.pm blib/lib/Bio/Tools/Run/AnalysisFactory.pm +cp lib/Bio/Tools/Run/GenericParameters.pm blib/lib/Bio/Tools/Run/GenericParameters.pm +cp lib/Bio/Tree/Tree.pm blib/lib/Bio/Tree/Tree.pm cp lib/Bio/Tree/NodeNHX.pm blib/lib/Bio/Tree/NodeNHX.pm -cp lib/Bio/Tools/Spidey/Exon.pm blib/lib/Bio/Tools/Spidey/Exon.pm -cp lib/Bio/Tree/DistanceFactory.pm blib/lib/Bio/Tree/DistanceFactory.pm cp lib/Bio/Tools/tRNAscanSE.pm blib/lib/Bio/Tools/tRNAscanSE.pm -cp lib/Bio/Tools/RandomDistFunctions.pm blib/lib/Bio/Tools/RandomDistFunctions.pm -cp lib/Bio/Tools/RepeatMasker.pm blib/lib/Bio/Tools/RepeatMasker.pm -cp lib/Bio/Tools/QRNA.pm blib/lib/Bio/Tools/QRNA.pm -cp lib/Bio/Tools/SeqPattern/Backtranslate.pm blib/lib/Bio/Tools/SeqPattern/Backtranslate.pm -cp lib/Bio/Tools/pICalculator.pm blib/lib/Bio/Tools/pICalculator.pm -cp lib/Bio/Tools/Spidey/Results.pm blib/lib/Bio/Tools/Spidey/Results.pm -cp lib/Bio/Tools/Sim4/Results.pm blib/lib/Bio/Tools/Sim4/Results.pm -cp lib/Bio/Tools/Signalp/ExtendedSignalp.pm blib/lib/Bio/Tools/Signalp/ExtendedSignalp.pm -cp lib/Bio/Tools/Sigcleave.pm blib/lib/Bio/Tools/Sigcleave.pm -cp lib/Bio/WebAgent.pm blib/lib/Bio/WebAgent.pm +cp lib/Bio/Tools/Run/WrapperBase/CommandExts.pm blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm cp lib/Bio/UpdateableSeqI.pm blib/lib/Bio/UpdateableSeqI.pm -cp lib/Bio/TreeIO/nhx.pm blib/lib/Bio/TreeIO/nhx.pm -cp lib/Bio/TreeIO.pm blib/lib/Bio/TreeIO.pm -cp lib/Bio/TreeIO/pag.pm blib/lib/Bio/TreeIO/pag.pm -cp lib/Bio/Tree/TreeFunctionsI.pm blib/lib/Bio/Tree/TreeFunctionsI.pm +cp lib/Bio/TreeIO/TreeEventBuilder.pm blib/lib/Bio/TreeIO/TreeEventBuilder.pm +cp lib/Bio/TreeIO/nexus.pm blib/lib/Bio/TreeIO/nexus.pm +cp lib/Bio/WebAgent.pm blib/lib/Bio/WebAgent.pm cp lib/BioPerl.pm blib/lib/BioPerl.pm -cp lib/Bio/TreeIO/NewickParser.pm blib/lib/Bio/TreeIO/NewickParser.pm -cp lib/Bio/TreeIO/phyloxml.pm blib/lib/Bio/TreeIO/phyloxml.pm +cp lib/Bio/Tree/TreeFunctionsI.pm blib/lib/Bio/Tree/TreeFunctionsI.pm +cp lib/Bio/TreeIO/cluster.pm blib/lib/Bio/TreeIO/cluster.pm +cp lib/Bio/TreeIO.pm blib/lib/Bio/TreeIO.pm cp lib/Bio/TreeIO/lintree.pm blib/lib/Bio/TreeIO/lintree.pm +cp lib/Bio/TreeIO/phyloxml.pm blib/lib/Bio/TreeIO/phyloxml.pm +cp lib/Bio/TreeIO/tabtree.pm blib/lib/Bio/TreeIO/tabtree.pm +cp lib/Bio/TreeIO/nhx.pm blib/lib/Bio/TreeIO/nhx.pm +cp lib/Bio/TreeIO/NewickParser.pm blib/lib/Bio/TreeIO/NewickParser.pm cp lib/Bio/Tree/TreeI.pm blib/lib/Bio/Tree/TreeI.pm +cp lib/Bio/TreeIO/pag.pm blib/lib/Bio/TreeIO/pag.pm cp lib/Bio/TreeIO/newick.pm blib/lib/Bio/TreeIO/newick.pm -cp lib/Bio/TreeIO/cluster.pm blib/lib/Bio/TreeIO/cluster.pm -cp lib/Bio/TreeIO/TreeEventBuilder.pm blib/lib/Bio/TreeIO/TreeEventBuilder.pm -cp lib/Bio/TreeIO/tabtree.pm blib/lib/Bio/TreeIO/tabtree.pm -cp lib/Bio/TreeIO/nexus.pm blib/lib/Bio/TreeIO/nexus.pm cp bin/bp_aacomp blib/script/bp_aacomp -cp bin/bp_bioflat_index blib/script/bp_bioflat_index -cp bin/bp_biogetseq blib/script/bp_biogetseq "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_aacomp +cp bin/bp_bioflat_index blib/script/bp_bioflat_index "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_bioflat_index +cp bin/bp_biogetseq blib/script/bp_biogetseq "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_biogetseq cp bin/bp_dbsplit blib/script/bp_dbsplit -cp bin/bp_extract_feature_seq blib/script/bp_extract_feature_seq -cp bin/bp_fastam9_to_table blib/script/bp_fastam9_to_table "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_dbsplit +cp bin/bp_extract_feature_seq blib/script/bp_extract_feature_seq "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_extract_feature_seq +cp bin/bp_fastam9_to_table blib/script/bp_fastam9_to_table "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_fastam9_to_table cp bin/bp_fetch blib/script/bp_fetch -cp bin/bp_filter_search blib/script/bp_filter_search "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_fetch +cp bin/bp_filter_search blib/script/bp_filter_search "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_filter_search cp bin/bp_find-blast-matches blib/script/bp_find-blast-matches -cp bin/bp_gccalc blib/script/bp_gccalc -cp bin/bp_genbank2gff3 blib/script/bp_genbank2gff3 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_find-blast-matches -cp bin/bp_index blib/script/bp_index +cp bin/bp_gccalc blib/script/bp_gccalc "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_gccalc +cp bin/bp_genbank2gff3 blib/script/bp_genbank2gff3 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_genbank2gff3 +cp bin/bp_index blib/script/bp_index "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_index cp bin/bp_local_taxonomydb_query blib/script/bp_local_taxonomydb_query -cp bin/bp_make_mrna_protein blib/script/bp_make_mrna_protein -cp bin/bp_mask_by_search blib/script/bp_mask_by_search "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_local_taxonomydb_query +cp bin/bp_make_mrna_protein blib/script/bp_make_mrna_protein "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_make_mrna_protein +cp bin/bp_mask_by_search blib/script/bp_mask_by_search "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mask_by_search cp bin/bp_mrtrans blib/script/bp_mrtrans "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mrtrans @@ -2080,8 +2123,8 @@ cp bin/bp_nrdb blib/script/bp_nrdb "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_nrdb cp bin/bp_oligo_count blib/script/bp_oligo_count -cp bin/bp_process_gadfly blib/script/bp_process_gadfly "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_oligo_count +cp bin/bp_process_gadfly blib/script/bp_process_gadfly "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_process_gadfly cp bin/bp_process_sgd blib/script/bp_process_sgd "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_process_sgd @@ -2096,22 +2139,22 @@ cp bin/bp_search2tribe blib/script/bp_search2tribe "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2tribe cp bin/bp_seq_length blib/script/bp_seq_length -cp bin/bp_seqconvert blib/script/bp_seqconvert "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seq_length +cp bin/bp_seqconvert blib/script/bp_seqconvert "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqconvert cp bin/bp_seqcut blib/script/bp_seqcut "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqcut cp bin/bp_seqpart blib/script/bp_seqpart "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqpart cp bin/bp_seqret blib/script/bp_seqret -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqret cp bin/bp_seqretsplit blib/script/bp_seqretsplit -cp bin/bp_split_seq blib/script/bp_split_seq +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqret "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqretsplit +cp bin/bp_split_seq blib/script/bp_split_seq "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_split_seq cp bin/bp_sreformat blib/script/bp_sreformat -cp bin/bp_taxid4species blib/script/bp_taxid4species "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_sreformat +cp bin/bp_taxid4species blib/script/bp_taxid4species "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_taxid4species cp bin/bp_taxonomy2tree blib/script/bp_taxonomy2tree "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_taxonomy2tree @@ -2139,7 +2182,7 @@ Manifying 15 pod documents make[1]: Leaving directory '/build/bioperl-1.7.8' dh_auto_test - make -j8 test TEST_VERBOSE=1 + make -j15 test TEST_VERBOSE=1 make[1]: Entering directory '/build/bioperl-1.7.8' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t t/Align/*.t t/AlignIO/*.t t/Annotation/*.t t/LocalDB/*.t t/LocalDB/Index/*.t t/LocalDB/Taxonomy/*.t t/Matrix/*.t t/Matrix/IO/*.t t/Ontology/*.t t/Ontology/IO/*.t t/RemoteDB/*.t t/Root/*.t t/SearchIO/*.t t/SearchIO/Writer/*.t t/Seq/*.t t/SeqFeature/*.t t/SeqIO/*.t t/SeqTools/*.t t/Tools/*.t t/Tools/Alignment/*.t t/Tools/EMBOSS/*.t t/Tools/Phylo/*.t t/Tools/Phylo/Phylip/*.t t/Tools/Signalp/*.t t/Tools/Spidey/*.t t/Tree/*.t t/Tree/TreeIO/*.t t/00-compile.t ...................... @@ -3000,31 +3043,31 @@ 1..27 ok 1 - use Bio::AlignIO; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::AnnotatableI' -ok 3 - input filehandle method test : pfam -ok 4 - input filehandle method test : selex -ok 5 - input filehandle method test : arp -ok 6 - input filehandle method test : msf -ok 7 - input filehandle method test : po -ok 8 - input filehandle method test : nexus -ok 9 - input filehandle method test : mase -ok 10 - input filehandle method test : phylip -ok 11 - input filehandle method test : fasta -ok 12 - input filehandle method test : prodom -ok 13 - input filehandle method test : metafasta -ok 14 - input filehandle method test : psi -ok 15 - input filehandle method test : clustalw -ok 16 - input filehandle method test : xmfa -ok 17 - filehandle output test : pfam -ok 18 - filehandle output test : selex -ok 19 - filehandle output test : msf +ok 3 - input filehandle method test : prodom +ok 4 - input filehandle method test : mase +ok 5 - input filehandle method test : phylip +ok 6 - input filehandle method test : arp +ok 7 - input filehandle method test : clustalw +ok 8 - input filehandle method test : psi +ok 9 - input filehandle method test : po +ok 10 - input filehandle method test : fasta +ok 11 - input filehandle method test : xmfa +ok 12 - input filehandle method test : metafasta +ok 13 - input filehandle method test : nexus +ok 14 - input filehandle method test : selex +ok 15 - input filehandle method test : msf +ok 16 - input filehandle method test : pfam +ok 17 - filehandle output test : phylip +ok 18 - filehandle output test : clustalw +ok 19 - filehandle output test : psi ok 20 - filehandle output test : po -ok 21 - filehandle output test : nexus -ok 22 - filehandle output test : phylip -ok 23 - filehandle output test : fasta -ok 24 - filehandle output test : metafasta -ok 25 - filehandle output test : psi -ok 26 - filehandle output test : clustalw -ok 27 - filehandle output test : xmfa +ok 21 - filehandle output test : fasta +ok 22 - filehandle output test : xmfa +ok 23 - filehandle output test : metafasta +ok 24 - filehandle output test : nexus +ok 25 - filehandle output test : selex +ok 26 - filehandle output test : msf +ok 27 - filehandle output test : pfam ok t/AlignIO/arp.t ..................... 1..48 @@ -4442,25 +4485,25 @@ ok 17 - to_string looks reasonable ok 18 - There are 8 root InterPro terms ok 19 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 20 - term Conserved Site in ontology InterPro +ok 20 - term Kringle in ontology InterPro ok 21 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 22 - term Cdc20/Fizzy in ontology InterPro +ok 22 - term Helix-turn-helix, AraC type in ontology InterPro ok 23 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 24 - term Helix-turn-helix, AraC type in ontology InterPro +ok 24 - term Conserved Site in ontology InterPro ok 25 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 26 - term Repeat in ontology InterPro +ok 26 - term Integrins alpha chain in ontology InterPro ok 27 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 28 - term Active Site in ontology InterPro +ok 28 - term Repeat in ontology InterPro ok 29 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 30 - term Region in ontology InterPro +ok 30 - term Binding Site in ontology InterPro ok 31 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 32 - term post-translational modification in ontology InterPro ok 33 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 34 - term Integrins alpha chain in ontology InterPro +ok 34 - term Region in ontology InterPro ok 35 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 36 - term Kringle in ontology InterPro +ok 36 - term Active Site in ontology InterPro ok 37 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 38 - term Binding Site in ontology InterPro +ok 38 - term Cdc20/Fizzy in ontology InterPro ok 39 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 40 - term Active Site in ontology InterPro ok 41 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' @@ -4483,14 +4526,14 @@ ok 58 ok 59 ok 60 -ok 61 - Cdc20/Fizzy term has one parent -ok 62 - Cdc20/Fizzy term has one ancestor +ok 61 - Kringle term has one parent +ok 62 - Kringle term has one ancestor ok 63 - Helix-turn-helix, AraC type term has one parent ok 64 - Helix-turn-helix, AraC type term has one ancestor ok 65 - Integrins alpha chain term has one parent ok 66 - Integrins alpha chain term has one ancestor -ok 67 - Kringle term has one parent -ok 68 - Kringle term has one ancestor +ok 67 - Cdc20/Fizzy term has one parent +ok 68 - Cdc20/Fizzy term has one ancestor ok 69 - secondary accession map has 2 keys ok t/Ontology/IO/obo.t ................. @@ -5061,12 +5104,17 @@ ok 106 ok 107 ok 108 -ok 109 # TODO Sporadic test failures when running using PerlIO::eol on Linux w/Windows line endings: # +not ok 109 # TODO Sporadic test failures when running using PerlIO::eol on Linux w/Windows line endings: # +# Failed (TODO) test at t/Root/IO.t line 289. +# got: 'DEFINITIN Desmognathus quadrammaculatu 12S ribosomal NNA gene, partial +# ' +# expected: 'DEFINITION Desmognathus quadramaculatus 12S ribosomal RNA gene, partial +# ' ok 110 ok 111 not ok 112 # TODO Sporadic test failures when running using PerlIO::eol on Linux w/Windows line endings: # # Failed (TODO) test at t/Root/IO.t line 298. -# got: ' seququence; tRNA-Val gene, complete sequence; and 16S ribosomal RNA +# got: ' suence; tRNA-Val g gene, comple sequence; and6S6S riribosomal RNA # ' # expected: ' sequence; tRNA-Val gene, complete sequence; and 16S ribosomal RNA # ' @@ -5074,7 +5122,7 @@ ok 114 not ok 115 # TODO Sporadic test failures when running using PerlIO::eol on Linux w/Windows line endings: # # Failed (TODO) test at t/Root/IO.t line 307. -# got: ' geneene, partial sequence, mitochondrial genes for mitochondrial RNAs. +# got: ' genpartial sequenuence, mitochonal genes for ochochochondrial RNAs. # ' # expected: ' gene, partial sequence, mitochondrial genes for mitochondrial RNAs. # ' @@ -5203,6 +5251,26 @@ ok 34 ok 35 ok + +--------------------- WARNING --------------------- +MSG: find_exe: Multiple paths to 'gzip' found. Using /usr/bin/gzip. +--------------------------------------------------- + +--------------------- WARNING --------------------- +MSG: find_exe: Multiple paths to 'gzip' found. Using /usr/bin/gzip. +--------------------------------------------------- + +--------------------- WARNING --------------------- +MSG: find_exe: Multiple paths to 'gunzip' found. Using /usr/bin/gunzip. +--------------------------------------------------- + +--------------------- WARNING --------------------- +MSG: find_exe: Multiple paths to 'gzip' found. Using /usr/bin/gzip. +--------------------------------------------------- + +--------------------- WARNING --------------------- +MSG: find_exe: Multiple paths to 'gunzip' found. Using /usr/bin/gunzip. +--------------------------------------------------- t/Root/Utilities.t .................. 1..56 ok 1 - use Bio::Root::Utilities; @@ -6376,24 +6444,24 @@ ok 1080 ok 1081 ok 1082 -ok 1083 - blastxml for f.blastxml -ok 1084 - fasta for f.fasta -ok 1085 - blast for f.tblx -ok 1086 - fasta for f.m9 -ok 1087 - fasta for f.psearch -ok 1088 - blast for f.blx -ok 1089 - exonerate for f.exon +ok 1083 - fasta for f.fasta +ok 1084 - fasta for f.fa +ok 1085 - exonerate for f.exonerate +ok 1086 - fasta for f.fx +ok 1087 - blastxml for f.xml +ok 1088 - blast for fast.bls +ok 1089 - fasta for f.osearch ok 1090 - blast for filename.bls -ok 1091 - fasta for f.osearch -ok 1092 - fasta for f.fa -ok 1093 - blast for filename.blast -ok 1094 - blast for fast.bls -ok 1095 - fasta for f.fx -ok 1096 - fasta for f.SSEARCH.m9 -ok 1097 - blastxml for f.xml -ok 1098 - fasta for f.ssearch -ok 1099 - exonerate for f.exonerate -ok 1100 - fasta for f.fy +ok 1091 - fasta for f.SSEARCH.m9 +ok 1092 - blast for filename.blast +ok 1093 - fasta for f.fy +ok 1094 - blast for f.tblx +ok 1095 - blast for f.blx +ok 1096 - fasta for f.psearch +ok 1097 - blastxml for f.blastxml +ok 1098 - exonerate for f.exon +ok 1099 - fasta for f.m9 +ok 1100 - fasta for f.ssearch ok 1101 ok 1102 ok 1103 @@ -8342,24 +8410,24 @@ t/SearchIO/SearchIO.t ............... 1..19 ok 1 - use Bio::SearchIO; -ok 2 - fasta for f.m9 -ok 3 - blast for f.blx -ok 4 - blastxml for f.xml -ok 5 - fasta for f.osearch -ok 6 - fasta for f.fx -ok 7 - blastxml for f.blastxml -ok 8 - fasta for f.fa -ok 9 - exonerate for f.exon -ok 10 - exonerate for f.exonerate +ok 2 - fasta for f.osearch +ok 3 - blast for filename.bls +ok 4 - exonerate for f.exon +ok 5 - fasta for f.ssearch +ok 6 - fasta for f.SSEARCH.m9 +ok 7 - blast for fast.bls +ok 8 - blast for f.tblx +ok 9 - blast for f.blx +ok 10 - fasta for f.fx ok 11 - blast for filename.blast -ok 12 - fasta for f.SSEARCH.m9 -ok 13 - fasta for f.ssearch -ok 14 - fasta for f.fy -ok 15 - blast for f.tblx -ok 16 - blast for fast.bls -ok 17 - blast for filename.bls -ok 18 - fasta for f.fasta -ok 19 - fasta for f.psearch +ok 12 - fasta for f.psearch +ok 13 - blastxml for f.xml +ok 14 - fasta for f.m9 +ok 15 - fasta for f.fasta +ok 16 - fasta for f.fy +ok 17 - blastxml for f.blastxml +ok 18 - exonerate for f.exonerate +ok 19 - fasta for f.fa ok t/SearchIO/sim4.t ................... 1..102 @@ -9395,14 +9463,14 @@ ok 910 - h cn: exact (0.92885) <= max (0.92885) ok 911 - bl2seq.blastx.out ok 912 - tile bl2seq.blastx.out hit 1 \#hsps 6 -ok 913 - q id: exact (0.70536) ~ est (0.70495) -ok 914 - q id: exact (0.70536) <= max (0.94286) -ok 915 - q cn: exact (0.78810) ~ est (0.78803) -ok 916 - q cn: exact (0.78810) <= max (0.96429) -ok 917 - q id: est (0.35714) = fast (0.35714) -ok 918 - q cn: est (0.57143) = fast (0.57143) -ok 919 - q id: est (0.71429) = fast (0.71429) -ok 920 - q cn: est (1.00000) = fast (1.00000) +ok 913 - q id: est (0.71429) = fast (0.71429) +ok 914 - q cn: est (1.00000) = fast (1.00000) +ok 915 - q id: est (0.35714) = fast (0.35714) +ok 916 - q cn: est (0.57143) = fast (0.57143) +ok 917 - q id: exact (0.70536) ~ est (0.70495) +ok 918 - q id: exact (0.70536) <= max (0.94286) +ok 919 - q cn: exact (0.78810) ~ est (0.78803) +ok 920 - q cn: exact (0.78810) <= max (0.96429) ok 921 - h id: exact (0.61923) ~ est (0.61955) ok 922 - h id: exact (0.61923) <= max (0.64231) ok 923 - h cn: exact (0.73077) ~ est (0.73077) @@ -9428,10 +9496,10 @@ ok 943 - q id: exact (0.68750) <= max (0.68750) ok 944 - q cn: exact (0.81250) ~ est (0.81250) ok 945 - q cn: exact (0.81250) <= max (0.81250) -ok 946 - h id: est (0.71429) = fast (0.71429) -ok 947 - h cn: est (0.85714) = fast (0.85714) -ok 948 - h id: est (0.66667) = fast (0.66667) -ok 949 - h cn: est (0.77778) = fast (0.77778) +ok 946 - h id: est (0.66667) = fast (0.66667) +ok 947 - h cn: est (0.77778) = fast (0.77778) +ok 948 - h id: est (0.71429) = fast (0.71429) +ok 949 - h cn: est (0.85714) = fast (0.85714) ok 950 - dnaEbsub_ecoli.wutblastn ok 951 - tile dnaEbsub_ecoli.wutblastn hit 1 \#hsps 1 ok 952 - q id: est (0.36386) = fast (0.36386) @@ -9545,37 +9613,37 @@ ok 1060 - h cn: est (0.60000) = fast (0.60000) ok 1061 - dnaEbsub_ecoli.wutblastx ok 1062 - tile dnaEbsub_ecoli.wutblastx hit 1 \#hsps 12 -ok 1063 - q id: est (0.37500) = fast (0.37500) -ok 1064 - q cn: est (0.62500) = fast (0.62500) +ok 1063 - q id: est (0.25352) = fast (0.25352) +ok 1064 - q cn: est (0.47887) = fast (0.47887) ok 1065 - q id: exact (0.40224) ~ est (0.40912) ok 1066 - q id: exact (0.40224) <= max (0.42628) ok 1067 - q cn: exact (0.58494) ~ est (0.58968) ok 1068 - q cn: exact (0.58494) <= max (0.62179) -ok 1069 - q id: est (0.25352) = fast (0.25352) -ok 1070 - q cn: est (0.47887) = fast (0.47887) +ok 1069 - q id: est (0.37500) = fast (0.37500) +ok 1070 - q cn: est (0.62500) = fast (0.62500) ok 1071 - q id: exact (0.44118) ~ est (0.44118) ok 1072 - q id: exact (0.44118) <= max (0.44118) ok 1073 - q cn: exact (0.54412) ~ est (0.54412) ok 1074 - q cn: exact (0.54412) <= max (0.54412) -ok 1075 - h id: exact (0.39848) ~ est (0.40304) -ok 1076 - h id: exact (0.39848) <= max (0.40355) -ok 1077 - h cn: exact (0.58376) ~ est (0.58889) -ok 1078 - h cn: exact (0.58376) <= max (0.58883) -ok 1079 - h id: exact (0.44118) ~ est (0.44118) -ok 1080 - h id: exact (0.44118) <= max (0.44118) -ok 1081 - h cn: exact (0.54412) ~ est (0.54412) -ok 1082 - h cn: exact (0.54412) <= max (0.54412) -ok 1083 - h id: est (0.25352) = fast (0.25352) -ok 1084 - h cn: est (0.47887) = fast (0.47887) +ok 1075 - h id: exact (0.44118) ~ est (0.44118) +ok 1076 - h id: exact (0.44118) <= max (0.44118) +ok 1077 - h cn: exact (0.54412) ~ est (0.54412) +ok 1078 - h cn: exact (0.54412) <= max (0.54412) +ok 1079 - h id: est (0.25352) = fast (0.25352) +ok 1080 - h cn: est (0.47887) = fast (0.47887) +ok 1081 - h id: exact (0.39848) ~ est (0.40304) +ok 1082 - h id: exact (0.39848) <= max (0.40355) +ok 1083 - h cn: exact (0.58376) ~ est (0.58889) +ok 1084 - h cn: exact (0.58376) <= max (0.58883) ok 1085 - tile dnaEbsub_ecoli.wutblastx hit 2 \#hsps 2 ok 1086 - q id: exact (0.41818) ~ est (0.41818) ok 1087 - q id: exact (0.41818) <= max (0.41818) ok 1088 - q cn: exact (0.52727) ~ est (0.52727) ok 1089 - q cn: exact (0.52727) <= max (0.52727) -ok 1090 - h id: est (0.53333) = fast (0.53333) -ok 1091 - h cn: est (0.66667) = fast (0.66667) -ok 1092 - h id: est (0.37500) = fast (0.37500) -ok 1093 - h cn: est (0.47500) = fast (0.47500) +ok 1090 - h id: est (0.37500) = fast (0.37500) +ok 1091 - h cn: est (0.47500) = fast (0.47500) +ok 1092 - h id: est (0.53333) = fast (0.53333) +ok 1093 - h cn: est (0.66667) = fast (0.66667) ok 1094 - bug2942: query m0: range correct ok 1095 - bug2942: query m1: range correct ok 1096 - bug2942: query m2: range correct @@ -10007,7 +10075,7 @@ ok 19 not ok 20 # TODO Need to fix columns before start of seq w/ start > 1 # Failed (TODO) test at t/Seq/LocatableSeq.t line 46. -# got: 'Bio::Location::Simple=HASH(0x1aac9ac)' +# got: 'Bio::Location::Simple=HASH(0x572efbbc)' # expected: undef ok 21 ok 22 - An object of class 'Bio::AlignIO::pfam' isa 'Bio::AlignIO' @@ -11692,7 +11760,7 @@ 1..325 ok 1 - use Bio::Factory::FTLocationFactory; ok 2 - An object of class 'Bio::Factory::FTLocationFactory' isa 'Bio::Factory::LocationFactoryI' -ok 3 - Bio::Location::Simple +ok 3 - Bio::Location::Split ok 4 ok 5 ok 6 @@ -11701,7 +11769,7 @@ ok 9 ok 10 ok 11 -ok 12 - Location String: J00194:100..202 +ok 12 - Location String: complement(join(94468..94578,94578..>94889)) ok 13 ok 14 - Bio::Location::Fuzzy ok 15 @@ -11712,7 +11780,7 @@ ok 20 ok 21 ok 22 -ok 23 - Location String: ?..536 +ok 23 - Location String: 22..?64 ok 24 ok 25 - Bio::Location::Fuzzy ok 26 @@ -11725,7 +11793,7 @@ ok 33 ok 34 - Location String: (122.133)..(204.221) ok 35 -ok 36 - Bio::Location::Split +ok 36 - Bio::Location::Fuzzy ok 37 ok 38 ok 39 @@ -11734,9 +11802,9 @@ ok 42 ok 43 ok 44 -ok 45 - Location String: join(12..78,134..202) +ok 45 - Location String: ?2465..2774 ok 46 -ok 47 - Bio::Location::Simple +ok 47 - Bio::Location::Fuzzy ok 48 ok 49 ok 50 @@ -11745,7 +11813,7 @@ ok 53 ok 54 ok 55 -ok 56 - Location String: 340..565 +ok 56 - Location String: ?..536 ok 57 ok 58 - Bio::Location::Fuzzy ok 59 @@ -11767,9 +11835,9 @@ ok 75 ok 76 ok 77 -ok 78 - Location String: (23.45)..600 +ok 78 - Location String: 1..>888 ok 79 -ok 80 - Bio::Location::Split +ok 80 - Bio::Location::Fuzzy ok 81 ok 82 ok 83 @@ -11778,7 +11846,7 @@ ok 86 ok 87 ok 88 -ok 89 - Location String: join(1..100,J00194.1:100..202) +ok 89 - Location String: (23.45)..600 ok 90 ok 91 - Bio::Location::Fuzzy ok 92 @@ -11789,9 +11857,9 @@ ok 97 ok 98 ok 99 -ok 100 - Location String: (122.133)..(204.221) +ok 100 - Location String: <1..? ok 101 -ok 102 - Bio::Location::Simple +ok 102 - Bio::Location::Fuzzy ok 103 ok 104 ok 105 @@ -11800,7 +11868,7 @@ ok 108 ok 109 ok 110 -ok 111 - Location String: 467 +ok 111 - Location String: ?..? ok 112 ok 113 - Bio::Location::Fuzzy ok 114 @@ -11811,9 +11879,9 @@ ok 119 ok 120 ok 121 -ok 122 - Location String: ?1..12 +ok 122 - Location String: 145^177 ok 123 -ok 124 - Bio::Location::Split +ok 124 - Bio::Location::Fuzzy ok 125 ok 126 ok 127 @@ -11822,7 +11890,7 @@ ok 130 ok 131 ok 132 -ok 133 - Location String: complement(join(2691..4571,4918..5163)) +ok 133 - Location String: complement(34..(122.126)) ok 134 ok 135 - Bio::Location::Fuzzy ok 136 @@ -11833,7 +11901,7 @@ ok 141 ok 142 ok 143 -ok 144 - Location String: 145^177 +ok 144 - Location String: <1..888 ok 145 ok 146 - Bio::Location::Fuzzy ok 147 @@ -11844,9 +11912,9 @@ ok 152 ok 153 ok 154 -ok 155 - Location String: ?..? +ok 155 - Location String: ?1..12 ok 156 -ok 157 - Bio::Location::Fuzzy +ok 157 - Bio::Location::Simple ok 158 ok 159 ok 160 @@ -11855,9 +11923,9 @@ ok 163 ok 164 ok 165 -ok 166 - Location String: <1..? +ok 166 - Location String: 467 ok 167 -ok 168 - Bio::Location::Split +ok 168 - Bio::Location::Fuzzy ok 169 ok 170 ok 171 @@ -11866,9 +11934,9 @@ ok 174 ok 175 ok 176 -ok 177 - Location String: join(AY016290.1:108..185,AY016291.1:1546..1599) +ok 177 - Location String: 1..? ok 178 -ok 179 - Bio::Location::Simple +ok 179 - Bio::Location::Split ok 180 ok 181 ok 182 @@ -11877,9 +11945,9 @@ ok 185 ok 186 ok 187 -ok 188 - Location String: 123^124 +ok 188 - Location String: join(12..78,134..202) ok 189 -ok 190 - Bio::Location::Fuzzy +ok 190 - Bio::Location::Split ok 191 ok 192 ok 193 @@ -11888,7 +11956,7 @@ ok 196 ok 197 ok 198 -ok 199 - Location String: (102.110) +ok 199 - Location String: complement(join(2691..4571,4918..5163)) ok 200 ok 201 - Bio::Location::Fuzzy ok 202 @@ -11899,9 +11967,9 @@ ok 207 ok 208 ok 209 -ok 210 - Location String: ?2465..2774 +ok 210 - Location String: ?22..?64 ok 211 -ok 212 - Bio::Location::Fuzzy +ok 212 - Bio::Location::Simple ok 213 ok 214 ok 215 @@ -11910,9 +11978,9 @@ ok 218 ok 219 ok 220 -ok 221 - Location String: 1..? +ok 221 - Location String: 123^124 ok 222 -ok 223 - Bio::Location::Split +ok 223 - Bio::Location::Fuzzy ok 224 ok 225 ok 226 @@ -11921,9 +11989,9 @@ ok 229 ok 230 ok 231 -ok 232 - Location String: complement(join(94468..94578,94578..>94889)) +ok 232 - Location String: (122.133)..(204.221) ok 233 -ok 234 - Bio::Location::Fuzzy +ok 234 - Bio::Location::Simple ok 235 ok 236 ok 237 @@ -11932,9 +12000,9 @@ ok 240 ok 241 ok 242 -ok 243 - Location String: <1..888 +ok 243 - Location String: J00194:100..202 ok 244 -ok 245 - Bio::Location::Fuzzy +ok 245 - Bio::Location::Split ok 246 ok 247 ok 248 @@ -11943,9 +12011,9 @@ ok 251 ok 252 ok 253 -ok 254 - Location String: 22..?64 +ok 254 - Location String: join(1..100,J00194.1:100..202) ok 255 -ok 256 - Bio::Location::Simple +ok 256 - Bio::Location::Fuzzy ok 257 ok 258 ok 259 @@ -11954,9 +12022,9 @@ ok 262 ok 263 ok 264 -ok 265 - Location String: J00194:100..202 +ok 265 - Location String: <345..500 ok 266 -ok 267 - Bio::Location::Fuzzy +ok 267 - Bio::Location::Split ok 268 ok 269 ok 270 @@ -11965,7 +12033,7 @@ ok 273 ok 274 ok 275 -ok 276 - Location String: complement(34..(122.126)) +ok 276 - Location String: join(AY016290.1:108..185,AY016291.1:1546..1599) ok 277 ok 278 - Bio::Location::Fuzzy ok 279 @@ -11976,9 +12044,9 @@ ok 284 ok 285 ok 286 -ok 287 - Location String: <345..500 +ok 287 - Location String: (102.110) ok 288 -ok 289 - Bio::Location::Fuzzy +ok 289 - Bio::Location::Simple ok 290 ok 291 ok 292 @@ -11987,9 +12055,9 @@ ok 295 ok 296 ok 297 -ok 298 - Location String: 1..>888 +ok 298 - Location String: J00194:100..202 ok 299 -ok 300 - Bio::Location::Fuzzy +ok 300 - Bio::Location::Simple ok 301 ok 302 ok 303 @@ -11998,7 +12066,7 @@ ok 306 ok 307 ok 308 -ok 309 - Location String: ?22..?64 +ok 309 - Location String: 340..565 ok 310 ok 311 - complement(join(2691..4571,4918..5163)) ok 312 - join(complement(4918..5163),complement(2691..4571)) @@ -12637,7 +12705,7 @@ not ok 9 - primary_id # TODO possible bug: RichSeq not setting primary_id? # Failed (TODO) test 'primary_id' # at t/SeqIO/gcg.t line 53. -# got: 'Bio::PrimarySeq=HASH(0x133ebfc)' +# got: 'Bio::PrimarySeq=HASH(0x57bb3a48)' # expected: 'roa1_drome' ok 10 - description ok 11 @@ -13594,20 +13662,20 @@ ok 2 - Bio::SeqIO::mbsout is at least api version 1.1.3 ok 3 - An object of class 'Bio::SeqIO::mbsout' isa 'Bio::SeqIO::mbsout' ok 4 - An object of class 'Bio::SeqIO::mbsout' isa 'Bio::SeqIO::mbsout' -ok 5 - Get TOT_RUN_HAPS -ok 6 - Get SEGSITES -ok 7 - Get POP_MUT_PARAM_PER_SITE -ok 8 - Get SELPOS -ok 9 - Get LAST_READ_HAP_NUM -ok 10 - Get NEXT_RUN_NUM -ok 11 - Get POSITIONS +ok 5 - Get POP_RECOMB_PARAM_PER_SITE +ok 6 - Get NFILES +ok 7 - Get MBS_INFO_LINE +ok 8 - Get POP_MUT_PARAM_PER_SITE +ok 9 - Get NSITES +ok 10 - Get SEGSITES +ok 11 - Get CURRENT_RUN_SEGSITES ok 12 - Get TRAJ_FILENAME -ok 13 - Get NREPS -ok 14 - Get MBS_INFO_LINE -ok 15 - Get NSITES -ok 16 - Get POP_RECOMB_PARAM_PER_SITE -ok 17 - Get CURRENT_RUN_SEGSITES -ok 18 - Get NFILES +ok 13 - Get LAST_READ_HAP_NUM +ok 14 - Get POSITIONS +ok 15 - Get TOT_RUN_HAPS +ok 16 - Get NREPS +ok 17 - Get NEXT_RUN_NUM +ok 18 - Get SELPOS ok 19 - Get RUNS ok 20 - Get next_hap at beginning of run ok 21 - Get next_hap after beginning of run @@ -13619,21 +13687,21 @@ ok 27 - Get next_run at beginning of run ok 28 - have all lines been read? ok 29 - An object of class 'Bio::SeqIO::mbsout' isa 'Bio::SeqIO::mbsout' -ok 30 - Get TOT_RUN_HAPS -ok 31 - Get SEGSITES +ok 30 - Get NFILES +ok 31 - Get POP_RECOMB_PARAM_PER_SITE ok 32 - Get POP_MUT_PARAM_PER_SITE -ok 33 - Get SELPOS -ok 34 - Get POSITIONS -ok 35 - Get NEXT_RUN_NUM -ok 36 - Get LAST_READ_HAP_NUM -ok 37 - Get TRAJ_FILENAME -ok 38 - Get MBS_INFO_LINE -ok 39 - Get NREPS -ok 40 - Get NSITES -ok 41 - Get CURRENT_RUN_SEGSITES -ok 42 - Get POP_RECOMB_PARAM_PER_SITE -ok 43 - Get NFILES -ok 44 - Get RUNS +ok 33 - Get NSITES +ok 34 - Get MBS_INFO_LINE +ok 35 - Get LAST_READ_HAP_NUM +ok 36 - Get TOT_RUN_HAPS +ok 37 - Get POSITIONS +ok 38 - Get CURRENT_RUN_SEGSITES +ok 39 - Get TRAJ_FILENAME +ok 40 - Get SEGSITES +ok 41 - Get RUNS +ok 42 - Get SELPOS +ok 43 - Get NREPS +ok 44 - Get NEXT_RUN_NUM ok 45 - Get next_hap at beginning of run ok 46 - Get next_hap after beginning of run ok 47 - Testing mbsout::outgroup @@ -13644,20 +13712,20 @@ ok 52 - Get next_run after hap ok 53 - next run should be 5. ok 54 - An object of class 'Bio::SeqIO::mbsout' isa 'Bio::SeqIO::mbsout' -ok 55 - Get POP_MUT_PARAM_PER_SITE -ok 56 - Get SEGSITES -ok 57 - Get SELPOS -ok 58 - Get TOT_RUN_HAPS +ok 55 - Get NSITES +ok 56 - Get POP_MUT_PARAM_PER_SITE +ok 57 - Get MBS_INFO_LINE +ok 58 - Get NFILES ok 59 - Get POP_RECOMB_PARAM_PER_SITE -ok 60 - Get CURRENT_RUN_SEGSITES -ok 61 - Get NSITES -ok 62 - Get RUNS -ok 63 - Get NFILES -ok 64 - Get LAST_READ_HAP_NUM -ok 65 - Get NEXT_RUN_NUM -ok 66 - Get POSITIONS -ok 67 - Get NREPS -ok 68 - Get MBS_INFO_LINE +ok 60 - Get RUNS +ok 61 - Get NEXT_RUN_NUM +ok 62 - Get NREPS +ok 63 - Get SELPOS +ok 64 - Get POSITIONS +ok 65 - Get TOT_RUN_HAPS +ok 66 - Get LAST_READ_HAP_NUM +ok 67 - Get SEGSITES +ok 68 - Get CURRENT_RUN_SEGSITES ok 69 - Get TRAJ_FILENAME ok 70 - Get next_run at end/beginning of run ok 71 - have all lines been read? @@ -13679,17 +13747,17 @@ ok 1 - use Bio::SeqIO::msout; ok 2 - Bio::SeqIO::msout is at least api version 1.1.5 ok 3 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 4 - Get POSITIONS -ok 5 - Get SEGSITES -ok 6 - Get LAST_READ_HAP_NUM -ok 7 - Get MS_INFO_LINE -ok 8 - Get NEXT_RUN_NUM -ok 9 - Get SEEDS -ok 10 - Get N_SITES -ok 11 - Get POPS -ok 12 - Get RUNS -ok 13 - Get CURRENT_RUN_SEGSITES -ok 14 - Get TOT_RUN_HAPS +ok 4 - Get N_SITES +ok 5 - Get LAST_READ_HAP_NUM +ok 6 - Get NEXT_RUN_NUM +ok 7 - Get POSITIONS +ok 8 - Get SEGSITES +ok 9 - Get CURRENT_RUN_SEGSITES +ok 10 - Get RUNS +ok 11 - Get TOT_RUN_HAPS +ok 12 - Get POPS +ok 13 - Get MS_INFO_LINE +ok 14 - Get SEEDS ok 15 - Get next_hap at beginning of run ok 16 - Get next_hap after beginning of run ok 17 - Testing msout::outgroup @@ -13702,17 +13770,17 @@ ok 24 - Get next_run at beginning of run ok 25 - have all lines been read? ok 26 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 27 - Get TOT_RUN_HAPS -ok 28 - Get CURRENT_RUN_SEGSITES -ok 29 - Get RUNS +ok 27 - Get MS_INFO_LINE +ok 28 - Get SEEDS +ok 29 - Get TOT_RUN_HAPS ok 30 - Get POPS -ok 31 - Get N_SITES -ok 32 - Get SEEDS -ok 33 - Get NEXT_RUN_NUM -ok 34 - Get MS_INFO_LINE -ok 35 - Get LAST_READ_HAP_NUM -ok 36 - Get SEGSITES -ok 37 - Get POSITIONS +ok 31 - Get POSITIONS +ok 32 - Get SEGSITES +ok 33 - Get CURRENT_RUN_SEGSITES +ok 34 - Get RUNS +ok 35 - Get N_SITES +ok 36 - Get LAST_READ_HAP_NUM +ok 37 - Get NEXT_RUN_NUM ok 38 - Get next_hap at beginning of run ok 39 - Get next_hap after beginning of run ok 40 - Testing msout::outgroup @@ -13724,16 +13792,16 @@ ok 46 - next run should be 5. ok 47 - Get last hap through next_hap ok 48 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 49 - Get NEXT_RUN_NUM -ok 50 - Get POPS -ok 51 - Get MS_INFO_LINE -ok 52 - Get LAST_READ_HAP_NUM -ok 53 - Get SEGSITES -ok 54 - Get POSITIONS -ok 55 - Get SEEDS -ok 56 - Get RUNS -ok 57 - Get CURRENT_RUN_SEGSITES -ok 58 - Get TOT_RUN_HAPS +ok 49 - Get POPS +ok 50 - Get TOT_RUN_HAPS +ok 51 - Get SEEDS +ok 52 - Get MS_INFO_LINE +ok 53 - Get NEXT_RUN_NUM +ok 54 - Get LAST_READ_HAP_NUM +ok 55 - Get RUNS +ok 56 - Get CURRENT_RUN_SEGSITES +ok 57 - Get SEGSITES +ok 58 - Get POSITIONS ok 59 - Get next_pop at end of run ok 60 - have all lines been read? ok 61 - Get next_pop at eof @@ -13741,17 +13809,17 @@ ok 63 - Get next_hap at eof ok 64 - Get next_seq at eof ok 65 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 66 - Get SEGSITES -ok 67 - Get POSITIONS -ok 68 - Get NEXT_RUN_NUM +ok 66 - Get POPS +ok 67 - Get TOT_RUN_HAPS +ok 68 - Get SEEDS ok 69 - Get MS_INFO_LINE -ok 70 - Get LAST_READ_HAP_NUM -ok 71 - Get SEEDS +ok 70 - Get NEXT_RUN_NUM +ok 71 - Get LAST_READ_HAP_NUM ok 72 - Get N_SITES -ok 73 - Get POPS -ok 74 - Get TOT_RUN_HAPS -ok 75 - Get CURRENT_RUN_SEGSITES -ok 76 - Get RUNS +ok 73 - Get RUNS +ok 74 - Get CURRENT_RUN_SEGSITES +ok 75 - Get SEGSITES +ok 76 - Get POSITIONS ok 77 - Get next_hap at beginning of run ok 78 - Get next_hap after beginning of run ok 79 - Testing msout::outgroup @@ -13768,17 +13836,17 @@ ok 90 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' ok 91 - Caught error in bad msout file 2 ok 92 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 93 - Get CURRENT_RUN_SEGSITES -ok 94 - Get TOT_RUN_HAPS -ok 95 - Get RUNS -ok 96 - Get POPS +ok 93 - Get POSITIONS +ok 94 - Get SEGSITES +ok 95 - Get CURRENT_RUN_SEGSITES +ok 96 - Get RUNS ok 97 - Get N_SITES -ok 98 - Get SEEDS +ok 98 - Get LAST_READ_HAP_NUM ok 99 - Get NEXT_RUN_NUM ok 100 - Get MS_INFO_LINE -ok 101 - Get LAST_READ_HAP_NUM -ok 102 - Get SEGSITES -ok 103 - Get POSITIONS +ok 101 - Get SEEDS +ok 102 - Get TOT_RUN_HAPS +ok 103 - Get POPS ok 104 - Get next_hap at beginning of run ok 105 - Get next_hap after beginning of run ok 106 - Testing msout::outgroup @@ -13791,17 +13859,17 @@ ok 113 - Get next_run at beginning of run ok 114 - have all lines been read? ok 115 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 116 - Get SEEDS -ok 117 - Get MS_INFO_LINE -ok 118 - Get LAST_READ_HAP_NUM -ok 119 - Get NEXT_RUN_NUM -ok 120 - Get POSITIONS -ok 121 - Get SEGSITES -ok 122 - Get TOT_RUN_HAPS -ok 123 - Get CURRENT_RUN_SEGSITES -ok 124 - Get RUNS -ok 125 - Get POPS -ok 126 - Get N_SITES +ok 116 - Get LAST_READ_HAP_NUM +ok 117 - Get NEXT_RUN_NUM +ok 118 - Get N_SITES +ok 119 - Get CURRENT_RUN_SEGSITES +ok 120 - Get RUNS +ok 121 - Get POSITIONS +ok 122 - Get SEGSITES +ok 123 - Get POPS +ok 124 - Get TOT_RUN_HAPS +ok 125 - Get MS_INFO_LINE +ok 126 - Get SEEDS ok 127 - Get next_hap at beginning of run ok 128 - Get next_hap after beginning of run ok 129 - Testing msout::outgroup @@ -13814,16 +13882,16 @@ ok 136 - Get last hap through next_hap ok 137 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' ok 138 - Get NEXT_RUN_NUM -ok 139 - Get MS_INFO_LINE -ok 140 - Get LAST_READ_HAP_NUM -ok 141 - Get POSITIONS -ok 142 - Get SEGSITES -ok 143 - Get SEEDS -ok 144 - Get POPS -ok 145 - Get N_SITES -ok 146 - Get CURRENT_RUN_SEGSITES -ok 147 - Get TOT_RUN_HAPS -ok 148 - Get RUNS +ok 139 - Get LAST_READ_HAP_NUM +ok 140 - Get N_SITES +ok 141 - Get RUNS +ok 142 - Get CURRENT_RUN_SEGSITES +ok 143 - Get SEGSITES +ok 144 - Get POSITIONS +ok 145 - Get POPS +ok 146 - Get TOT_RUN_HAPS +ok 147 - Get SEEDS +ok 148 - Get MS_INFO_LINE ok 149 - Get next_hap at beginning of run ok 150 - Get next_hap after beginning of run ok 151 - Testing msout::outgroup @@ -13983,7 +14051,7 @@ not ok 29 - accuracies # TODO documentation and code for accuracies() do not match # Failed (TODO) test 'accuracies' # at t/SeqIO/scf.t line 77. -# got: 'ARRAY(0x1bd877c)' +# got: 'ARRAY(0x57e3ad54)' # expected: '482' ok 30 ok 31 - sub_peak_index @@ -14286,9 +14354,9 @@ ok 19 - dblink source ok 20 - dblink ID ok 21 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' -ok 22 - boolean property +ok 22 - property with value ok 23 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' -ok 24 - property with value +ok 24 - boolean property ok 25 - writer ok ok 26 - outfile is created ok 27 - seqXML version @@ -14309,9 +14377,9 @@ ok 42 - dblink source ok 43 - dblink ID ok 44 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' -ok 45 - property with value +ok 45 - boolean property ok 46 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' -ok 47 - boolean property +ok 47 - property with value ok 48 - outfile is created ok 49 - seqXML version ok 50 - source @@ -15286,9 +15354,9 @@ ok 100 ok 101 ok 102 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 103 - gcgblast format -ok 104 - blast format -ok 105 - vcf format +ok 103 - blast format +ok 104 - vcf format +ok 105 - gcgblast format ok t/SeqTools/OddCodes.t ............... 1..11 @@ -17706,14 +17774,14 @@ Test Summary Report ------------------- t/Root/IO.t (Wstat: 0 Tests: 154 Failed: 0) - TODO passed: 109, 118 -Files=211, Tests=14791, 151 wallclock secs ( 2.03 usr 0.45 sys + 139.39 cusr 10.15 csys = 152.02 CPU) + TODO passed: 118 +Files=211, Tests=14791, 195 wallclock secs ( 1.92 usr 0.40 sys + 147.18 cusr 10.58 csys = 160.08 CPU) Result: PASS make[1]: Leaving directory '/build/bioperl-1.7.8' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j8 install DESTDIR=/build/bioperl-1.7.8/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr + make -j15 install DESTDIR=/build/bioperl-1.7.8/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/bioperl-1.7.8' Manifying 40 pod documents Manifying 35 pod documents @@ -17732,1027 +17800,1027 @@ Manifying 33 pod documents Manifying 15 pod documents Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/BioPerl.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnnotatableI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnalysisI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnnotationCollectionI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/RangeI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/LocationI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnalysisResultI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Range.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/LocatableSeq.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/PrimarySeqI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/HandlerBaseI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/IdentifiableI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/PullParserI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnnotatableI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/UpdateableSeqI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnalysisParserI.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SimpleAlign.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/WebAgent.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Taxon.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/RangeI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DescribableI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/PullParserI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Range.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DBLinkContainerI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnnotationCollectionI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqAnalysisParserI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/IdCollectionI.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/PrimarySeq.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/UpdateableSeqI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnnotationI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DasI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SimpleAnalysisI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/ParameterBaseI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnalysisI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnnotationI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DBLinkContainerI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DescribableI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Species.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/PrimarySeq.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/LocatableSeq.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnalysisParserI.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqUtils.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/IdCollectionI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Species.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/LocationI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/HandlerBaseI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/WebAgent.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/FeatureHolderI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/IdentifiableI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/ParameterBaseI.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeatureI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/Tree.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/RandomFactory.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/NodeNHX.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/Statistics.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/Compatible.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/DistanceFactory.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/NodeI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/TreeI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/Node.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/TreeFunctionsI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/AnnotatableNode.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/tRNAscanSE.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqAnalysisParserI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/FeatureHolderI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tab.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/fasta.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/msout.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/FTHelper.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/bsml_sax.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/mbsout.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/embl.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/embldriver.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/fastq.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/scf.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/swissdriver.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tinyseq.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/MultiFile.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/swiss.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/table.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/kegg.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/ace.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/raw.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/metafasta.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/phd.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/seqxml.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/asciitree.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/qual.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/locuslink.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/genbank.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/bsml.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/pir.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tigrxml.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tigr.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/gbxml.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/gbdriver.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/gcg.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/largefasta.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tinyseq/tinyseqHandler.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/seqHandler.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/gameSubs.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/gameWriter.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/featHandler.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/gameHandler.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/Handler/GenericRichSeqHandler.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/MatrixI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/Scoring.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/Generic.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/Mlagan.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PhylipDist.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/PsmI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/SiteMatrix.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/ProtMatrix.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/ProtPsm.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/InstanceSiteI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/Psm.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/InstanceSite.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/PsmHeader.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/SiteMatrixI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/PsmHeaderI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/psiblast.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/meme.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/transfac.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/mast.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/masta.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO/phylip.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO/scoring.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO/mlagan.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/MZEF.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genomewise.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/TandemRepeatsFinder.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Grail.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Sigcleave.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Match.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/GuessSeqFormat.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Fgenesh.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/pICalculator.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/SeqStats.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Profile.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/SeqPattern.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Pseudowise.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/ipcress.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Signalp.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer3.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Prints.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/TargetP.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/GuessSeqFormat.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Seg.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/IUPAC.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genewise.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/OddCodes.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/GFF.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/AnalysisResult.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Promoterwise.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/RepeatMasker.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Eponine.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Prints.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Tmhmm.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Blat.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genscan.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Fgenesh.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/SeqWords.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/ESTScan.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/GFF.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Lucy.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Signalp.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Coil.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/ECnumber.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/ipcress.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/FootPrinter.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/AnalysisResult.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/TandemRepeatsFinder.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/pICalculator.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/tRNAscanSE.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Profile.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/QRNA.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genemark.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/EPCR.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/SeqStats.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Tmhmm.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Geneid.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Pseudowise.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genewise.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/CodonTable.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Est2Genome.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Sigcleave.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/PrositeScan.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/RandomDistFunctions.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Glimmer.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Promoterwise.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Est2Genome.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/EPCR.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Grail.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/SeqPattern.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Blat.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Eponine.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/ESTScan.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Lucy.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/ECnumber.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/isPcr.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/RandomDistFunctions.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/MZEF.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/OddCodes.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genemark.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/AmpliconSearch.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/TargetP.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Seg.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer/Feature.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer/Pair.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer/AssessorI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer/Assessor/Base.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Signalp/ExtendedSignalp.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Analysis/SimpleAnalysisBase.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Prediction/Gene.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Prediction/Exon.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/EMBOSS/Palindrome.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Alignment/Consed.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/FootPrinter.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/CodonTable.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genscan.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Alignment/Trim.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Alignment/Consed.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Analysis/SimpleAnalysisBase.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/WrapperBase.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/ParametersI.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/Analysis.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/AnalysisFactory.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/GenericParameters.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/WrapperBase/CommandExts.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/AnalysisFactory.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/PhyloBase.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Sim4/Results.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Sim4/Exon.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/SeqPattern/Backtranslate.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Spidey/Results.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/WrapperBase/CommandExts.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Spidey/Exon.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Spidey/Results.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer/Feature.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer/Pair.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer/AssessorI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer/Assessor/Base.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Signalp/ExtendedSignalp.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Phylo/Gerp.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Phylo/Molphy.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Phylo/Molphy/Result.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Phylo/Phylip/ProtDist.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Tree.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Reference.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/AnnotationFactory.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/TagTree.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/SimpleValue.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/DBLink.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Relation.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/TypeManager.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/OntologyTerm.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Collection.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Target.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/StructuredValue.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Comment.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/AlignI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/Utilities.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/ProteinStatistics.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/PairwiseStatistics.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/DNAStatistics.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/StatisticsI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/MetaI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SequenceTrace.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/Meta.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SeqBuilder.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/LargePrimarySeq.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/LargeSeq.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Phylo/Molphy/Result.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/SeqPattern/Backtranslate.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Prediction/Exon.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Prediction/Gene.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/EMBOSS/Palindrome.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Sim4/Exon.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Sim4/Results.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SequenceFactoryI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SeqAnalysisParserFactory.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/AnalysisI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SequenceStreamI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SequenceProcessorI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/ObjectFactory.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/ApplicationFactoryI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/ObjectFactoryI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/DriverFactory.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/TreeFactoryI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/LocationFactoryI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SeqAnalysisParserFactoryI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/ObjectBuilderI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/FTLocationFactory.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/TreeFunctionsI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/Compatible.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/TreeI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/Statistics.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/DistanceFactory.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/NodeNHX.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/Node.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/AnnotatableNode.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/Tree.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/NodeI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/RandomFactory.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/WidestCoordPolicy.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/NarrowestCoordPolicy.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Simple.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/SplitLocationI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/AvWithinCoordPolicy.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/CoordinatePolicyI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/FuzzyLocationI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Split.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Atomic.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Fuzzy.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/InterProParser.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/goflat.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/obo.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/soflat.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/dagflat.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/simplehierarchy.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/Handlers/BaseSAXHandler.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/Handlers/InterProHandler.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/SwissPfam.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Abstract.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Qual.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/BlastTable.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/GenBank.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Fastq.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/AbstractSeq.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Blast.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/EMBL.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Swissprot.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Fasta.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/QualI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SimulatedRead.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/TraceI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/PrimedSeq.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SeqBuilder.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/LargeSeqI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/Quality.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/PrimaryQual.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SimulatedRead.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SeqFastaSpeedFactory.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/RichSeq.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/BaseSeqProcessor.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/Meta.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/LargePrimarySeq.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/RichSeqI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/PrimaryQual.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/LargeSeq.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/PrimedSeq.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SeqFactory.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/EncodedSeq.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/MetaI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/Quality.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SeqFastaSpeedFactory.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/LargeLocatableSeq.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/QualI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SequenceTrace.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/BaseSeqProcessor.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/Meta/Array.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/Mlagan.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/Generic.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PhylipDist.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/Scoring.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/MatrixI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/SiteMatrixI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/PsmI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/SiteMatrix.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/PsmHeader.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/ProtPsm.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/ProtMatrix.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/Psm.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/PsmHeaderI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/InstanceSiteI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/InstanceSite.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/transfac.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/meme.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/masta.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/mast.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/psiblast.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO/phylip.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO/scoring.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO/mlagan.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Exception.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/TestObject.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/RootI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Exception.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Version.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/IO.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Utilities.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Root.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Version.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Test.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/TestObject.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Storable.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Test.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/HTTPget.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Relationship.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/InterProTerm.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/infernal.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/fasta.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/blast.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/SearchResultEventBuilder.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/exonerate.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/blast_pull.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/EventHandlerI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/blasttable.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/sim4.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/wise.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/gmap_f9.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/megablast.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/waba.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/rnamotif.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/FastHitEventBuilder.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/erpin.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/psl.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/IteratedSearchResultEventBuilder.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/cross_match.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/SearchWriterI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/axt.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/HTMLResultWriter.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/GbrowseGFF.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/HSPTableWriter.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/TextResultWriter.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/HitTableWriter.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/ResultTableWriter.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Event/EventHandlerI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Event/EventGeneratorI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OntologyStore.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OBOterm.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/TermI.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/PathI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/DocumentRegistry.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/SimpleOntologyEngine.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/TermFactory.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/InterProTerm.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/RelationshipFactory.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/GOterm.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Ontology.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/RelationshipType.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Term.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/TermFactory.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/SimpleOntologyEngine.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/DocumentRegistry.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OBOEngine.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OntologyI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Path.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Relationship.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/RelationshipI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/TermI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OBOterm.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OntologyStore.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OntologyEngineI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OBOEngine.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Path.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OntologyI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/RelationshipType.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Term.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/lintree.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/TreeEventBuilder.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/nexus.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/cluster.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/nhx.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/NewickParser.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/lintree.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/nexus.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/pag.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/cluster.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/tabtree.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/nhx.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/phyloxml.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/newick.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/BlastStatistics.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/GenericDatabase.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/phyloxml.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/CodonUsage/IO.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/CodonUsage/Table.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/maf.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/psi.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/fasta.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/xmfa.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/pfam.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/emboss.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/meme.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/mega.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/nexus.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/prodom.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/clustalw.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/phylip.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/selex.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/msf.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/metafasta.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/po.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/mase.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/largemultifasta.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/arp.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/bl2seq.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/proda.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/Handler/GenericAlignHandler.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/StatisticsI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/ProteinStatistics.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/AlignI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/DNAStatistics.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/Utilities.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/PairwiseStatistics.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Relation.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/DBLink.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/SimpleValue.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/StructuredValue.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Target.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/TypeManager.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Collection.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/OntologyTerm.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/AnnotationFactory.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/TagTree.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Tree.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Comment.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Reference.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/DatabaseI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/SearchUtils.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Processor.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/StatisticsI.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/BlastUtils.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/GenericStatistics.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/StatisticsI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/PsiBlastHSP.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/HSPFactory.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/PullHSPI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/FastaHSP.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/WABAHSP.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/HSPI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/PSLHSP.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/BlastPullHSP.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/BlastHSP.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/GenericHSP.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/ModelHSP.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Iteration/IterationI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Iteration/GenericIteration.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/ResultFactory.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/WABAResult.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/CrossMatchResult.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/PullResultI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/ResultI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/INFERNALResult.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/BlastResult.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/BlastPullResult.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/GenericResult.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/HitI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/PsiBlastHit.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/BlastStatistics.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/GenericDatabase.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Processor.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/SearchUtils.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/PullHitI.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/BlastHit.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/GenericHit.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/HitFactory.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/BlastPullHit.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/ModelHit.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/PullHitI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/HitI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/BlastPullHit.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/Fasta.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/PsiBlastHit.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Tiling/MapTiling.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Tiling/MapTileUtils.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Tiling/TilingI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Similarity.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/AnnotationAdaptor.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Primer.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/TypedSeqFeatureI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/SimilarityPair.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Amplicon.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/CollectionI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Generic.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/FeaturePair.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Computation.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/PositionProxy.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Lite.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/SubSeq.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Collection.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Tools/FeatureNamer.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Tools/TypeMapper.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Tools/Unflattener.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Tools/IDHandler.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/TranscriptI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/NC_Feature.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/GeneStructure.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/GeneStructureI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/ExonI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Exon.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Transcript.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Poly_A_site.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Promoter.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/UTR.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Intron.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/pfam.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/nexus.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/largemultifasta.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/po.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/proda.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/phylip.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/maf.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/meme.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/fasta.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/arp.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/bl2seq.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/selex.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/clustalw.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/psi.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/prodom.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/emboss.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/metafasta.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/msf.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/mega.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/xmfa.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/mase.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/Handler/GenericAlignHandler.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/HSPI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/GenericHSP.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/BlastPullHSP.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/PullHSPI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/FastaHSP.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/BlastHSP.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/PsiBlastHSP.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/ModelHSP.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/PSLHSP.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/HSPFactory.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/WABAHSP.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/WABAResult.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/ResultI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/PullResultI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/BlastResult.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/CrossMatchResult.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/GenericResult.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/BlastPullResult.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/INFERNALResult.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/ResultFactory.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Iteration/IterationI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Iteration/GenericIteration.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Qual.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/GenericWebAgent.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Registry.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/LocationI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/SeqI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/ReferenceI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/FileCache.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/IndexedBase.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/RandomAccessI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/DBFetch.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/IndexedBase.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/UpdateableSeqI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Registry.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Qual.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/InMemoryCache.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/WebDBSeqI.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Failover.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/FileCache.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/GenericWebAgent.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/ReferenceI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/SeqI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/LocationI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/DBFetch.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/WebDBSeqI.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/QueryI.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Fasta.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/InMemoryCache.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/silva.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/flatfile.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/greengenes.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/list.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/GFF/Util/Binning.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/GFF/Util/Rearrange.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Query/WebQuery.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BinarySearch.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB/fasta.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB/embl.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB/genbank.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB/swiss.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/obo.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/goflat.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/InterProParser.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/dagflat.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/soflat.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/simplehierarchy.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/Handlers/InterProHandler.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/Handlers/BaseSAXHandler.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SequenceFactoryI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/ApplicationFactoryI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/TreeFactoryI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/ObjectFactory.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/FTLocationFactory.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/ObjectBuilderI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SeqAnalysisParserFactory.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SequenceStreamI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/LocationFactoryI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SeqAnalysisParserFactoryI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SequenceProcessorI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/AnalysisI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/ObjectFactoryI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/DriverFactory.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Event/EventGeneratorI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Event/EventHandlerI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Fastq.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/GenBank.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Abstract.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/SwissPfam.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Blast.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Qual.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Swissprot.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/BlastTable.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/AbstractSeq.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/EMBL.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Fasta.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/sim4.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/fasta.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/IteratedSearchResultEventBuilder.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/blast_pull.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/infernal.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/blasttable.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/waba.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/psl.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/FastHitEventBuilder.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/rnamotif.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/exonerate.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/EventHandlerI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/gmap_f9.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/SearchResultEventBuilder.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/erpin.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/cross_match.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/blast.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/megablast.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/SearchWriterI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/wise.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/axt.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/TextResultWriter.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/GbrowseGFF.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/HSPTableWriter.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/HTMLResultWriter.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/HitTableWriter.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/ResultTableWriter.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB/genbank.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/GFF/Util/Binning.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/GFF/Util/Rearrange.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Das/SegmentI.pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Das/FeatureTypeI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Fuzzy.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/AvWithinCoordPolicy.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/FuzzyLocationI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/WidestCoordPolicy.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Split.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/SplitLocationI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/NarrowestCoordPolicy.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Simple.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Atomic.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/CoordinatePolicyI.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/CodonUsage/IO.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/CodonUsage/Table.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/swissdriver.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/pir.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/MultiFile.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/embldriver.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/largefasta.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/table.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/fasta.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/FTHelper.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/embl.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/scf.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/genbank.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/fastq.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/gbdriver.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tigr.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/gcg.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/kegg.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tinyseq.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tigrxml.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/gbxml.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/bsml_sax.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/asciitree.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tab.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/swiss.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/mbsout.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/seqxml.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/locuslink.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/metafasta.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/msout.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/phd.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/qual.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/ace.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/raw.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/bsml.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/seqHandler.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/gameHandler.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/gameWriter.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/featHandler.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/gameSubs.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/Handler/GenericRichSeqHandler.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tinyseq/tinyseqHandler.pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_nexus2nh.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_make_mrna_protein.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_dbsplit.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_local_taxonomydb_query.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_aacomp.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_genbank2gff3.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_fastam9_to_table.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_mask_by_search.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_taxonomy2tree.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_bioflat_index.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_oligo_count.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_find-blast-matches.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_process_gadfly.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Amplicon.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Lite.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/PositionProxy.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Computation.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Primer.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/SubSeq.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/CollectionI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/TypedSeqFeatureI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/AnnotationAdaptor.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Similarity.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Collection.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/FeaturePair.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/SimilarityPair.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Generic.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Tools/IDHandler.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Tools/Unflattener.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Tools/FeatureNamer.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Tools/TypeMapper.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Intron.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/NC_Feature.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/GeneStructure.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Promoter.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Transcript.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Poly_A_site.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Exon.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/TranscriptI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/UTR.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/ExonI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/GeneStructureI.pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_mrtrans.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_mutate.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_seqconvert.1p Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_biogetseq.1p Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_process_sgd.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_mutate.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_sreformat.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_seqretsplit.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_revtrans-motif.1p Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_split_seq.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_taxid4species.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_filter_search.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_seqret.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_seq_length.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_fetch.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_local_taxonomydb_query.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_revtrans-motif.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_nexus2nh.1p Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_index.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_seqpart.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_mrtrans.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_unflatten_seq.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_search2tribe.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_nrdb.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_seqretsplit.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_fastam9_to_table.1p Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_search2alnblocks.1p Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_search2table.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_seqcut.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_gccalc.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_seqconvert.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_nrdb.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_translate_seq.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_filter_search.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_find-blast-matches.1p Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_search2gff.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_oligo_count.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_unflatten_seq.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_search2tribe.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_process_gadfly.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_genbank2gff3.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_gccalc.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_sreformat.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_seqpart.1p Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_extract_feature_seq.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_translate_seq.1p Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_tree2pag.1p -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Align::Utilities.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Flat::BDB.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::PathI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::selex.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Fgenesh.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::LargeLocatableSeq.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Root::TestObject.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::TandemRepeatsFinder.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::gmap_f9.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Iteration::IterationI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::rnamotif.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::ProtMatrix.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::RepeatMasker.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Fasta.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::Relation.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Taxonomy::list.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::LargePrimarySeq.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Phylo::Phylip::ProtDist.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO::phyloxml.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Analysis::SimpleAnalysisBase.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::OntologyIO::Handlers::InterProHandler.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::SearchWriterI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Similarity.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_dbsplit.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_fetch.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_seqcut.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_taxonomy2tree.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_mask_by_search.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_taxid4species.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_make_mrna_protein.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_bioflat_index.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_seq_length.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_aacomp.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_seqret.1p +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::msf.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Phylo::Gerp.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::TreeFunctionsI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::IO::psiblast.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::LocationI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::AnnotationAdaptor.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Genemark.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::SimpleOntologyEngine.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::GOterm.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::Tree.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Hit::HitI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::Writer::GbrowseGFF.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::game::seqHandler.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::WABAHSP.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PhylipDist.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Spidey::Exon.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::waba.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::psl.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::tinyseq::tinyseqHandler.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::ProtPsm.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Flat.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Location::WidestCoordPolicy.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Result::WABAResult.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::AbstractSeq.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::PrositeScan.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::fasta.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::PullHSPI.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::TargetP.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::QualI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::SearchUtils.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::qual.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Primer3.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::exonerate.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Hit::PsiBlastHit.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Result::ResultI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::DBLink.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::SeqAnalysisParserFactoryI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::Tree.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::tab.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::proda.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::SeqI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::OntologyTerm.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::BlastStatistics.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::NC_Feature.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::IUPAC.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::CodonUsage::Table.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO::newick.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::SubSeq.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Alignment::Trim.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::Fastq.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::mase.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::HSPI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::clustalw.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::AnnotationFactory.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Sim4::Results.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::RandomFactory.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Tools::Unflattener.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Das::SegmentI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::swissdriver.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::GenericWebAgent.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::PrimarySeq.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Failover.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::StatisticsI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Alignment::Trim.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Lite.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Root::Version.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Iteration::GenericIteration.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::Psm.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Flat::BDB::genbank.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::Compatible.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::fastq.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::FileCache.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Location::CoordinatePolicyI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::RelationshipFactory.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::game::featHandler.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::AnnotationAdaptor.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::SearchResultEventBuilder.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::QueryI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::psl.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO::nexus.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Primer.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Lucy.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::prodom.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::game::gameSubs.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::psi.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::Swissprot.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::Scoring.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Root::Storable.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::phylip.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::IO::mast.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Flat::BDB::fasta.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::po.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::SequenceProcessorI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::Writer::HTMLResultWriter.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Result::PullResultI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::BlastUtils.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Alignment::Consed.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::largefasta.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::pICalculator.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::DriverFactory.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::ApplicationFactoryI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::Exon.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::Promoter.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Blat.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::AnalysisI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::OntologyIO::obo.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DescribableI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::BlastTable.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::Tree.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Sigcleave.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::GuessSeqFormat.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Registry.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Root::Test.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::NodeNHX.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::GFF.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Species.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Iteration::IterationI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::LocationI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO::cluster.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Prints.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Pseudowise.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::Intron.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::OntologyIO::simplehierarchy.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::EPCR.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::EventHandlerI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::RangeI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Tiling::TilingI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Align::PairwiseStatistics.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PhylipDist.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::raw.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::SimpleValue.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::embldriver.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::LargeLocatableSeq.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Location::SplitLocationI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::tigrxml.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SimpleAnalysisI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::SequenceProcessorI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Align::Utilities.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::QualI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Location::Atomic.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Run::ParametersI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::qual.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::fasta.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::PositionProxy.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::fasta.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::prodom.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::emboss.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DBLinkContainerI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::OntologyTerm.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::SequenceStreamI.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::SeqPattern::Backtranslate.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::BlastPullHSP.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::IO::mlagan.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::IdentifiableI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Registry.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO::NewickParser.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::cross_match.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::PSLHSP.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::MetaI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Taxonomy.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::SiteMatrixI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::TagTree.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::SequenceTrace.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Align::AlignI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::scf.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::clustalw.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::arp.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::ModelHSP.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::Mlagan.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::msout.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::QueryI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::SeqAnalysisParserFactoryI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::SeqFactory.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Result::BlastPullResult.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Root::RootI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::OntologyI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::mbsout.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Das::FeatureTypeI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::tinyseq.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Location::FuzzyLocationI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Das::SegmentI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::GenericWebAgent.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::Path.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::OntologyEngineI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::Writer::TextResultWriter.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::OntologyIO.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::PathI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Genomewise.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::gmap_f9.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::WebAgent.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::Quality.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::PrimarySeqI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::gbdriver.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::RelationshipFactory.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::ESTScan.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::LargeSeqI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Flat::BDB::swiss.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::SeqFastaSpeedFactory.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::Writer::ResultTableWriter.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AnalysisI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Tools::IDHandler.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::cross_match.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::selex.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Glimmer.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::game::gameWriter.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::Writer::HTMLResultWriter.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::TraceI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Run::GenericParameters.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::IUPAC.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::SimpleGOEngine::GraphAdaptor.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::Intron.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Event::EventHandlerI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::LocatableSeq.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::SiteMatrix.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::Collection.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::FastHitEventBuilder.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::ApplicationFactoryI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Event::EventGeneratorI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::locuslink.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Signalp.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Location::NarrowestCoordPolicy.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::PsiBlastHSP.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::tigr.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::GeneStructure.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::CodonUsage::IO.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Taxon.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::erpin.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AnalysisResultI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Taxonomy::greengenes.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::OntologyIO::InterProParser.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::tinyseq.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::game::featHandler.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::Node.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::xmfa.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::Collection.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::phd.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO::TreeEventBuilder.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Seg.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Est2Genome.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AnalysisResultI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::AnalysisResult.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::EncodedSeq.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::CodonTable.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::IdentifiableI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO::phyloxml.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::Swissprot.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::InstanceSiteI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::GOterm.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::metafasta.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::Abstract.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::OntologyIO::dagflat.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::WebDBSeqI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::FootPrinter.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::Writer::HitTableWriter.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::SeqI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::MatrixI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::FileCache.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::CodonUsage::Table.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::NodeI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::BlastUtils.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::HSPFactory.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::CollectionI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::LargeSeq.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::bsml_sax.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::IndexedBase.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SimpleAlign.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::Meta::Array.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::AnalysisI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::psi.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::DriverFactory.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::ObjectFactory.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::GeneStructureI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Taxonomy::list.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::OntologyIO::soflat.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::PrimarySeq.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Grail.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::SimpleGOEngine::GraphAdaptor.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::BlastHSP.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO::pag.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::OntologyIO::goflat.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::game::gameWriter.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Root::Exception.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::largemultifasta.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::SequenceFactoryI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::HandlerBaseI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Tmhmm.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::kegg.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::game::seqHandler.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::embl.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::metafasta.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Taxonomy.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AnalysisParserI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::Comment.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Align::ProteinStatistics.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::SeqStats.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::MultiFile.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::FeatureHolderI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::gbxml.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Eponine.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::Handler::GenericRichSeqHandler.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::SearchWriterI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::gcg.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::pfam.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Query::WebQuery.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Seg.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::EPCR.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::OddCodes.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Collection.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::isPcr.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Phylo::Molphy.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::OntologyEngineI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Fasta.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::PhyloBase.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::IO::transfac.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Computation.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Result::CrossMatchResult.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::RichSeq.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::SwissPfam.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Hit::ModelHit.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::Fasta.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Hit::PullHitI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::IO::psiblast.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Root::Root.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Result::BlastResult.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::FootPrinter.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::ReferenceI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::GFF.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::AmpliconSearch.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::DBLink.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::PsmHeaderI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::infernal.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::blast_pull.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::NC_Feature.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::Target.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::bsml.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Analysis.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::LargeSeq.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::ParameterBaseI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::ObjectFactory.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::Writer::HitTableWriter.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::Generic.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Hit::GenericHit.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Processor.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::IdCollectionI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Tiling::MapTileUtils.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::blast.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::WebAgent.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Generic.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::RandomDistFunctions.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::PsmI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::mbsout.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::DatabaseI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::RandomAccessI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::fasta.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Species.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::SeqBuilder.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::QRNA.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::Relationship.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SimpleAnalysisI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::FastHitEventBuilder.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Result::ResultFactory.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Glimmer.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Run::WrapperBase::CommandExts.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::IO::mlagan.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Prediction::Gene.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO::lintree.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::maf.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Sigcleave.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AnalysisParserI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::DistanceFactory.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::Comment.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Similarity.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqUtils.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::msf.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Location::AvWithinCoordPolicy.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::Term.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO::tabtree.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::PsmHeader.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Tools::FeatureNamer.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::WebDBSeqI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::ObjectBuilderI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::emboss.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::waba.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Computation.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Phylo::Gerp.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Hit::ModelHit.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::locuslink.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::FeaturePair.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Sim4::Results.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::genbank.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::IO::scoring.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::FTHelper.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Run::WrapperBase.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Lucy.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::GeneStructure.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::DocumentRegistry.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::InMemoryCache.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Tiling::TilingI.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Prediction::Exon.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::WABAHSP.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Hit::BlastHit.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Root::HTTPget.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Coil.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::SimpleOntologyEngine.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::DBFetch.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Primer::Assessor::Base.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Genemark.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Primer::AssessorI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Promoterwise.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::TypedSeqFeatureI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::GenBank.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::LocationI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Phylo::Molphy.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::MZEF.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::asciitree.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Spidey::Results.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Root::Version.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::SeqPattern.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::EncodedSeq.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Root::IO.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::tigrxml.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Lite.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/BioPerl.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::PrositeScan.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Spidey::Exon.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Location::WidestCoordPolicy.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO::nhx.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::Fasta.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::RichSeq.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Root::RootI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::meme.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::TreeI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqAnalysisParserI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::swiss.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Match.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::LocationI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::ESTScan.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::TranscriptI.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::IteratedSearchResultEventBuilder.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Result::GenericResult.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::tRNAscanSE.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::SeqFastaSpeedFactory.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::Statistics.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::SeqFactory.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::SequenceFactoryI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::fasta.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::OntologyStore.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Align::ProteinStatistics.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::blasttable.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::BlastHSP.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::LocationFactoryI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::OntologyIO::goflat.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AnnotationI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::ipcress.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeatureI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::Fastq.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Result::BlastResult.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::UpdateableSeqI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Phylo::Phylip::ProtDist.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::SubSeq.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::Ontology.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::nexus.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::bl2seq.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Amplicon.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::IO::phylip.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Tiling::MapTileUtils.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/BioPerl.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Qual.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Profile.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::ProtMatrix.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::IO.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::Handler::GenericAlignHandler.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::IO::masta.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Flat::BinarySearch.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Align::DNAStatistics.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::Qual.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::AnnotatableNode.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::PrimaryQual.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::erpin.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::RelationshipI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::Path.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Align::StatisticsI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::AbstractSeq.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::Blast.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::IndexedBase.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::Writer::HSPTableWriter.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Collection.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::LocatableSeq.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Match.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::Handler::GenericAlignHandler.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Primer3.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::GenericDatabase.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::Reference.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Iteration::GenericIteration.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Tools::TypeMapper.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Flat::BDB::embl.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::PullHSPI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::SiteMatrix.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::table.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Location::SplitLocationI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::arp.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::Handler::GenericRichSeqHandler.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Taxonomy::flatfile.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::Statistics.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::IdCollectionI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Primer::Feature.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::FTLocationFactory.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Align::PairwiseStatistics.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Taxon.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::EventHandlerI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::ExonI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO::TreeEventBuilder.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Sim4::Exon.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::blast.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::Scoring.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::Writer::TextResultWriter.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::game::gameSubs.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::OBOEngine.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::FastaHSP.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::swiss.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AnnotationCollectionI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::CollectionI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Das::FeatureTypeI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Taxonomy::silva.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Phylo::Molphy::Result.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::IO::meme.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::Relation.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::meme.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AnnotatableI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Root::Utilities.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::PrimaryQual.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Genewise.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::PrimedSeq.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::SwissPfam.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::LocationFactoryI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::tab.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Genscan.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::DBFetch.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Location::Split.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::SeqAnalysisParserFactory.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::SearchUtils.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Flat::BDB::embl.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Range.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::embl.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::MZEF.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::pir.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Blat.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::megablast.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::Term.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::OntologyIO::obo.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Root::Exception.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Hit::BlastPullHit.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::ParameterBaseI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::TypedSeqFeatureI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::InterProTerm.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::ReferenceI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::genbank.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::exonerate.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::Tree.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::IO.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::GenericHSP.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Root::IO.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::game::gameHandler.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::HandlerBaseI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Genomewise.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::NodeI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Signalp::ExtendedSignalp.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::TandemRepeatsFinder.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Root::Storable.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::rnamotif.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::tigr.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::PrimedSeq.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Result::INFERNALResult.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::metafasta.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::SeqPattern.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Location::AvWithinCoordPolicy.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::RelationshipType.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Pseudowise.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::GenericStatistics.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Flat::BDB.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::EMBOSS::Palindrome.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::RepeatMasker.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::StructuredValue.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Run::AnalysisFactory.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::GenBank.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::UpdateableSeqI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Root::HTTPget.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Genewise.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::ECnumber.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::SeqWords.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::pICalculator.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Analysis::SimpleAnalysisBase.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::SimulatedRead.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::OntologyIO::dagflat.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::OntologyIO::InterProParser.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::tRNAscanSE.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Result::ResultI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::SimilarityPair.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::GFF::Util::Binning.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::scf.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::megablast.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::nexus.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Primer::Feature.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::ProtPsm.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::Target.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::HSPFactory.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::TraceI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Run::WrapperBase::CommandExts.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeatureI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Geneid.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::msout.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Prediction::Gene.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::ModelHSP.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::RandomDistFunctions.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::EMBL.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::QRNA.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Location::Fuzzy.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::OntologyIO::Handlers::InterProHandler.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DasI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Hit::Fasta.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::Blast.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Root::Root.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::ObjectBuilderI.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Location::Simple.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Flat::BDB::genbank.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO::lintree.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::NodeNHX.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::GFF::Util::Rearrange.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Taxonomy::flatfile.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::po.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO::nhx.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::OBOterm.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::raw.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::CodonUsage::IO.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Primer::AssessorI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Generic.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::SeqBuilder.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::phd.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::Relationship.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::LargePrimarySeq.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Taxonomy::greengenes.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::table.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Tiling::MapTiling.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::TagTree.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::fasta.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::Writer::GbrowseGFF.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::Ontology.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::Quality.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::DocumentRegistry.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::ipcress.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::sim4.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::bl2seq.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::game.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::AnnotatableNode.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::ECnumber.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Query::WebQuery.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DasI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::CodonTable.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Run::GenericParameters.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqAnalysisParserI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Flat::BDB::fasta.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::TermI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO::pag.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::phylip.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Result::PullResultI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Result::GenericResult.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::GFF::Util::Rearrange.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::wise.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Root::TestObject.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::PSLHSP.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::asciitree.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::RandomAccessI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::Exon.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::xmfa.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DescribableI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::Writer::HSPTableWriter.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::Promoter.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO::newick.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO::NewickParser.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::AnnotationFactory.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO::nexus.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::mega.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Location::NarrowestCoordPolicy.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::axt.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::ObjectFactoryI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::GenericStatistics.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Genscan.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::TypeManager.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::RelationshipType.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::SimilarityPair.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Align::AlignI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::gbxml.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::OddCodes.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::OntologyI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::IO::transfac.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::maf.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Primer::Assessor::Base.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::RichSeqI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Processor.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Promoterwise.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::BlastTable.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Primer::Pair.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::InstanceSite.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::RangeI.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::OntologyIO::Handlers::BaseSAXHandler.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::IO.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::Meta.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::IO::meme.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::swissdriver.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::FastaHSP.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Qual.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Failover.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Hit::BlastPullHit.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::UTR.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Flat.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::EMBOSS::Palindrome.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::EMBL.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::Transcript.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Root::Utilities.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Hit::HitFactory.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::OBOEngine.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SimpleAlign.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Event::EventHandlerI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::infernal.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::PsiBlastHSP.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::sim4.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::IO::mast.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::FeaturePair.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Tools::FeatureNamer.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::largefasta.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::PsmI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::BaseSeqProcessor.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::PsmHeader.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::HSPI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::mase.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::game.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Location::CoordinatePolicyI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::DatabaseI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Geneid.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Spidey::Results.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Fgenesh.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::largemultifasta.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::metafasta.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Alignment::Consed.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Result::ResultFactory.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::seqxml.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::TreeI.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::Poly_A_site.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::TreeFunctionsI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Amplicon.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::GenericDatabase.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Run::WrapperBase.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::bsml.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::MultiFile.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::PhyloBase.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Location::Fuzzy.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Location::Atomic.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Run::AnalysisFactory.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Tools::Unflattener.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::IO::masta.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::TranscriptI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::TermFactory.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::isPcr.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Hit::Fasta.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Event::EventGeneratorI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Root::Test.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DBLinkContainerI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Signalp::ExtendedSignalp.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::InMemoryCache.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::Generic.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::FTLocationFactory.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Eponine.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::Mlagan.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::RichSeqI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::proda.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::Abstract.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO::tabtree.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::OntologyIO::simplehierarchy.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::OntologyStore.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::MetaI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::Meta.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::ace.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Tools::IDHandler.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Result::WABAResult.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::Compatible.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::SimpleValue.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::gcg.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::RandomFactory.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Index::Qual.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::GenericHSP.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::StructuredValue.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::IO::phylip.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::AnalysisResult.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::TreeFactoryI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::PrimarySeqI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AnalysisI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Result::BlastPullResult.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Tmhmm.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::SeqAnalysisParserFactory.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Sim4::Exon.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::pfam.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Align::DNAStatistics.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::blasttable.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::InstanceSite.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::LargeSeqI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::InterProTerm.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::embldriver.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Result::INFERNALResult.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Profile.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Est2Genome.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Run::ParametersI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Hit::HitI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::PsmHeaderI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Phylo::Molphy::Result.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::UpdateableSeqI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::FeatureHolderI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Flat::BinarySearch.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::SeqWords.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::SequenceTrace.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::bsml_sax.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::MatrixI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::wise.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Primer::Pair.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Taxonomy::silva.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::tinyseq::tinyseqHandler.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::GeneStructureI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::blast_pull.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::gbdriver.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::SeqStats.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::Transcript.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::Meta::Array.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Range.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Primer.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::TermFactory.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::OntologyIO.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::Coil.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::IO::scoring.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::UTR.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Hit::BlastHit.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::HSP::BlastPullHSP.3pm Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::PullParserI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::seqxml.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::SequenceStreamI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::AmpliconSearch.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AnnotationI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::TermI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::SimulatedRead.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::Psm.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tools::GuessSeqFormat.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::Result::CrossMatchResult.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Tree::DistanceFactory.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Location::Split.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::Flat::BDB::swiss.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Gene::ExonI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Matrix::PSM::SiteMatrixI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Seq::BaseSeqProcessor.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::Writer::ResultTableWriter.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::DB::UpdateableSeqI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::pir.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::OBOterm.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Ontology::RelationshipI.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::TreeIO::cluster.3pm -Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::AlignIO::mega.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Factory::ObjectFactoryI.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqFeature::Tools::TypeMapper.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SearchIO::SearchResultEventBuilder.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Search::BlastStatistics.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::SeqIO::FTHelper.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Annotation::TypeManager.3pm +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_tree2pag +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_aacomp Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_local_taxonomydb_query -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2gff +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqret Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_nrdb -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_seq_length -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_mutate -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2alnblocks -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_process_sgd +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_bioflat_index +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqpart Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_index +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_mask_by_search +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_mrtrans +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2alnblocks +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_unflatten_seq +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_mutate +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_find-blast-matches +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqretsplit +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_fetch +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_biogetseq Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_translate_seq -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_split_seq +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_process_sgd +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_taxid4species Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_dbsplit -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_nexus2nh -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_taxonomy2tree -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_find-blast-matches -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_genbank2gff3 -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_unflatten_seq Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_gccalc -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_sreformat -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqretsplit -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_mrtrans Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_process_gadfly -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqret Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_revtrans-motif -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_fetch -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_aacomp Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2tribe +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_sreformat +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2gff Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqconvert -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_bioflat_index -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_filter_search -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_tree2pag -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_biogetseq -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2table -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_mask_by_search -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_extract_feature_seq +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_taxonomy2tree Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_oligo_count +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_split_seq +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2table Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqcut -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqpart -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_make_mrna_protein Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_fastam9_to_table -Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_taxid4species +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_make_mrna_protein +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_seq_length +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_filter_search +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_extract_feature_seq +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_nexus2nh +Installing /build/bioperl-1.7.8/debian/tmp/usr/bin/bp_genbank2gff3 make[1]: Leaving directory '/build/bioperl-1.7.8' dh_install dh_installdocs @@ -18790,12 +18858,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/104887/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/104887/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/18702 and its subdirectories -I: Current time: Fri Apr 28 23:22:15 -12 2023 -I: pbuilder-time-stamp: 1682767335 +I: removing directory /srv/workspace/pbuilder/104887 and its subdirectories +I: Current time: Sat Jun 1 07:50:59 +14 2024 +I: pbuilder-time-stamp: 1717177859