RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux gumiho 2.6.24-32-xen #1 SMP Mon Dec 3 16:12:25 UTC 2012 x86_64 Buildd toolchain package versions: launchpad-buildd_118~0.IS.08.04 python-lpbuildd_118~0.IS.08.04 bzr-builder_0.7.2+bzr156-0ubuntu1~1.IS.8.04 bzr_2.4.0-0ubuntu2~11.IS.8.04. Syncing the system clock with the buildd NTP service... 8 Oct 21:59:20 ntpdate[3371]: step time server 10.211.37.1 offset -21993.196528 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-5085631', '/home/buildd/filecache-default/a773c5bc5bb042a1c5e3ddeccf21e58b47cfbf39'] Uncompressing the tarball... Unpacking chroot for build PACKAGEBUILD-5085631 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-5085631'] Mounting chroot for build PACKAGEBUILD-5085631 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-5085631', 'deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main', 'deb http://ppa.launchpad.net/marutter/rrutter/ubuntu precise main', 'deb http://ftpmaster.internal/ubuntu precise main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu precise-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu precise-updates main restricted universe multiverse'] Overriding sources.list in build-PACKAGEBUILD-5085631 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-5085631', 'i386'] Updating debian chroot for build PACKAGEBUILD-5085631 Ign http://ppa.launchpad.net precise InRelease Ign http://ppa.launchpad.net precise InRelease Ign http://ftpmaster.internal precise InRelease Ign http://ftpmaster.internal precise-security InRelease Ign http://ftpmaster.internal precise-updates InRelease Get:1 http://ppa.launchpad.net precise Release.gpg [316 B] Get:2 http://ppa.launchpad.net precise Release.gpg [316 B] Get:3 http://ppa.launchpad.net precise Release [11.9 kB] Get:4 http://ppa.launchpad.net precise Release [11.9 kB] Ign http://ppa.launchpad.net precise Release Get:5 http://ppa.launchpad.net precise/main i386 Packages [59.5 kB] Ign http://ppa.launchpad.net precise Release Get:6 http://ftpmaster.internal precise Release.gpg [198 B] Get:7 http://ftpmaster.internal precise-security Release.gpg [198 B] Ign http://ppa.launchpad.net precise/main TranslationIndex Get:8 http://ppa.launchpad.net precise/main i386 Packages [45.5 kB] Ign http://ppa.launchpad.net precise/main TranslationIndex Get:9 http://ftpmaster.internal precise-updates Release.gpg [198 B] Get:10 http://ftpmaster.internal precise Release [49.6 kB] Ign http://ppa.launchpad.net precise/main Translation-en Get:11 http://ftpmaster.internal precise-security Release [49.6 kB] Ign http://ppa.launchpad.net precise/main Translation-en Get:12 http://ftpmaster.internal precise-updates Release [49.6 kB] Get:13 http://ftpmaster.internal precise/main i386 Packages [1274 kB] Get:14 http://ftpmaster.internal precise/restricted i386 Packages [8431 B] Get:15 http://ftpmaster.internal precise/universe i386 Packages [4796 kB] Get:16 http://ftpmaster.internal precise/multiverse i386 Packages [121 kB] Get:17 http://ftpmaster.internal precise/main TranslationIndex [3706 B] Get:18 http://ftpmaster.internal precise/multiverse TranslationIndex [2676 B] Get:19 http://ftpmaster.internal precise/restricted TranslationIndex [2596 B] Get:20 http://ftpmaster.internal precise/universe TranslationIndex [2922 B] Get:21 http://ftpmaster.internal precise-security/main i386 Packages [343 kB] Get:22 http://ftpmaster.internal precise-security/restricted i386 Packages [4620 B] Get:23 http://ftpmaster.internal precise-security/universe i386 Packages [86.3 kB] Get:24 http://ftpmaster.internal precise-security/multiverse i386 Packages [2640 B] Get:25 http://ftpmaster.internal precise-security/main TranslationIndex [74 B] Get:26 http://ftpmaster.internal precise-security/multiverse TranslationIndex [72 B] Get:27 http://ftpmaster.internal precise-security/restricted TranslationIndex [72 B] Get:28 http://ftpmaster.internal precise-security/universe TranslationIndex [73 B] Get:29 http://ftpmaster.internal precise-updates/main i386 Packages [714 kB] Get:30 http://ftpmaster.internal precise-updates/restricted i386 Packages [11.4 kB] Get:31 http://ftpmaster.internal precise-updates/universe i386 Packages [221 kB] Get:32 http://ftpmaster.internal precise-updates/multiverse i386 Packages [14.0 kB] Get:33 http://ftpmaster.internal precise-updates/main TranslationIndex [3564 B] Get:34 http://ftpmaster.internal precise-updates/multiverse TranslationIndex [2605 B] Get:35 http://ftpmaster.internal precise-updates/restricted TranslationIndex [2461 B] Get:36 http://ftpmaster.internal precise-updates/universe TranslationIndex [2850 B] Get:37 http://ftpmaster.internal precise/main Translation-en [726 kB] Get:38 http://ftpmaster.internal precise/multiverse Translation-en [93.4 kB] Get:39 http://ftpmaster.internal precise/restricted Translation-en [2395 B] Get:40 http://ftpmaster.internal precise/universe Translation-en [3341 kB] Get:41 http://ftpmaster.internal precise-security/main Translation-en [156 kB] Get:42 http://ftpmaster.internal precise-security/multiverse Translation-en [1299 B] Get:43 http://ftpmaster.internal precise-security/restricted Translation-en [1253 B] Get:44 http://ftpmaster.internal precise-security/universe Translation-en [52.6 kB] Get:45 http://ftpmaster.internal precise-updates/main Translation-en [313 kB] Get:46 http://ftpmaster.internal precise-updates/multiverse Translation-en [8064 B] Get:47 http://ftpmaster.internal precise-updates/restricted Translation-en [2637 B] Get:48 http://ftpmaster.internal precise-updates/universe Translation-en [127 kB] Fetched 12.7 MB in 7s (1615 kB/s) Reading package lists... W: GPG error: http://ppa.launchpad.net precise Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 759A8E0E5BA15160 W: GPG error: http://ppa.launchpad.net precise Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 5E25F516B04C661B Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: apt apt-transport-https base-files bash binutils build-essential busybox-initramfs coreutils dpkg dpkg-dev gnupg gpgv ifupdown initramfs-tools initramfs-tools-bin initscripts libapt-pkg4.12 libasn1-8-heimdal libc-bin libc-dev-bin libc6 libc6-dev libcurl3-gnutls libdbus-1-3 libdpkg-perl libdrm-intel1 libdrm-nouveau1a libdrm-radeon1 libdrm2 libgcrypt11 libglib2.0-0 libgnutls26 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libk5crypto3 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libnih-dbus1 libnih1 libpciaccess0 libplymouth2 libroken18-heimdal libsasl2-2 libsqlite3-0 libssl1.0.0 libtasn1-3 libudev0 libwind0-heimdal linux-libc-dev login lsb-base make mountall multiarch-support openssl passwd perl perl-base perl-modules plymouth python-minimal python2.7-minimal sysv-rc sysvinit-utils tzdata ubuntu-keyring udev upstart 74 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 41.7 MB of archives. After this operation, 74.8 kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! base-files bash dpkg coreutils login perl perl-base perl-modules sysv-rc plymouth libplymouth2 initramfs-tools-bin initramfs-tools mountall initscripts upstart libc-dev-bin libc6-dev libc-bin libc6 sysvinit-utils libdbus-1-3 libdrm2 libpciaccess0 libdrm-intel1 libdrm-nouveau1a libdrm-radeon1 libglib2.0-0 libudev0 busybox-initramfs udev libnih-dbus1 libnih1 lsb-base passwd ifupdown linux-libc-dev tzdata libssl1.0.0 python2.7-minimal python-minimal libapt-pkg4.12 ubuntu-keyring gpgv gnupg apt libsqlite3-0 libroken18-heimdal libasn1-8-heimdal libgcrypt11 libtasn1-3 libgnutls26 libk5crypto3 libgssapi-krb5-2 libkrb5-3 libkrb5support0 libhcrypto4-heimdal libheimbase1-heimdal libwind0-heimdal libhx509-5-heimdal libkrb5-26-heimdal libheimntlm0-heimdal libgssapi3-heimdal libsasl2-2 libldap-2.4-2 libcurl3-gnutls multiarch-support apt-transport-https openssl binutils make dpkg-dev libdpkg-perl build-essential Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ precise-updates/main base-files i386 6.5ubuntu6.6 [65.8 kB] Get:2 http://ftpmaster.internal/ubuntu/ precise-updates/main bash i386 4.2-2ubuntu2.1 [616 kB] Get:3 http://ftpmaster.internal/ubuntu/ precise-updates/main dpkg i386 1.16.1.2ubuntu7.1 [1815 kB] Get:4 http://ftpmaster.internal/ubuntu/ precise-updates/main coreutils i386 8.13-3ubuntu3.2 [2181 kB] Get:5 http://ftpmaster.internal/ubuntu/ precise-updates/main login i386 1:4.1.4.2+svn3283-3ubuntu5.1 [286 kB] Get:6 http://ftpmaster.internal/ubuntu/ precise-security/main perl i386 5.14.2-6ubuntu2.3 [3697 kB] Get:7 http://ftpmaster.internal/ubuntu/ precise-security/main perl-base i386 5.14.2-6ubuntu2.3 [1471 kB] Get:8 http://ftpmaster.internal/ubuntu/ precise-security/main perl-modules all 5.14.2-6ubuntu2.3 [3389 kB] Get:9 http://ftpmaster.internal/ubuntu/ precise-updates/main sysv-rc all 2.88dsf-13.10ubuntu11.1 [44.6 kB] Get:10 http://ftpmaster.internal/ubuntu/ precise-updates/main plymouth i386 0.8.2-2ubuntu31.1 [125 kB] Get:11 http://ftpmaster.internal/ubuntu/ precise-updates/main libplymouth2 i386 0.8.2-2ubuntu31.1 [91.9 kB] Get:12 http://ftpmaster.internal/ubuntu/ precise-updates/main initramfs-tools-bin i386 0.99ubuntu13.2 [9758 B] Get:13 http://ftpmaster.internal/ubuntu/ precise-updates/main initramfs-tools all 0.99ubuntu13.2 [49.2 kB] Get:14 http://ftpmaster.internal/ubuntu/ precise-updates/main mountall i386 2.36.4 [70.2 kB] Get:15 http://ftpmaster.internal/ubuntu/ precise-updates/main initscripts i386 2.88dsf-13.10ubuntu11.1 [28.1 kB] Get:16 http://ftpmaster.internal/ubuntu/ precise-updates/main upstart i386 1.5-0ubuntu7.2 [313 kB] Get:17 http://ftpmaster.internal/ubuntu/ precise-updates/main libc-dev-bin i386 2.15-0ubuntu10.4 [77.7 kB] Get:18 http://ftpmaster.internal/ubuntu/ precise-updates/main libc6-dev i386 2.15-0ubuntu10.4 [5098 kB] Get:19 http://ftpmaster.internal/ubuntu/ precise-updates/main libc-bin i386 2.15-0ubuntu10.4 [1131 kB] Get:20 http://ftpmaster.internal/ubuntu/ precise-updates/main libc6 i386 2.15-0ubuntu10.4 [3941 kB] Get:21 http://ftpmaster.internal/ubuntu/ precise-updates/main sysvinit-utils i386 2.88dsf-13.10ubuntu11.1 [58.4 kB] Get:22 http://ftpmaster.internal/ubuntu/ precise-security/main libdbus-1-3 i386 1.4.18-1ubuntu1.4 [148 kB] Get:23 http://ftpmaster.internal/ubuntu/ precise-updates/main libdrm2 i386 2.4.43-0ubuntu0.0.2 [27.6 kB] Get:24 http://ftpmaster.internal/ubuntu/ precise-updates/main libpciaccess0 i386 0.12.902-1ubuntu0.2 [22.5 kB] Get:25 http://ftpmaster.internal/ubuntu/ precise-updates/main libdrm-intel1 i386 2.4.43-0ubuntu0.0.2 [64.9 kB] Get:26 http://ftpmaster.internal/ubuntu/ precise-updates/main libdrm-nouveau1a i386 2.4.43-0ubuntu0.0.2 [14.2 kB] Get:27 http://ftpmaster.internal/ubuntu/ precise-updates/main libdrm-radeon1 i386 2.4.43-0ubuntu0.0.2 [24.7 kB] Get:28 http://ftpmaster.internal/ubuntu/ precise-updates/main libglib2.0-0 i386 2.32.3-0ubuntu1 [1187 kB] Get:29 http://ftpmaster.internal/ubuntu/ precise-updates/main libudev0 i386 175-0ubuntu9.4 [32.3 kB] Get:30 http://ftpmaster.internal/ubuntu/ precise-updates/main busybox-initramfs i386 1:1.18.5-1ubuntu4.1 [172 kB] Get:31 http://ftpmaster.internal/ubuntu/ precise-updates/main udev i386 175-0ubuntu9.4 [350 kB] Get:32 http://ftpmaster.internal/ubuntu/ precise-updates/main libnih-dbus1 i386 1.0.3-4ubuntu9.1 [15.4 kB] Get:33 http://ftpmaster.internal/ubuntu/ precise-updates/main libnih1 i386 1.0.3-4ubuntu9.1 [53.7 kB] Get:34 http://ftpmaster.internal/ubuntu/ precise-updates/main lsb-base all 4.0-0ubuntu20.3 [10.5 kB] Get:35 http://ftpmaster.internal/ubuntu/ precise-updates/main passwd i386 1:4.1.4.2+svn3283-3ubuntu5.1 [940 kB] Get:36 http://ftpmaster.internal/ubuntu/ precise-updates/main ifupdown i386 0.7~beta2ubuntu10 [48.8 kB] Get:37 http://ftpmaster.internal/ubuntu/ precise-security/main linux-libc-dev i386 3.2.0-54.82 [858 kB] Get:38 http://ftpmaster.internal/ubuntu/ precise-updates/main tzdata all 2013d-0ubuntu0.12.04 [483 kB] Get:39 http://ftpmaster.internal/ubuntu/ precise-security/main libssl1.0.0 i386 1.0.1-4ubuntu5.10 [1008 kB] Get:40 http://ftpmaster.internal/ubuntu/ precise-security/main python2.7-minimal i386 2.7.3-0ubuntu3.4 [1690 kB] Get:41 http://ftpmaster.internal/ubuntu/ precise-updates/main python-minimal i386 2.7.3-0ubuntu2.2 [29.2 kB] Get:42 http://ftpmaster.internal/ubuntu/ precise-updates/main libapt-pkg4.12 i386 0.8.16~exp12ubuntu10.14 [944 kB] Get:43 http://ftpmaster.internal/ubuntu/ precise-updates/main ubuntu-keyring all 2011.11.21.1 [16.7 kB] Get:44 http://ftpmaster.internal/ubuntu/ precise-security/main gpgv i386 1.4.11-3ubuntu2.3 [179 kB] Get:45 http://ftpmaster.internal/ubuntu/ precise-security/main gnupg i386 1.4.11-3ubuntu2.3 [789 kB] Get:46 http://ftpmaster.internal/ubuntu/ precise-updates/main apt i386 0.8.16~exp12ubuntu10.14 [1096 kB] Get:47 http://ftpmaster.internal/ubuntu/ precise-updates/main libsqlite3-0 i386 3.7.9-2ubuntu1.1 [354 kB] Get:48 http://ftpmaster.internal/ubuntu/ precise-updates/main libroken18-heimdal i386 1.6~git20120311.dfsg.1-2ubuntu0.1 [47.5 kB] Get:49 http://ftpmaster.internal/ubuntu/ precise-updates/main libasn1-8-heimdal i386 1.6~git20120311.dfsg.1-2ubuntu0.1 [242 kB] Get:50 http://ftpmaster.internal/ubuntu/ precise-security/main libgcrypt11 i386 1.5.0-3ubuntu0.2 [281 kB] Get:51 http://ftpmaster.internal/ubuntu/ precise-security/main libtasn1-3 i386 2.10-1ubuntu1.1 [43.8 kB] Get:52 http://ftpmaster.internal/ubuntu/ precise-updates/main libgnutls26 i386 2.12.14-5ubuntu3.5 [448 kB] Get:53 http://ftpmaster.internal/ubuntu/ precise-security/main libk5crypto3 i386 1.10+dfsg~beta1-2ubuntu0.3 [77.4 kB] Get:54 http://ftpmaster.internal/ubuntu/ precise-security/main libgssapi-krb5-2 i386 1.10+dfsg~beta1-2ubuntu0.3 [120 kB] Get:55 http://ftpmaster.internal/ubuntu/ precise-security/main libkrb5-3 i386 1.10+dfsg~beta1-2ubuntu0.3 [366 kB] Get:56 http://ftpmaster.internal/ubuntu/ precise-security/main libkrb5support0 i386 1.10+dfsg~beta1-2ubuntu0.3 [23.9 kB] Get:57 http://ftpmaster.internal/ubuntu/ precise-updates/main libhcrypto4-heimdal i386 1.6~git20120311.dfsg.1-2ubuntu0.1 [104 kB] Get:58 http://ftpmaster.internal/ubuntu/ precise-updates/main libheimbase1-heimdal i386 1.6~git20120311.dfsg.1-2ubuntu0.1 [33.3 kB] Get:59 http://ftpmaster.internal/ubuntu/ precise-updates/main libwind0-heimdal i386 1.6~git20120311.dfsg.1-2ubuntu0.1 [77.8 kB] Get:60 http://ftpmaster.internal/ubuntu/ precise-updates/main libhx509-5-heimdal i386 1.6~git20120311.dfsg.1-2ubuntu0.1 [127 kB] Get:61 http://ftpmaster.internal/ubuntu/ precise-updates/main libkrb5-26-heimdal i386 1.6~git20120311.dfsg.1-2ubuntu0.1 [240 kB] Get:62 http://ftpmaster.internal/ubuntu/ precise-updates/main libheimntlm0-heimdal i386 1.6~git20120311.dfsg.1-2ubuntu0.1 [16.8 kB] Get:63 http://ftpmaster.internal/ubuntu/ precise-updates/main libgssapi3-heimdal i386 1.6~git20120311.dfsg.1-2ubuntu0.1 [112 kB] Get:64 http://ftpmaster.internal/ubuntu/ precise-updates/main libsasl2-2 i386 2.1.25.dfsg1-3ubuntu0.1 [69.0 kB] Get:65 http://ftpmaster.internal/ubuntu/ precise-updates/main libldap-2.4-2 i386 2.4.28-1.1ubuntu4.4 [185 kB] Get:66 http://ftpmaster.internal/ubuntu/ precise-updates/main libcurl3-gnutls i386 7.22.0-3ubuntu4.3 [232 kB] Get:67 http://ftpmaster.internal/ubuntu/ precise-updates/main multiarch-support i386 2.15-0ubuntu10.4 [4482 B] Get:68 http://ftpmaster.internal/ubuntu/ precise-updates/main apt-transport-https i386 0.8.16~exp12ubuntu10.14 [16.3 kB] Get:69 http://ftpmaster.internal/ubuntu/ precise-security/main openssl i386 1.0.1-4ubuntu5.10 [520 kB] Get:70 http://ftpmaster.internal/ubuntu/ precise-security/main binutils i386 2.22-6ubuntu1.1 [2387 kB] Get:71 http://ftpmaster.internal/ubuntu/ precise-updates/main make i386 3.81-8.1ubuntu1.1 [116 kB] Get:72 http://ftpmaster.internal/ubuntu/ precise-updates/main dpkg-dev all 1.16.1.2ubuntu7.1 [469 kB] Get:73 http://ftpmaster.internal/ubuntu/ precise-updates/main libdpkg-perl all 1.16.1.2ubuntu7.1 [180 kB] Get:74 http://ftpmaster.internal/ubuntu/ precise-updates/main build-essential i386 11.5ubuntu2.1 [5796 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 41.7 MB in 4s (10.3 MB/s) (Reading database ... 12281 files and directories currently installed.) Preparing to replace base-files 6.5ubuntu6 (using .../base-files_6.5ubuntu6.6_i386.deb) ... Unpacking replacement base-files ... Setting up base-files (6.5ubuntu6.6) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... (Reading database ... 12282 files and directories currently installed.) Preparing to replace bash 4.2-2ubuntu2 (using .../bash_4.2-2ubuntu2.1_i386.deb) ... Unpacking replacement bash ... Setting up bash (4.2-2ubuntu2.1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode. (Reading database ... 12282 files and directories currently installed.) Preparing to replace dpkg 1.16.1.2ubuntu7 (using .../dpkg_1.16.1.2ubuntu7.1_i386.deb) ... Unpacking replacement dpkg ... Setting up dpkg (1.16.1.2ubuntu7.1) ... (Reading database ... 12283 files and directories currently installed.) Preparing to replace coreutils 8.13-3ubuntu3 (using .../coreutils_8.13-3ubuntu3.2_i386.deb) ... Unpacking replacement coreutils ... Setting up coreutils (8.13-3ubuntu3.2) ... (Reading database ... 12283 files and directories currently installed.) Preparing to replace login 1:4.1.4.2+svn3283-3ubuntu5 (using .../login_1%3a4.1.4.2+svn3283-3ubuntu5.1_i386.deb) ... Unpacking replacement login ... Setting up login (1:4.1.4.2+svn3283-3ubuntu5.1) ... (Reading database ... 12283 files and directories currently installed.) Preparing to replace perl 5.14.2-6ubuntu2 (using .../perl_5.14.2-6ubuntu2.3_i386.deb) ... Unpacking replacement perl ... Preparing to replace perl-base 5.14.2-6ubuntu2 (using .../perl-base_5.14.2-6ubuntu2.3_i386.deb) ... Unpacking replacement perl-base ... Setting up perl-base (5.14.2-6ubuntu2.3) ... (Reading database ... 12283 files and directories currently installed.) Preparing to replace perl-modules 5.14.2-6ubuntu2 (using .../perl-modules_5.14.2-6ubuntu2.3_all.deb) ... Unpacking replacement perl-modules ... Preparing to replace sysv-rc 2.88dsf-13.10ubuntu11 (using .../sysv-rc_2.88dsf-13.10ubuntu11.1_all.deb) ... Unpacking replacement sysv-rc ... Preparing to replace plymouth 0.8.2-2ubuntu30 (using .../plymouth_0.8.2-2ubuntu31.1_i386.deb) ... Unpacking replacement plymouth ... Preparing to replace libplymouth2 0.8.2-2ubuntu30 (using .../libplymouth2_0.8.2-2ubuntu31.1_i386.deb) ... Unpacking replacement libplymouth2 ... Preparing to replace initramfs-tools-bin 0.99ubuntu13 (using .../initramfs-tools-bin_0.99ubuntu13.2_i386.deb) ... Unpacking replacement initramfs-tools-bin ... Preparing to replace initramfs-tools 0.99ubuntu13 (using .../initramfs-tools_0.99ubuntu13.2_all.deb) ... Unpacking replacement initramfs-tools ... Preparing to replace mountall 2.36 (using .../mountall_2.36.4_i386.deb) ... Unpacking replacement mountall ... Preparing to replace initscripts 2.88dsf-13.10ubuntu11 (using .../initscripts_2.88dsf-13.10ubuntu11.1_i386.deb) ... Unpacking replacement initscripts ... Preparing to replace upstart 1.5-0ubuntu5 (using .../upstart_1.5-0ubuntu7.2_i386.deb) ... Unpacking replacement upstart ... Preparing to replace libc-dev-bin 2.15-0ubuntu10 (using .../libc-dev-bin_2.15-0ubuntu10.4_i386.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libc6-dev 2.15-0ubuntu10 (using .../libc6-dev_2.15-0ubuntu10.4_i386.deb) ... Unpacking replacement libc6-dev ... Preparing to replace libc-bin 2.15-0ubuntu10 (using .../libc-bin_2.15-0ubuntu10.4_i386.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.15-0ubuntu10.4) ... (Reading database ... 12283 files and directories currently installed.) Preparing to replace libc6 2.15-0ubuntu10 (using .../libc6_2.15-0ubuntu10.4_i386.deb) ... Unpacking replacement libc6 ... Setting up libc6 (2.15-0ubuntu10.4) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12283 files and directories currently installed.) Preparing to replace sysvinit-utils 2.88dsf-13.10ubuntu11 (using .../sysvinit-utils_2.88dsf-13.10ubuntu11.1_i386.deb) ... Unpacking replacement sysvinit-utils ... Preparing to replace libdbus-1-3 1.4.18-1ubuntu1 (using .../libdbus-1-3_1.4.18-1ubuntu1.4_i386.deb) ... Unpacking replacement libdbus-1-3 ... Preparing to replace libdrm2 2.4.32-1ubuntu1 (using .../libdrm2_2.4.43-0ubuntu0.0.2_i386.deb) ... Unpacking replacement libdrm2 ... Preparing to replace libpciaccess0 0.12.902-1 (using .../libpciaccess0_0.12.902-1ubuntu0.2_i386.deb) ... Unpacking replacement libpciaccess0 ... Preparing to replace libdrm-intel1 2.4.32-1ubuntu1 (using .../libdrm-intel1_2.4.43-0ubuntu0.0.2_i386.deb) ... Unpacking replacement libdrm-intel1 ... 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No schema files found: doing nothing. Setting up initramfs-tools-bin (0.99ubuntu13.2) ... Setting up busybox-initramfs (1:1.18.5-1ubuntu4.1) ... Setting up libdrm2 (2.4.43-0ubuntu0.0.2) ... Setting up libpciaccess0 (0.12.902-1ubuntu0.2) ... Setting up libdrm-intel1 (2.4.43-0ubuntu0.0.2) ... Setting up libdrm-nouveau1a (2.4.43-0ubuntu0.0.2) ... Setting up libdrm-radeon1 (2.4.43-0ubuntu0.0.2) ... Setting up libplymouth2 (0.8.2-2ubuntu31.1) ... Setting up upstart (1.5-0ubuntu7.2) ... Installing new version of config file /etc/logrotate.d/upstart ... Setting up passwd (1:4.1.4.2+svn3283-3ubuntu5.1) ... Setting up initramfs-tools (0.99ubuntu13.2) ... update-initramfs: deferring update (trigger activated) Setting up udev (175-0ubuntu9.4) ... invoke-rc.d: policy-rc.d denied execution of restart. Removing 'diversion of /sbin/udevadm to /sbin/udevadm.upgrade by fake-udev' update-initramfs: deferring update (trigger activated) Setting up plymouth (0.8.2-2ubuntu31.1) ... update-initramfs: deferring update (trigger activated) Setting up mountall (2.36.4) ... Setting up initscripts (2.88dsf-13.10ubuntu11.1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Processing triggers for initramfs-tools ... (Reading database ... 12292 files and directories currently installed.) Preparing to replace ifupdown 0.7~beta2ubuntu8 (using .../ifupdown_0.7~beta2ubuntu10_i386.deb) ... Unpacking replacement ifupdown ... Preparing to replace linux-libc-dev 3.2.0-23.36 (using .../linux-libc-dev_3.2.0-54.82_i386.deb) ... Unpacking replacement linux-libc-dev ... Preparing to replace tzdata 2012b-1 (using .../tzdata_2013d-0ubuntu0.12.04_all.deb) ... Unpacking replacement tzdata ... Setting up tzdata (2013d-0ubuntu0.12.04) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Oct 8 15:55:52 UTC 2013. Universal Time is now: Tue Oct 8 15:55:52 UTC 2013. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 12303 files and directories currently installed.) Preparing to replace libssl1.0.0 1.0.1-4ubuntu3 (using .../libssl1.0.0_1.0.1-4ubuntu5.10_i386.deb) ... Unpacking replacement libssl1.0.0 ... Setting up libssl1.0.0 (1.0.1-4ubuntu5.10) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12303 files and directories currently installed.) Preparing to replace python2.7-minimal 2.7.3-0ubuntu3 (using .../python2.7-minimal_2.7.3-0ubuntu3.4_i386.deb) ... Unpacking replacement python2.7-minimal ... Setting up python2.7-minimal (2.7.3-0ubuntu3.4) ... (Reading database ... 12303 files and directories currently installed.) Preparing to replace python-minimal 2.7.3-0ubuntu2 (using .../python-minimal_2.7.3-0ubuntu2.2_i386.deb) ... Unpacking replacement python-minimal ... Setting up python-minimal (2.7.3-0ubuntu2.2) ... (Reading database ... 12303 files and directories currently installed.) Preparing to replace libapt-pkg4.12 0.8.16~exp12ubuntu10 (using .../libapt-pkg4.12_0.8.16~exp12ubuntu10.14_i386.deb) ... Unpacking replacement libapt-pkg4.12 ... Setting up libapt-pkg4.12 (0.8.16~exp12ubuntu10.14) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12303 files and directories currently installed.) Preparing to replace ubuntu-keyring 2011.11.21 (using .../ubuntu-keyring_2011.11.21.1_all.deb) ... Unpacking replacement ubuntu-keyring ... Setting up ubuntu-keyring (2011.11.21.1) ... gpg: key 437D05B5: "Ubuntu Archive Automatic Signing Key " not changed gpg: key FBB75451: "Ubuntu CD Image Automatic Signing Key " not changed gpg: key C0B21F32: public key "Ubuntu Archive Automatic Signing Key (2012) " imported gpg: key EFE21092: public key "Ubuntu CD Image Automatic Signing Key (2012) " imported gpg: Total number processed: 4 gpg: imported: 2 (RSA: 2) gpg: unchanged: 2 gpg: no ultimately trusted keys found (Reading database ... 12303 files and directories currently installed.) Preparing to replace gpgv 1.4.11-3ubuntu2 (using .../gpgv_1.4.11-3ubuntu2.3_i386.deb) ... Unpacking replacement gpgv ... Setting up gpgv (1.4.11-3ubuntu2.3) ... (Reading database ... 12303 files and directories currently installed.) Preparing to replace gnupg 1.4.11-3ubuntu2 (using .../gnupg_1.4.11-3ubuntu2.3_i386.deb) ... Unpacking replacement gnupg ... Setting up gnupg (1.4.11-3ubuntu2.3) ... (Reading database ... 12303 files and directories currently installed.) Preparing to replace apt 0.8.16~exp12ubuntu10 (using .../apt_0.8.16~exp12ubuntu10.14_i386.deb) ... Unpacking replacement apt ... Setting up apt (0.8.16~exp12ubuntu10.14) ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... gpg: key 437D05B5: "Ubuntu Archive Automatic Signing Key " not changed gpg: key FBB75451: "Ubuntu CD Image Automatic Signing Key " not changed gpg: key C0B21F32: "Ubuntu Archive Automatic Signing Key (2012) " not changed gpg: key EFE21092: "Ubuntu CD Image Automatic Signing Key (2012) " not changed gpg: Total number processed: 4 gpg: unchanged: 4 No packages found matching linux-image-[0-9]*. (Reading database ... 12304 files and directories currently installed.) Preparing to replace libsqlite3-0 3.7.9-2ubuntu1 (using .../libsqlite3-0_3.7.9-2ubuntu1.1_i386.deb) ... Unpacking replacement libsqlite3-0 ... 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Preparing to replace libwind0-heimdal 1.6~git20120311.dfsg.1-2 (using .../libwind0-heimdal_1.6~git20120311.dfsg.1-2ubuntu0.1_i386.deb) ... Unpacking replacement libwind0-heimdal ... Preparing to replace libhx509-5-heimdal 1.6~git20120311.dfsg.1-2 (using .../libhx509-5-heimdal_1.6~git20120311.dfsg.1-2ubuntu0.1_i386.deb) ... Unpacking replacement libhx509-5-heimdal ... Preparing to replace libkrb5-26-heimdal 1.6~git20120311.dfsg.1-2 (using .../libkrb5-26-heimdal_1.6~git20120311.dfsg.1-2ubuntu0.1_i386.deb) ... Unpacking replacement libkrb5-26-heimdal ... Preparing to replace libheimntlm0-heimdal 1.6~git20120311.dfsg.1-2 (using .../libheimntlm0-heimdal_1.6~git20120311.dfsg.1-2ubuntu0.1_i386.deb) ... Unpacking replacement libheimntlm0-heimdal ... Preparing to replace libgssapi3-heimdal 1.6~git20120311.dfsg.1-2 (using .../libgssapi3-heimdal_1.6~git20120311.dfsg.1-2ubuntu0.1_i386.deb) ... Unpacking replacement libgssapi3-heimdal ... 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Setting up libsqlite3-0 (3.7.9-2ubuntu1.1) ... Setting up libroken18-heimdal (1.6~git20120311.dfsg.1-2ubuntu0.1) ... Setting up libasn1-8-heimdal (1.6~git20120311.dfsg.1-2ubuntu0.1) ... Setting up libgcrypt11 (1.5.0-3ubuntu0.2) ... Setting up libtasn1-3 (2.10-1ubuntu1.1) ... Setting up libgnutls26 (2.12.14-5ubuntu3.5) ... Setting up libkrb5support0 (1.10+dfsg~beta1-2ubuntu0.3) ... Setting up libk5crypto3 (1.10+dfsg~beta1-2ubuntu0.3) ... Setting up libkrb5-3 (1.10+dfsg~beta1-2ubuntu0.3) ... Setting up libgssapi-krb5-2 (1.10+dfsg~beta1-2ubuntu0.3) ... Setting up libhcrypto4-heimdal (1.6~git20120311.dfsg.1-2ubuntu0.1) ... Setting up libheimbase1-heimdal (1.6~git20120311.dfsg.1-2ubuntu0.1) ... Setting up libwind0-heimdal (1.6~git20120311.dfsg.1-2ubuntu0.1) ... Setting up libhx509-5-heimdal (1.6~git20120311.dfsg.1-2ubuntu0.1) ... Setting up libkrb5-26-heimdal (1.6~git20120311.dfsg.1-2ubuntu0.1) ... Setting up libheimntlm0-heimdal (1.6~git20120311.dfsg.1-2ubuntu0.1) ... 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Processing triggers for libc-bin ... ldconfig deferred processing now taking place RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-5085631', 'i386', 'precise', '--nolog', '--batch', '--archive=ubuntu', '--dist=precise', '-A', '--purpose=PPA', '--architecture=i386', '--comp=main', 'python-cogent_1.5.3-1biolinux1.dsc'] Initiating build PACKAGEBUILD-5085631 with 1 jobs across 1 processor cores. Kernel reported to sbuild: 2.6.24-32-xen #1 SMP Mon Dec 3 16:12:25 UTC 2012 i686 Automatic build of python-cogent_1.5.3-1biolinux1 on gumiho by sbuild/i386 1.170.5 Build started at 20131008-1557 ****************************************************************************** python-cogent_1.5.3-1biolinux1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 8), python-all-dev (>= 2.6), python-support, python-numpy (>= 1.3.0), python-sphinx, cython Checking for already installed source dependencies... debhelper: missing python-all-dev: missing python-support: missing python-numpy: missing python-sphinx: missing cython: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper python-all-dev python-support python-numpy python-sphinx cython Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils dh-apparmor docutils-common file gettext gettext-base groff-base html2text intltool-debian libblas3gf libcroco3 libexpat1 libexpat1-dev libgettextpo0 libgfortran3 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3gf libmagic1 libpipeline1 libpython2.7 libssl-dev libunistring0 libxml2 man-db mime-support po-debconf python python-all python-dev python-docutils python-jinja2 python-markupsafe python-pygments python-roman python2.7 python2.7-dev sgml-base sphinx-common xml-core zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff javascript-common less www-browser libmail-box-perl python-doc python-tk texlive-latex-recommended texlive-latex-base texlive-lang-french ttf-linux-libertine python-jinja2-doc python-numpy-doc python-numpy-dbg python-nose gfortran ttf-bitstream-vera jsmath libjs-mathjax texlive-latex-extra texlive-fonts-recommended python2.7-doc sgml-base-doc Recommended packages: curl wget lynx-cur libssl-doc libmail-sendmail-perl python-imaging libpaper-utils python-lxml docutils-doc python-pkg-resources python-chardet sphinx-doc The following NEW packages will be installed: bsdmainutils cython debhelper dh-apparmor docutils-common file gettext gettext-base groff-base html2text intltool-debian libblas3gf libcroco3 libexpat1 libexpat1-dev libgettextpo0 libgfortran3 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3gf libmagic1 libpipeline1 libpython2.7 libssl-dev libunistring0 libxml2 man-db mime-support po-debconf python python-all python-all-dev python-dev python-docutils python-jinja2 python-markupsafe python-numpy python-pygments python-roman python-sphinx python-support python2.7 python2.7-dev sgml-base sphinx-common xml-core zlib1g-dev 0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded. Need to get 49.7 MB of archives. After this operation, 105 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libxml2 libcroco3 libexpat1 libunistring0 libgettextpo0 libgfortran3 libmagic1 file mime-support python2.7 python bsdmainutils gettext-base groff-base man-db sgml-base xml-core python-support cython html2text gettext intltool-debian po-debconf dh-apparmor debhelper docutils-common libblas3gf libexpat1-dev libjs-jquery libjs-underscore libjs-sphinxdoc liblapack3gf libpython2.7 zlib1g-dev libssl-dev python-all python2.7-dev python-dev python-all-dev python-roman python-docutils python-markupsafe python-jinja2 python-numpy python-pygments sphinx-common python-sphinx Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ precise/main libpipeline1 i386 1.2.1-1 [26.1 kB] Get:2 http://ftpmaster.internal/ubuntu/ precise-security/main libxml2 i386 2.7.8.dfsg-5.1ubuntu4.6 [662 kB] Get:3 http://ftpmaster.internal/ubuntu/ precise-updates/main libcroco3 i386 0.6.5-1ubuntu0.1 [100 kB] Get:4 http://ftpmaster.internal/ubuntu/ precise-security/main libexpat1 i386 2.0.1-7.2ubuntu1.1 [130 kB] Get:5 http://ftpmaster.internal/ubuntu/ precise/main libunistring0 i386 0.9.3-5 [432 kB] Get:6 http://ftpmaster.internal/ubuntu/ precise/main libgettextpo0 i386 0.18.1.1-5ubuntu3 [118 kB] Get:7 http://ftpmaster.internal/ubuntu/ precise/main libgfortran3 i386 4.6.3-1ubuntu5 [355 kB] Get:8 http://ftpmaster.internal/ubuntu/ precise/main libmagic1 i386 5.09-2 [219 kB] Get:9 http://ftpmaster.internal/ubuntu/ precise/main file i386 5.09-2 [19.4 kB] Get:10 http://ftpmaster.internal/ubuntu/ precise/main mime-support all 3.51-1ubuntu1 [30.7 kB] Get:11 http://ftpmaster.internal/ubuntu/ precise-security/main python2.7 i386 2.7.3-0ubuntu3.4 [2647 kB] Get:12 http://ftpmaster.internal/ubuntu/ precise-updates/main python i386 2.7.3-0ubuntu2.2 [166 kB] Get:13 http://ftpmaster.internal/ubuntu/ precise/main bsdmainutils i386 8.2.3ubuntu1 [194 kB] Get:14 http://ftpmaster.internal/ubuntu/ precise/main gettext-base i386 0.18.1.1-5ubuntu3 [58.2 kB] Get:15 http://ftpmaster.internal/ubuntu/ precise/main groff-base i386 1.21-7 [1024 kB] Get:16 http://ftpmaster.internal/ubuntu/ precise-updates/main man-db i386 2.6.1-2ubuntu1 [742 kB] Get:17 http://ftpmaster.internal/ubuntu/ precise/main sgml-base all 1.26+nmu1ubuntu1 [8360 B] Get:18 http://ftpmaster.internal/ubuntu/ precise/main xml-core all 0.13 [23.4 kB] Get:19 http://ftpmaster.internal/ubuntu/ precise/universe python-support all 1.0.14ubuntu2 [26.1 kB] Get:20 http://ftpmaster.internal/ubuntu/ precise/universe cython i386 0.15.1-1ubuntu1 [1162 kB] Get:21 http://ftpmaster.internal/ubuntu/ precise/main html2text i386 1.3.2a-15 [101 kB] Get:22 http://ftpmaster.internal/ubuntu/ precise/main gettext i386 0.18.1.1-5ubuntu3 [1122 kB] Get:23 http://ftpmaster.internal/ubuntu/ precise/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:24 http://ftpmaster.internal/ubuntu/ precise/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:25 http://ftpmaster.internal/ubuntu/ precise-updates/main dh-apparmor all 2.7.102-0ubuntu3.9 [8950 B] Get:26 http://ftpmaster.internal/ubuntu/ precise/main debhelper all 9.20120115ubuntu3 [616 kB] Get:27 http://ftpmaster.internal/ubuntu/ precise/main docutils-common all 0.8.1-4ubuntu1 [153 kB] Get:28 http://ftpmaster.internal/ubuntu/ precise/main libblas3gf i386 1.2.20110419-2ubuntu1 [204 kB] Get:29 http://ftpmaster.internal/ubuntu/ precise-security/main libexpat1-dev i386 2.0.1-7.2ubuntu1.1 [208 kB] Get:30 http://ftpmaster.internal/ubuntu/ precise/main libjs-jquery all 1.7.1-1ubuntu1 [111 kB] Get:31 http://ftpmaster.internal/ubuntu/ precise/main libjs-underscore all 1.1.6-1ubuntu2 [31.3 kB] Get:32 http://ftpmaster.internal/ubuntu/ precise-updates/main libjs-sphinxdoc all 1.1.3+dfsg-2ubuntu2.1 [45.1 kB] Get:33 http://ftpmaster.internal/ubuntu/ precise/main liblapack3gf i386 3.3.1-1 [3209 kB] Get:34 http://ftpmaster.internal/ubuntu/ precise-security/main libpython2.7 i386 2.7.3-0ubuntu3.4 [1148 kB] Get:35 http://ftpmaster.internal/ubuntu/ precise/main zlib1g-dev i386 1:1.2.3.4.dfsg-3ubuntu4 [162 kB] Get:36 http://ftpmaster.internal/ubuntu/ precise-security/main libssl-dev i386 1.0.1-4ubuntu5.10 [1422 kB] Get:37 http://ftpmaster.internal/ubuntu/ precise-updates/main python-all i386 2.7.3-0ubuntu2.2 [912 B] Get:38 http://ftpmaster.internal/ubuntu/ precise-security/main python2.7-dev i386 2.7.3-0ubuntu3.4 [29.3 MB] Get:39 http://ftpmaster.internal/ubuntu/ precise-updates/main python-dev i386 2.7.3-0ubuntu2.2 [1098 B] Get:40 http://ftpmaster.internal/ubuntu/ precise-updates/main python-all-dev i386 2.7.3-0ubuntu2.2 [926 B] Get:41 http://ftpmaster.internal/ubuntu/ precise/main python-roman all 0.8.1-4ubuntu1 [12.6 kB] Get:42 http://ftpmaster.internal/ubuntu/ precise/main python-docutils all 0.8.1-4ubuntu1 [382 kB] Get:43 http://ftpmaster.internal/ubuntu/ precise/main python-markupsafe i386 0.15-1 [13.6 kB] Get:44 http://ftpmaster.internal/ubuntu/ precise/main python-jinja2 i386 2.6-1 [158 kB] Get:45 http://ftpmaster.internal/ubuntu/ precise/main python-numpy i386 1:1.6.1-6ubuntu1 [1839 kB] Get:46 http://ftpmaster.internal/ubuntu/ precise/main python-pygments all 1.4+dfsg-2 [353 kB] Get:47 http://ftpmaster.internal/ubuntu/ precise-updates/main sphinx-common all 1.1.3+dfsg-2ubuntu2.1 [412 kB] Get:48 http://ftpmaster.internal/ubuntu/ precise-updates/main python-sphinx all 1.1.3+dfsg-2ubuntu2.1 [312 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 49.7 MB in 2s (17.6 MB/s) Selecting previously unselected package libpipeline1. (Reading database ... 12304 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_i386.deb) ... Selecting previously unselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1ubuntu4.6_i386.deb) ... Selecting previously unselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.5-1ubuntu0.1_i386.deb) ... Selecting previously unselected package libexpat1. Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2ubuntu1.1_i386.deb) ... Selecting previously unselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-5_i386.deb) ... Selecting previously unselected package libgettextpo0. Unpacking libgettextpo0 (from .../libgettextpo0_0.18.1.1-5ubuntu3_i386.deb) ... Selecting previously unselected package libgfortran3. Unpacking libgfortran3 (from .../libgfortran3_4.6.3-1ubuntu5_i386.deb) ... Selecting previously unselected package libmagic1. 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Selecting previously unselected package sphinx-common. Unpacking sphinx-common (from .../sphinx-common_1.1.3+dfsg-2ubuntu2.1_all.deb) ... Selecting previously unselected package python-sphinx. Unpacking python-sphinx (from .../python-sphinx_1.1.3+dfsg-2ubuntu2.1_all.deb) ... Setting up libpipeline1 (1.2.1-1) ... Setting up libxml2 (2.7.8.dfsg-5.1ubuntu4.6) ... Setting up libcroco3 (0.6.5-1ubuntu0.1) ... Setting up libexpat1 (2.0.1-7.2ubuntu1.1) ... Setting up libunistring0 (0.9.3-5) ... Setting up libgettextpo0 (0.18.1.1-5ubuntu3) ... Setting up libgfortran3 (4.6.3-1ubuntu5) ... Setting up libmagic1 (5.09-2) ... Setting up file (5.09-2) ... Setting up mime-support (3.51-1ubuntu1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode. Setting up python2.7 (2.7.3-0ubuntu3.4) ... Setting up python (2.7.3-0ubuntu2.2) ... Setting up bsdmainutils (8.2.3ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode. Setting up gettext-base (0.18.1.1-5ubuntu3) ... Setting up groff-base (1.21-7) ... Setting up man-db (2.6.1-2ubuntu1) ... Building database of manual pages ... Setting up sgml-base (1.26+nmu1ubuntu1) ... Setting up xml-core (0.13) ... Setting up python-support (1.0.14ubuntu2) ... Setting up cython (0.15.1-1ubuntu1) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2ubuntu1) ... Setting up dh-apparmor (2.7.102-0ubuntu3.9) ... Setting up debhelper (9.20120115ubuntu3) ... Setting up docutils-common (0.8.1-4ubuntu1) ... Setting up libblas3gf (1.2.20110419-2ubuntu1) ... update-alternatives: using /usr/lib/libblas/libblas.so.3gf to provide /usr/lib/libblas.so.3gf (libblas.so.3gf) in auto mode. Setting up libexpat1-dev (2.0.1-7.2ubuntu1.1) ... Setting up libjs-jquery (1.7.1-1ubuntu1) ... Setting up libjs-underscore (1.1.6-1ubuntu2) ... Setting up libjs-sphinxdoc (1.1.3+dfsg-2ubuntu2.1) ... Setting up liblapack3gf (3.3.1-1) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3gf to provide /usr/lib/liblapack.so.3gf (liblapack.so.3gf) in auto mode. Setting up libpython2.7 (2.7.3-0ubuntu3.4) ... Setting up zlib1g-dev (1:1.2.3.4.dfsg-3ubuntu4) ... Setting up libssl-dev (1.0.1-4ubuntu5.10) ... Setting up python-all (2.7.3-0ubuntu2.2) ... Setting up python2.7-dev (2.7.3-0ubuntu3.4) ... Setting up python-dev (2.7.3-0ubuntu2.2) ... Setting up python-all-dev (2.7.3-0ubuntu2.2) ... Setting up python-roman (0.8.1-4ubuntu1) ... Setting up python-docutils (0.8.1-4ubuntu1) ... update-alternatives: using /usr/share/docutils/scripts/python2/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode. Setting up python-markupsafe (0.15-1) ... Setting up python-jinja2 (2.6-1) ... Setting up python-numpy (1:1.6.1-6ubuntu1) ... Setting up python-pygments (1.4+dfsg-2) ... Setting up sphinx-common (1.1.3+dfsg-2ubuntu2.1) ... Setting up python-sphinx (1.1.3+dfsg-2ubuntu2.1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Processing triggers for python-support ... Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.15-0ubuntu10.4 make_3.81-8.1ubuntu1.1 dpkg-dev_1.16.1.2ubuntu7.1 gcc-4.6_4.6.3-1ubuntu5 g++-4.6_4.6.3-1ubuntu5 binutils_2.22-6ubuntu1.1 libstdc++6-4.6-dev_4.6.3-1ubuntu5 libstdc++6_4.6.3-1ubuntu5 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt gpgv: Signature made Tue Oct 8 15:47:17 2013 UTC using DSA key ID 113960C5 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./python-cogent_1.5.3-1biolinux1.dsc dpkg-source: info: extracting python-cogent in python-cogent-1.5.3 dpkg-source: info: unpacking python-cogent_1.5.3.orig.tar.gz dpkg-source: info: unpacking python-cogent_1.5.3-1biolinux1.debian.tar.gz dpkg-source: info: applying accept_newer_cdhit dpkg-source: info: applying fix_python_shebang_line.patch dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): -D_FORTIFY_SOURCE=2 dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): -Wl,-Bsymbolic-functions -Wl,-z,relro dpkg-buildpackage: source package python-cogent dpkg-buildpackage: source version 1.5.3-1biolinux1 dpkg-source --before-build python-cogent-1.5.3 dpkg-buildpackage: host architecture i386 /usr/bin/fakeroot debian/rules clean dh clean --with python2 dh_testdir dh_auto_clean running clean 'build/lib.linux-i686-2.7' does not exist -- can't clean it 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it debian/rules override_dh_clean make[1]: Entering directory `/build/buildd/python-cogent-1.5.3' #These files are rebuilt on-the-fly for f in `find -name '*.c'` ; do \ head -n 1 "$f" | grep -q '^/\* Generated by Cython' && rm "$f" ; \ done rm -rf build build-stamp rm -rf doc/_build dh_clean make[1]: Leaving directory `/build/buildd/python-cogent-1.5.3' debian/rules build dh build --with python2 dh_testdir dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory `/build/buildd/python-cogent-1.5.3' dh_auto_build running build running build_py creating build creating build/lib.linux-i686-2.7 creating build/lib.linux-i686-2.7/cogent copying cogent/__init__.py -> build/lib.linux-i686-2.7/cogent creating build/lib.linux-i686-2.7/cogent/align copying cogent/align/indel_model.py -> build/lib.linux-i686-2.7/cogent/align copying cogent/align/__init__.py -> build/lib.linux-i686-2.7/cogent/align copying cogent/align/progressive.py -> build/lib.linux-i686-2.7/cogent/align copying cogent/align/indel_positions.py -> build/lib.linux-i686-2.7/cogent/align copying cogent/align/align.py -> build/lib.linux-i686-2.7/cogent/align copying cogent/align/algorithm.py -> build/lib.linux-i686-2.7/cogent/align copying cogent/align/traceback.py -> build/lib.linux-i686-2.7/cogent/align copying cogent/align/pairwise.py -> build/lib.linux-i686-2.7/cogent/align copying cogent/align/dp_calculation.py -> build/lib.linux-i686-2.7/cogent/align copying cogent/align/pycompare.py -> build/lib.linux-i686-2.7/cogent/align creating build/lib.linux-i686-2.7/cogent/align/weights copying cogent/align/weights/__init__.py -> build/lib.linux-i686-2.7/cogent/align/weights copying cogent/align/weights/util.py -> build/lib.linux-i686-2.7/cogent/align/weights copying cogent/align/weights/methods.py -> build/lib.linux-i686-2.7/cogent/align/weights creating build/lib.linux-i686-2.7/cogent/app copying cogent/app/parsinsert.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/knetfold.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/mafft.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/rtax.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/gctmpca.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/formatdb.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/pplacer.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/__init__.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/ilm.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/dialign.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/usearch.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/rnaalifold.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/bwa.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/dynalign.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/foldalign.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/stride.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/cove.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/mfold.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/util.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/msms.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/pknotsrg.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/blast.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/rdp_classifier20.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/infernal.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/blat.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/contrafold.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/carnac.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/rdp_classifier.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/sfffile.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/muscle_v38.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/cmfinder.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/sffinfo.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/nupack.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/vienna_package.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/uclust.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/comrna.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/dotur.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/parameters.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/raxml.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/mothur.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/sfold.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/fasttree_v1.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/pfold.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/clearcut.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/consan.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/fasttree.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/rnashapes.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/muscle.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/clustalw.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/rnaview.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/cd_hit.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/raxml_v730.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/unafold.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/guppy.py -> build/lib.linux-i686-2.7/cogent/app copying cogent/app/rnaforester.py -> build/lib.linux-i686-2.7/cogent/app creating build/lib.linux-i686-2.7/cogent/cluster copying cogent/cluster/goodness_of_fit.py -> build/lib.linux-i686-2.7/cogent/cluster copying cogent/cluster/__init__.py -> build/lib.linux-i686-2.7/cogent/cluster copying cogent/cluster/approximate_mds.py -> build/lib.linux-i686-2.7/cogent/cluster copying cogent/cluster/procrustes.py -> build/lib.linux-i686-2.7/cogent/cluster copying cogent/cluster/metric_scaling.py -> build/lib.linux-i686-2.7/cogent/cluster copying cogent/cluster/nmds.py -> build/lib.linux-i686-2.7/cogent/cluster copying cogent/cluster/UPGMA.py -> build/lib.linux-i686-2.7/cogent/cluster creating build/lib.linux-i686-2.7/cogent/core copying cogent/core/bitvector.py -> build/lib.linux-i686-2.7/cogent/core copying cogent/core/sequence.py -> build/lib.linux-i686-2.7/cogent/core copying cogent/core/__init__.py -> build/lib.linux-i686-2.7/cogent/core copying cogent/core/info.py -> build/lib.linux-i686-2.7/cogent/core copying cogent/core/entity.py -> build/lib.linux-i686-2.7/cogent/core copying cogent/core/alphabet.py -> build/lib.linux-i686-2.7/cogent/core copying cogent/core/alignment.py -> build/lib.linux-i686-2.7/cogent/core copying cogent/core/usage.py -> build/lib.linux-i686-2.7/cogent/core copying cogent/core/tree.py -> build/lib.linux-i686-2.7/cogent/core copying cogent/core/genetic_code.py -> build/lib.linux-i686-2.7/cogent/core copying cogent/core/annotation.py -> build/lib.linux-i686-2.7/cogent/core copying cogent/core/moltype.py -> build/lib.linux-i686-2.7/cogent/core copying cogent/core/profile.py -> build/lib.linux-i686-2.7/cogent/core copying cogent/core/location.py -> build/lib.linux-i686-2.7/cogent/core creating build/lib.linux-i686-2.7/cogent/data copying cogent/data/__init__.py -> build/lib.linux-i686-2.7/cogent/data copying cogent/data/ligand_properties.py -> build/lib.linux-i686-2.7/cogent/data copying cogent/data/energy_params.py -> build/lib.linux-i686-2.7/cogent/data copying cogent/data/nucleic_properties.py -> build/lib.linux-i686-2.7/cogent/data copying cogent/data/molecular_weight.py -> build/lib.linux-i686-2.7/cogent/data copying cogent/data/protein_properties.py -> build/lib.linux-i686-2.7/cogent/data creating build/lib.linux-i686-2.7/cogent/db copying cogent/db/rfam.py -> build/lib.linux-i686-2.7/cogent/db copying cogent/db/__init__.py -> build/lib.linux-i686-2.7/cogent/db copying cogent/db/util.py -> build/lib.linux-i686-2.7/cogent/db copying cogent/db/pdb.py -> build/lib.linux-i686-2.7/cogent/db copying cogent/db/ncbi.py -> build/lib.linux-i686-2.7/cogent/db creating build/lib.linux-i686-2.7/cogent/db/ensembl copying cogent/db/ensembl/name.py -> build/lib.linux-i686-2.7/cogent/db/ensembl copying cogent/db/ensembl/database.py -> build/lib.linux-i686-2.7/cogent/db/ensembl copying cogent/db/ensembl/sequence.py -> build/lib.linux-i686-2.7/cogent/db/ensembl copying cogent/db/ensembl/host.py -> build/lib.linux-i686-2.7/cogent/db/ensembl copying cogent/db/ensembl/__init__.py -> build/lib.linux-i686-2.7/cogent/db/ensembl copying cogent/db/ensembl/genome.py -> build/lib.linux-i686-2.7/cogent/db/ensembl copying cogent/db/ensembl/species.py -> build/lib.linux-i686-2.7/cogent/db/ensembl copying cogent/db/ensembl/assembly.py -> build/lib.linux-i686-2.7/cogent/db/ensembl copying cogent/db/ensembl/util.py -> build/lib.linux-i686-2.7/cogent/db/ensembl copying cogent/db/ensembl/related_region.py -> build/lib.linux-i686-2.7/cogent/db/ensembl copying cogent/db/ensembl/region.py -> build/lib.linux-i686-2.7/cogent/db/ensembl copying cogent/db/ensembl/compara.py -> build/lib.linux-i686-2.7/cogent/db/ensembl copying cogent/db/ensembl/feature_level.py -> build/lib.linux-i686-2.7/cogent/db/ensembl creating build/lib.linux-i686-2.7/cogent/draw copying cogent/draw/__init__.py -> build/lib.linux-i686-2.7/cogent/draw copying cogent/draw/linear.py -> build/lib.linux-i686-2.7/cogent/draw copying cogent/draw/compatibility.py -> build/lib.linux-i686-2.7/cogent/draw copying cogent/draw/arrow_rates.py -> build/lib.linux-i686-2.7/cogent/draw copying cogent/draw/multivariate_plot.py -> build/lib.linux-i686-2.7/cogent/draw copying cogent/draw/distribution_plots.py -> build/lib.linux-i686-2.7/cogent/draw copying cogent/draw/codon_usage.py -> build/lib.linux-i686-2.7/cogent/draw copying cogent/draw/util.py -> build/lib.linux-i686-2.7/cogent/draw copying cogent/draw/dinuc.py -> build/lib.linux-i686-2.7/cogent/draw copying cogent/draw/dotplot.py -> build/lib.linux-i686-2.7/cogent/draw copying cogent/draw/legend.py -> build/lib.linux-i686-2.7/cogent/draw copying cogent/draw/dendrogram.py -> build/lib.linux-i686-2.7/cogent/draw copying cogent/draw/fancy_arrow.py -> build/lib.linux-i686-2.7/cogent/draw copying cogent/draw/rlg2mpl.py -> build/lib.linux-i686-2.7/cogent/draw creating build/lib.linux-i686-2.7/cogent/evolve copying cogent/evolve/bootstrap.py -> build/lib.linux-i686-2.7/cogent/evolve copying cogent/evolve/__init__.py -> build/lib.linux-i686-2.7/cogent/evolve copying cogent/evolve/likelihood_tree.py -> build/lib.linux-i686-2.7/cogent/evolve copying cogent/evolve/likelihood_calculation.py -> build/lib.linux-i686-2.7/cogent/evolve copying cogent/evolve/predicate.py -> build/lib.linux-i686-2.7/cogent/evolve copying cogent/evolve/substitution_model.py -> build/lib.linux-i686-2.7/cogent/evolve copying cogent/evolve/simulate.py -> build/lib.linux-i686-2.7/cogent/evolve copying cogent/evolve/discrete_markov.py -> build/lib.linux-i686-2.7/cogent/evolve copying cogent/evolve/best_likelihood.py -> build/lib.linux-i686-2.7/cogent/evolve copying cogent/evolve/solved_models.py -> build/lib.linux-i686-2.7/cogent/evolve copying cogent/evolve/parameter_controller.py -> build/lib.linux-i686-2.7/cogent/evolve copying cogent/evolve/motif_prob_model.py -> build/lib.linux-i686-2.7/cogent/evolve copying cogent/evolve/models.py -> build/lib.linux-i686-2.7/cogent/evolve copying cogent/evolve/likelihood_function.py -> build/lib.linux-i686-2.7/cogent/evolve copying cogent/evolve/pairwise_distance.py -> build/lib.linux-i686-2.7/cogent/evolve copying cogent/evolve/substitution_calculation.py -> build/lib.linux-i686-2.7/cogent/evolve copying cogent/evolve/coevolution.py -> build/lib.linux-i686-2.7/cogent/evolve creating build/lib.linux-i686-2.7/cogent/format copying cogent/format/mage.py -> build/lib.linux-i686-2.7/cogent/format copying cogent/format/pdb_color.py -> build/lib.linux-i686-2.7/cogent/format copying cogent/format/xyzrn.py -> build/lib.linux-i686-2.7/cogent/format copying cogent/format/__init__.py -> build/lib.linux-i686-2.7/cogent/format copying cogent/format/text_tree.py -> build/lib.linux-i686-2.7/cogent/format copying cogent/format/alignment.py -> build/lib.linux-i686-2.7/cogent/format copying cogent/format/pdb.py -> build/lib.linux-i686-2.7/cogent/format copying cogent/format/nexus.py -> build/lib.linux-i686-2.7/cogent/format copying cogent/format/table.py -> build/lib.linux-i686-2.7/cogent/format copying cogent/format/clustal.py -> build/lib.linux-i686-2.7/cogent/format copying cogent/format/motif.py -> build/lib.linux-i686-2.7/cogent/format copying cogent/format/phylip.py -> build/lib.linux-i686-2.7/cogent/format copying cogent/format/fasta.py -> build/lib.linux-i686-2.7/cogent/format copying cogent/format/structure.py -> build/lib.linux-i686-2.7/cogent/format copying cogent/format/stockholm.py -> build/lib.linux-i686-2.7/cogent/format copying cogent/format/rna_struct.py -> build/lib.linux-i686-2.7/cogent/format copying cogent/format/bedgraph.py -> build/lib.linux-i686-2.7/cogent/format creating build/lib.linux-i686-2.7/cogent/maths copying cogent/maths/scipy_optimize.py -> build/lib.linux-i686-2.7/cogent/maths copying cogent/maths/__init__.py -> build/lib.linux-i686-2.7/cogent/maths copying cogent/maths/matrix_logarithm.py -> build/lib.linux-i686-2.7/cogent/maths copying cogent/maths/geometry.py -> build/lib.linux-i686-2.7/cogent/maths copying cogent/maths/svd.py -> build/lib.linux-i686-2.7/cogent/maths copying cogent/maths/period.py -> build/lib.linux-i686-2.7/cogent/maths copying cogent/maths/solve.py -> build/lib.linux-i686-2.7/cogent/maths copying cogent/maths/scipy_optimisers.py -> build/lib.linux-i686-2.7/cogent/maths copying cogent/maths/optimisers.py -> build/lib.linux-i686-2.7/cogent/maths copying cogent/maths/markov.py -> build/lib.linux-i686-2.7/cogent/maths copying cogent/maths/fit_function.py -> build/lib.linux-i686-2.7/cogent/maths copying cogent/maths/function_optimisation.py -> build/lib.linux-i686-2.7/cogent/maths copying cogent/maths/distance_transform.py -> build/lib.linux-i686-2.7/cogent/maths copying cogent/maths/simannealingoptimiser.py -> build/lib.linux-i686-2.7/cogent/maths copying cogent/maths/matrix_exponentiation.py -> build/lib.linux-i686-2.7/cogent/maths creating build/lib.linux-i686-2.7/cogent/maths/matrix copying cogent/maths/matrix/__init__.py -> build/lib.linux-i686-2.7/cogent/maths/matrix copying cogent/maths/matrix/distance.py -> build/lib.linux-i686-2.7/cogent/maths/matrix creating build/lib.linux-i686-2.7/cogent/maths/stats copying cogent/maths/stats/rarefaction.py -> build/lib.linux-i686-2.7/cogent/maths/stats copying cogent/maths/stats/alpha_diversity.py -> build/lib.linux-i686-2.7/cogent/maths/stats copying cogent/maths/stats/jackknife.py -> build/lib.linux-i686-2.7/cogent/maths/stats copying cogent/maths/stats/__init__.py -> build/lib.linux-i686-2.7/cogent/maths/stats copying cogent/maths/stats/histogram.py -> build/lib.linux-i686-2.7/cogent/maths/stats copying cogent/maths/stats/test.py -> build/lib.linux-i686-2.7/cogent/maths/stats copying cogent/maths/stats/ks.py -> build/lib.linux-i686-2.7/cogent/maths/stats copying cogent/maths/stats/kendall.py -> build/lib.linux-i686-2.7/cogent/maths/stats copying cogent/maths/stats/period.py -> build/lib.linux-i686-2.7/cogent/maths/stats copying cogent/maths/stats/special.py -> build/lib.linux-i686-2.7/cogent/maths/stats copying cogent/maths/stats/util.py -> build/lib.linux-i686-2.7/cogent/maths/stats copying cogent/maths/stats/distribution.py -> build/lib.linux-i686-2.7/cogent/maths/stats copying cogent/maths/stats/information_criteria.py -> build/lib.linux-i686-2.7/cogent/maths/stats creating build/lib.linux-i686-2.7/cogent/maths/stats/cai copying cogent/maths/stats/cai/get_by_cai.py -> build/lib.linux-i686-2.7/cogent/maths/stats/cai copying cogent/maths/stats/cai/__init__.py -> build/lib.linux-i686-2.7/cogent/maths/stats/cai copying cogent/maths/stats/cai/adaptor.py -> build/lib.linux-i686-2.7/cogent/maths/stats/cai copying cogent/maths/stats/cai/util.py -> build/lib.linux-i686-2.7/cogent/maths/stats/cai creating build/lib.linux-i686-2.7/cogent/maths/unifrac copying cogent/maths/unifrac/__init__.py -> build/lib.linux-i686-2.7/cogent/maths/unifrac copying cogent/maths/unifrac/fast_unifrac.py -> build/lib.linux-i686-2.7/cogent/maths/unifrac copying cogent/maths/unifrac/fast_tree.py -> build/lib.linux-i686-2.7/cogent/maths/unifrac creating build/lib.linux-i686-2.7/cogent/maths/spatial copying cogent/maths/spatial/__init__.py -> build/lib.linux-i686-2.7/cogent/maths/spatial creating build/lib.linux-i686-2.7/cogent/motif copying cogent/motif/k_word.py -> build/lib.linux-i686-2.7/cogent/motif copying cogent/motif/__init__.py -> build/lib.linux-i686-2.7/cogent/motif copying cogent/motif/util.py -> build/lib.linux-i686-2.7/cogent/motif creating build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/mage.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/blast_xml.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/knetfold.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/rfam.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/kegg_pos.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/rna_fold.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/meme.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/ncbi_taxonomy.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/sequence.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/column.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/flowgram.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/agilent_microarray.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/__init__.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/tree_xml.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/ilm.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/greengenes.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/dialign.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/rnaalifold.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/unigene.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/dynalign.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/foldalign.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/cutg.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/locuslink.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/gcg.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/newick.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/stride.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/flowgram_parser.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/fastq.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/paml.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/kegg_ko.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/gibbs.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/flowgram_collection.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/cove.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/tinyseq.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/genbank.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/ct.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/mfold.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/macsim.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/binary_sff.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/psl.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/pdb.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/msms.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/rna_plot.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/pknotsrg.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/kegg_taxonomy.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/blast.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/nexus.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/infernal.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/sprinzl.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/table.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/contrafold.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/bpseq.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/carnac.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/gbseq.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/bowtie.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/clustal.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/kegg_fasta.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/aaindex.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/phylip.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/cut.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/tree.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/cmfinder.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/nupack.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/record.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/fasta.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/structure.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/comrna.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/dotur.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/mothur.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/sfold.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/rdb.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/stockholm.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/illumina_sequence.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/pfold.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/consan.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/ebi.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/rnashapes.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/record_finder.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/rnaview.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/gff.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/paml_matrix.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/unafold.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/cigar.py -> build/lib.linux-i686-2.7/cogent/parse copying cogent/parse/rnaforester.py -> build/lib.linux-i686-2.7/cogent/parse creating build/lib.linux-i686-2.7/cogent/phylo copying cogent/phylo/consensus.py -> build/lib.linux-i686-2.7/cogent/phylo copying cogent/phylo/nj.py -> build/lib.linux-i686-2.7/cogent/phylo copying cogent/phylo/maximum_likelihood.py -> build/lib.linux-i686-2.7/cogent/phylo copying cogent/phylo/__init__.py -> build/lib.linux-i686-2.7/cogent/phylo copying cogent/phylo/least_squares.py -> build/lib.linux-i686-2.7/cogent/phylo copying cogent/phylo/util.py -> build/lib.linux-i686-2.7/cogent/phylo copying cogent/phylo/tree_space.py -> build/lib.linux-i686-2.7/cogent/phylo copying cogent/phylo/tree_collection.py -> build/lib.linux-i686-2.7/cogent/phylo copying cogent/phylo/distance.py -> build/lib.linux-i686-2.7/cogent/phylo creating build/lib.linux-i686-2.7/cogent/recalculation copying cogent/recalculation/__init__.py -> build/lib.linux-i686-2.7/cogent/recalculation copying cogent/recalculation/scope.py -> build/lib.linux-i686-2.7/cogent/recalculation copying cogent/recalculation/setting.py -> build/lib.linux-i686-2.7/cogent/recalculation copying cogent/recalculation/calculation.py -> build/lib.linux-i686-2.7/cogent/recalculation copying cogent/recalculation/definition.py -> build/lib.linux-i686-2.7/cogent/recalculation creating build/lib.linux-i686-2.7/cogent/seqsim copying cogent/seqsim/microarray_normalize.py -> build/lib.linux-i686-2.7/cogent/seqsim copying cogent/seqsim/__init__.py -> build/lib.linux-i686-2.7/cogent/seqsim copying cogent/seqsim/randomization.py -> build/lib.linux-i686-2.7/cogent/seqsim copying cogent/seqsim/analysis.py -> build/lib.linux-i686-2.7/cogent/seqsim copying cogent/seqsim/usage.py -> build/lib.linux-i686-2.7/cogent/seqsim copying cogent/seqsim/tree.py -> build/lib.linux-i686-2.7/cogent/seqsim copying cogent/seqsim/searchpath.py -> build/lib.linux-i686-2.7/cogent/seqsim copying cogent/seqsim/sequence_generators.py -> build/lib.linux-i686-2.7/cogent/seqsim copying cogent/seqsim/birth_death.py -> build/lib.linux-i686-2.7/cogent/seqsim copying cogent/seqsim/markov.py -> build/lib.linux-i686-2.7/cogent/seqsim copying cogent/seqsim/microarray.py -> build/lib.linux-i686-2.7/cogent/seqsim creating build/lib.linux-i686-2.7/cogent/struct copying cogent/struct/__init__.py -> build/lib.linux-i686-2.7/cogent/struct copying cogent/struct/asa.py -> build/lib.linux-i686-2.7/cogent/struct copying cogent/struct/rna2d.py -> build/lib.linux-i686-2.7/cogent/struct copying cogent/struct/manipulation.py -> build/lib.linux-i686-2.7/cogent/struct copying cogent/struct/contact.py -> build/lib.linux-i686-2.7/cogent/struct copying cogent/struct/dihedral.py -> build/lib.linux-i686-2.7/cogent/struct copying cogent/struct/pairs_util.py -> build/lib.linux-i686-2.7/cogent/struct copying cogent/struct/annotation.py -> build/lib.linux-i686-2.7/cogent/struct copying cogent/struct/knots.py -> build/lib.linux-i686-2.7/cogent/struct copying cogent/struct/selection.py -> build/lib.linux-i686-2.7/cogent/struct creating build/lib.linux-i686-2.7/cogent/util copying cogent/util/warning.py -> build/lib.linux-i686-2.7/cogent/util copying cogent/util/unit_test.py -> build/lib.linux-i686-2.7/cogent/util copying cogent/util/terminal.py -> build/lib.linux-i686-2.7/cogent/util copying cogent/util/progress_display.py -> build/lib.linux-i686-2.7/cogent/util copying cogent/util/organizer.py -> build/lib.linux-i686-2.7/cogent/util copying cogent/util/trie.py -> build/lib.linux-i686-2.7/cogent/util copying cogent/util/__init__.py -> build/lib.linux-i686-2.7/cogent/util copying cogent/util/dict2d.py -> build/lib.linux-i686-2.7/cogent/util copying cogent/util/datatypes.py -> build/lib.linux-i686-2.7/cogent/util copying cogent/util/array.py -> build/lib.linux-i686-2.7/cogent/util copying cogent/util/recode_alignment.py -> build/lib.linux-i686-2.7/cogent/util copying cogent/util/update_version.py -> build/lib.linux-i686-2.7/cogent/util copying cogent/util/table.py -> build/lib.linux-i686-2.7/cogent/util copying cogent/util/transform.py -> build/lib.linux-i686-2.7/cogent/util copying cogent/util/checkpointing.py -> build/lib.linux-i686-2.7/cogent/util copying cogent/util/misc.py -> build/lib.linux-i686-2.7/cogent/util copying cogent/util/modules.py -> build/lib.linux-i686-2.7/cogent/util copying cogent/util/parallel.py -> build/lib.linux-i686-2.7/cogent/util copying cogent/util/dict_array.py -> build/lib.linux-i686-2.7/cogent/util copying cogent/util/option_parsing.py -> build/lib.linux-i686-2.7/cogent/util running build_ext cythoning cogent/align/_compare.pyx to cogent/align/_compare.c building 'cogent.align._compare' extension creating build/temp.linux-i686-2.7 creating build/temp.linux-i686-2.7/cogent creating build/temp.linux-i686-2.7/cogent/align gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -fPIC -I/build/buildd/python-cogent-1.5.3/include -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/align/_compare.c -o build/temp.linux-i686-2.7/cogent/align/_compare.o -w gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/cogent/align/_compare.o -o build/lib.linux-i686-2.7/cogent/align/_compare.so cythoning cogent/align/_pairwise_seqs.pyx to cogent/align/_pairwise_seqs.c building 'cogent.align._pairwise_seqs' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -fPIC -I/build/buildd/python-cogent-1.5.3/include -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/align/_pairwise_seqs.c -o build/temp.linux-i686-2.7/cogent/align/_pairwise_seqs.o -w gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/cogent/align/_pairwise_seqs.o -o build/lib.linux-i686-2.7/cogent/align/_pairwise_seqs.so cythoning cogent/align/_pairwise_pogs.pyx to cogent/align/_pairwise_pogs.c building 'cogent.align._pairwise_pogs' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -fPIC -I/build/buildd/python-cogent-1.5.3/include -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/align/_pairwise_pogs.c -o build/temp.linux-i686-2.7/cogent/align/_pairwise_pogs.o -w gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/cogent/align/_pairwise_pogs.o -o build/lib.linux-i686-2.7/cogent/align/_pairwise_pogs.so cythoning cogent/evolve/_solved_models.pyx to cogent/evolve/_solved_models.c building 'cogent.evolve._solved_models' extension creating build/temp.linux-i686-2.7/cogent/evolve gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -fPIC -I/build/buildd/python-cogent-1.5.3/include -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/evolve/_solved_models.c -o build/temp.linux-i686-2.7/cogent/evolve/_solved_models.o -w gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/cogent/evolve/_solved_models.o -o build/lib.linux-i686-2.7/cogent/evolve/_solved_models.so cythoning cogent/evolve/_likelihood_tree.pyx to cogent/evolve/_likelihood_tree.c building 'cogent.evolve._likelihood_tree' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -fPIC -I/build/buildd/python-cogent-1.5.3/include -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/evolve/_likelihood_tree.c -o build/temp.linux-i686-2.7/cogent/evolve/_likelihood_tree.o -w gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/cogent/evolve/_likelihood_tree.o -o build/lib.linux-i686-2.7/cogent/evolve/_likelihood_tree.so cythoning cogent/evolve/_pairwise_distance.pyx to cogent/evolve/_pairwise_distance.c building 'cogent.evolve._pairwise_distance' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -fPIC -I/build/buildd/python-cogent-1.5.3/include -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/evolve/_pairwise_distance.c -o build/temp.linux-i686-2.7/cogent/evolve/_pairwise_distance.o -w gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/cogent/evolve/_pairwise_distance.o -o build/lib.linux-i686-2.7/cogent/evolve/_pairwise_distance.so cythoning cogent/struct/_asa.pyx to cogent/struct/_asa.c warning: cogent/struct/_asa.pyx:6:0: 'stdlib' is deprecated, use 'libc.stdlib' building 'cogent.struct._asa' extension creating build/temp.linux-i686-2.7/cogent/struct gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -fPIC -I/build/buildd/python-cogent-1.5.3/include -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/struct/_asa.c -o build/temp.linux-i686-2.7/cogent/struct/_asa.o -w gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/cogent/struct/_asa.o -o build/lib.linux-i686-2.7/cogent/struct/_asa.so cythoning cogent/struct/_contact.pyx to cogent/struct/_contact.c warning: cogent/struct/_contact.pyx:6:0: 'stdlib' is deprecated, use 'libc.stdlib' building 'cogent.struct._contact' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -fPIC -I/build/buildd/python-cogent-1.5.3/include -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/struct/_contact.c -o build/temp.linux-i686-2.7/cogent/struct/_contact.o -w gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/cogent/struct/_contact.o -o build/lib.linux-i686-2.7/cogent/struct/_contact.so cythoning cogent/maths/_period.pyx to cogent/maths/_period.c building 'cogent.maths._period' extension creating build/temp.linux-i686-2.7/cogent/maths gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -fPIC -I/build/buildd/python-cogent-1.5.3/include -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/maths/_period.c -o build/temp.linux-i686-2.7/cogent/maths/_period.o -w gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/cogent/maths/_period.o -o build/lib.linux-i686-2.7/cogent/maths/_period.so cythoning cogent/maths/spatial/ckd3.pyx to cogent/maths/spatial/ckd3.c warning: cogent/maths/spatial/ckd3.pyx:14:0: 'stdlib' is deprecated, use 'libc.stdlib' building 'cogent.maths.spatial.ckd3' extension creating build/temp.linux-i686-2.7/cogent/maths/spatial gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -fPIC -I/build/buildd/python-cogent-1.5.3/include -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/maths/spatial/ckd3.c -o build/temp.linux-i686-2.7/cogent/maths/spatial/ckd3.o -w gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/cogent/maths/spatial/ckd3.o -o build/lib.linux-i686-2.7/cogent/maths/spatial/ckd3.so cd doc; /usr/bin/make html make[2]: Entering directory `/build/buildd/python-cogent-1.5.3/doc' sphinx-build -b html -d _build/doctrees . _build/html Making output directory... Running Sphinx v1.1.3 loading pickled environment... not yet created building [html]: targets for 99 source files that are out of date updating environment: 99 added, 0 changed, 0 removed reading sources... [ 1%] COGENT_LICENSE reading sources... [ 2%] ChangeLog reading sources... [ 3%] README reading sources... [ 4%] coding_guidelines reading sources... [ 5%] cookbook/DNA_and_RNA_sequences reading sources... [ 6%] cookbook/accessing_databases reading sources... [ 7%] cookbook/alignments reading sources... [ 8%] cookbook/alphabet reading sources... [ 9%] cookbook/analysis_of_sequence_composition reading sources... [ 10%] cookbook/annotations reading sources... [ 11%] cookbook/blast reading sources... [ 12%] cookbook/building_a_tree_of_life reading sources... [ 13%] cookbook/building_alignments reading sources... [ 14%] cookbook/building_phylogenies reading sources... [ 15%] cookbook/checkpointing_long_running reading sources... [ 16%] cookbook/code_development reading sources... [ 17%] cookbook/community_analysis reading sources... [ 18%] cookbook/controlling_third_party_applications reading sources... [ 19%] cookbook/dealing_with_hts_data reading sources... [ 20%] cookbook/genetic_code reading sources... [ 21%] cookbook/hpc_environments reading sources... [ 22%] cookbook/index reading sources... [ 23%] cookbook/introduction reading sources... [ 24%] cookbook/loading_sequences reading sources... [ 25%] cookbook/managing_trees reading sources... [ 26%] cookbook/manipulating_biological_data reading sources... [ 27%] cookbook/moltypesequence reading sources... [ 28%] cookbook/multivariate_data_analysis reading sources... [ 29%] cookbook/parallel_tasks_with_mpi reading sources... [ 30%] cookbook/parallel_tasks_with_multiprocess reading sources... [ 31%] cookbook/phylonodes reading sources... [ 32%] cookbook/protein_sequences reading sources... [ 33%] cookbook/sequence_similarity_search reading sources... [ 34%] cookbook/sequence_simulation reading sources... [ 35%] cookbook/simple_trees reading sources... [ 36%] cookbook/standard_statistical_analyses reading sources... [ 37%] cookbook/structural_contacts reading sources... [ 38%] cookbook/structural_data reading sources... [ 39%] cookbook/structural_data_2 reading sources... [ 40%] cookbook/tables reading sources... [ 41%] cookbook/tips_for_using_python reading sources... [ 42%] cookbook/useful_utilities reading sources... [ 43%] cookbook/using_likelihood_to_perform_evolutionary_analyses reading sources... [ 44%] data_file_links reading sources... [ 45%] developer_notes reading sources... [ 46%] examples/align_codons_to_protein reading sources... [ 47%] examples/alignment_app_controllers reading sources... [ 48%] examples/aln_profile reading sources... [ 49%] examples/application_controller_framework reading sources... [ 50%] examples/building_and_using_an_application_controller reading sources... [ 51%] examples/calculate_UPGMA_cluster reading sources... [ 52%] examples/calculate_neigbourjoining_tree reading sources... [ 53%] examples/calculate_pairwise_distances reading sources... [ 54%] examples/codon_models reading sources... [ 55%] examples/coevolution reading sources... [ 56%] examples/complete_seq_features reading sources... [ 57%] examples/draw_dendrogram reading sources... [ 58%] examples/draw_dotplot reading sources... [ 59%] examples/empirical_protein_models reading sources... [ 60%] examples/entity_selection reading sources... [ 61%] examples/estimate_startingpoint reading sources... [ 62%] examples/generating_app_commandlines reading sources... [ 63%] examples/genetic_code_aa_index reading sources... [ 64%] examples/goodness_of_fit reading sources... [ 65%] examples/handling_3dstructures reading sources... [ 66%] examples/handling_tabular_data reading sources... [ 67%] examples/hmm_par_heterogeneity reading sources... [ 68%] examples/index reading sources... [ 69%] examples/maketree_from_proteinseqs reading sources... [ 70%] examples/manipulating_tree_nodes reading sources... [ 71%] examples/motif_results reading sources... [ 72%] examples/neutral_test reading sources... [ 73%] examples/parametric_bootstrap reading sources... [ 74%] examples/perform_PCoA_analysis reading sources... [ 75%] examples/perform_nmds reading sources... [ 76%] examples/period_estimation reading sources... [ 77%] examples/phylo_by_ls reading sources... [ 78%] examples/phylogeny_app_controllers reading sources... [ 79%] examples/query_ensembl reading sources... [ 80%] examples/query_ncbi reading sources... [ 81%] examples/rate_heterogeneity reading sources... [ 82%] examples/relative_rate reading sources... [ 83%] examples/reuse_results reading sources... [ 84%] examples/reverse_complement reading sources... [ 85%] examples/scope_model_params_on_trees reading sources... [ 86%] examples/seq_features reading sources... [ 87%] examples/seqsim_alignment_simulation reading sources... [ 88%] examples/seqsim_aln_sim_user_alphabet reading sources... [ 89%] examples/seqsim_tree_sim reading sources... [ 90%] examples/simple reading sources... [ 91%] examples/simulate_alignment reading sources... [ 92%] examples/testing_multi_loci reading sources... [ 93%] examples/translate_dna reading sources... [ 94%] examples/unifrac reading sources... [ 95%] examples/unrestricted_nucleotide reading sources... [ 96%] index reading sources... [ 97%] install reading sources... [ 98%] licenses reading sources... [100%] scripting_guidelines looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 1%] COGENT_LICENSE writing output... [ 2%] ChangeLog writing output... [ 3%] README writing output... [ 4%] coding_guidelines writing output... [ 5%] cookbook/DNA_and_RNA_sequences writing output... [ 6%] cookbook/accessing_databases writing output... [ 7%] cookbook/alignments writing output... [ 8%] cookbook/alphabet writing output... [ 9%] cookbook/analysis_of_sequence_composition writing output... [ 10%] cookbook/annotations writing output... [ 11%] cookbook/blast writing output... [ 12%] cookbook/building_a_tree_of_life writing output... [ 13%] cookbook/building_alignments writing output... [ 14%] cookbook/building_phylogenies writing output... [ 15%] cookbook/checkpointing_long_running writing output... [ 16%] cookbook/code_development writing output... [ 17%] cookbook/community_analysis writing output... [ 18%] cookbook/controlling_third_party_applications writing output... [ 19%] cookbook/dealing_with_hts_data writing output... [ 20%] cookbook/genetic_code writing output... [ 21%] cookbook/hpc_environments writing output... [ 22%] cookbook/index writing output... [ 23%] cookbook/introduction writing output... [ 24%] cookbook/loading_sequences writing output... [ 25%] cookbook/managing_trees writing output... [ 26%] cookbook/manipulating_biological_data writing output... [ 27%] cookbook/moltypesequence writing output... [ 28%] cookbook/multivariate_data_analysis writing output... [ 29%] cookbook/parallel_tasks_with_mpi writing output... [ 30%] cookbook/parallel_tasks_with_multiprocess writing output... [ 31%] cookbook/phylonodes writing output... [ 32%] cookbook/protein_sequences writing output... [ 33%] cookbook/sequence_similarity_search writing output... [ 34%] cookbook/sequence_simulation writing output... [ 35%] cookbook/simple_trees writing output... [ 36%] cookbook/standard_statistical_analyses writing output... [ 37%] cookbook/structural_contacts writing output... [ 38%] cookbook/structural_data writing output... [ 39%] cookbook/structural_data_2 writing output... [ 40%] cookbook/tables writing output... [ 41%] cookbook/tips_for_using_python writing output... [ 42%] cookbook/useful_utilities writing output... [ 43%] cookbook/using_likelihood_to_perform_evolutionary_analyses writing output... [ 44%] data_file_links writing output... [ 45%] developer_notes writing output... [ 46%] examples/align_codons_to_protein writing output... [ 47%] examples/alignment_app_controllers writing output... [ 48%] examples/aln_profile writing output... [ 49%] examples/application_controller_framework writing output... [ 50%] examples/building_and_using_an_application_controller writing output... [ 51%] examples/calculate_UPGMA_cluster writing output... [ 52%] examples/calculate_neigbourjoining_tree writing output... [ 53%] examples/calculate_pairwise_distances writing output... [ 54%] examples/codon_models writing output... [ 55%] examples/coevolution writing output... [ 56%] examples/complete_seq_features writing output... [ 57%] examples/draw_dendrogram writing output... [ 58%] examples/draw_dotplot writing output... [ 59%] examples/empirical_protein_models writing output... [ 60%] examples/entity_selection writing output... [ 61%] examples/estimate_startingpoint writing output... [ 62%] examples/generating_app_commandlines writing output... [ 63%] examples/genetic_code_aa_index writing output... [ 64%] examples/goodness_of_fit writing output... [ 65%] examples/handling_3dstructures writing output... [ 66%] examples/handling_tabular_data writing output... [ 67%] examples/hmm_par_heterogeneity writing output... [ 68%] examples/index writing output... [ 69%] examples/maketree_from_proteinseqs writing output... [ 70%] examples/manipulating_tree_nodes writing output... [ 71%] examples/motif_results writing output... [ 72%] examples/neutral_test writing output... [ 73%] examples/parametric_bootstrap writing output... [ 74%] examples/perform_PCoA_analysis writing output... [ 75%] examples/perform_nmds writing output... [ 76%] examples/period_estimation writing output... [ 77%] examples/phylo_by_ls writing output... [ 78%] examples/phylogeny_app_controllers writing output... [ 79%] examples/query_ensembl writing output... [ 80%] examples/query_ncbi writing output... [ 81%] examples/rate_heterogeneity writing output... [ 82%] examples/relative_rate WARNING: LaTeX command 'latex' cannot be run (needed for math display), check the pngmath_latex setting writing output... [ 83%] examples/reuse_results writing output... [ 84%] examples/reverse_complement writing output... [ 85%] examples/scope_model_params_on_trees writing output... [ 86%] examples/seq_features writing output... [ 87%] examples/seqsim_alignment_simulation writing output... [ 88%] examples/seqsim_aln_sim_user_alphabet writing output... [ 89%] examples/seqsim_tree_sim writing output... [ 90%] examples/simple writing output... [ 91%] examples/simulate_alignment writing output... [ 92%] examples/testing_multi_loci writing output... [ 93%] examples/translate_dna writing output... [ 94%] examples/unifrac writing output... [ 95%] examples/unrestricted_nucleotide writing output... [ 96%] index writing output... [ 97%] install writing output... [ 98%] licenses writing output... [100%] scripting_guidelines writing additional files... genindex search copying images... [ 33%] cookbook/../images/tol_not_gap_filtered.png copying images... [ 66%] cookbook/../images/tol_gap_filtered.png copying images... [100%] cookbook/../images/tol_entropy_gap_filtered.png copying downloadable files... [ 4%] /build/buildd/python-cogent-1.5.3/doc/data/test2.fasta copying downloadable files... [ 9%] /build/buildd/python-cogent-1.5.3/doc/data/trna_profile.fasta copying downloadable files... [ 14%] /build/buildd/python-cogent-1.5.3/doc/data/dists_for_phylo.pickle copying downloadable files... [ 19%] /build/buildd/python-cogent-1.5.3/doc/data/refseqs.fasta copying downloadable files... [ 23%] /build/buildd/python-cogent-1.5.3/doc/data/abglobin_aa.phylip copying downloadable files... [ 28%] /build/buildd/python-cogent-1.5.3/doc/cookbook/../data/long_testseqs.fasta copying downloadable files... [ 33%] /build/buildd/python-cogent-1.5.3/doc/data/primate_brca1.tree copying downloadable files... [ 38%] /build/buildd/python-cogent-1.5.3/doc/data/refseqs_protein.fasta copying downloadable files... [ 42%] /build/buildd/python-cogent-1.5.3/doc/data/motif_example.fasta copying downloadable files... [ 47%] /build/buildd/python-cogent-1.5.3/doc/data/test.paml copying downloadable files... [ 52%] /build/buildd/python-cogent-1.5.3/doc/data/4TSV.pdb copying downloadable files... [ 57%] /build/buildd/python-cogent-1.5.3/doc/data/inseqs_protein.fasta copying downloadable files... [ 61%] /build/buildd/python-cogent-1.5.3/doc/data/motif_example_meme_results.txt copying downloadable files... [ 66%] /build/buildd/python-cogent-1.5.3/doc/data/test.tree copying downloadable files... [ 71%] /build/buildd/python-cogent-1.5.3/doc/../cogent-requirements.txt copying downloadable files... [ 76%] /build/buildd/python-cogent-1.5.3/doc/data/inseqs.fasta copying downloadable files... [ 80%] /build/buildd/python-cogent-1.5.3/doc/data/pycogent_script_template.py copying downloadable files... [ 85%] /build/buildd/python-cogent-1.5.3/doc/data/primate_cdx2_promoter.fasta copying downloadable files... [ 90%] /build/buildd/python-cogent-1.5.3/doc/data/count_seqs.py copying downloadable files... [ 95%] /build/buildd/python-cogent-1.5.3/doc/data/primate_brca1.fasta copying downloadable files... [100%] /build/buildd/python-cogent-1.5.3/doc/data/long_testseqs.fasta copying static files... done dumping search index... done dumping object inventory... done build succeeded, 1 warning. Build finished. The HTML pages are in _build/html. make[2]: Leaving directory `/build/buildd/python-cogent-1.5.3/doc' make[1]: Leaving directory `/build/buildd/python-cogent-1.5.3' dh_auto_test /usr/bin/fakeroot debian/rules binary dh binary --with python2 dh_testroot dh_prep dh_installdirs dh_auto_install running install running build running build_py running build_ext skipping 'cogent/align/_compare.c' Cython extension (up-to-date) skipping 'cogent/align/_pairwise_seqs.c' Cython extension (up-to-date) skipping 'cogent/align/_pairwise_pogs.c' Cython extension (up-to-date) skipping 'cogent/evolve/_solved_models.c' Cython extension (up-to-date) skipping 'cogent/evolve/_likelihood_tree.c' Cython extension (up-to-date) skipping 'cogent/evolve/_pairwise_distance.c' Cython extension (up-to-date) skipping 'cogent/struct/_asa.c' Cython extension (up-to-date) skipping 'cogent/struct/_contact.c' Cython extension (up-to-date) skipping 'cogent/maths/_period.c' Cython extension (up-to-date) skipping 'cogent/maths/spatial/ckd3.c' Cython extension (up-to-date) running install_lib creating /build/buildd/python-cogent-1.5.3/debian/tmp creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7 creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/struct copying build/lib.linux-i686-2.7/cogent/struct/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/struct copying build/lib.linux-i686-2.7/cogent/struct/asa.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/struct copying build/lib.linux-i686-2.7/cogent/struct/rna2d.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/struct copying build/lib.linux-i686-2.7/cogent/struct/manipulation.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/struct copying build/lib.linux-i686-2.7/cogent/struct/_contact.so -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/struct copying build/lib.linux-i686-2.7/cogent/struct/contact.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/struct copying build/lib.linux-i686-2.7/cogent/struct/dihedral.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/struct copying build/lib.linux-i686-2.7/cogent/struct/pairs_util.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/struct copying build/lib.linux-i686-2.7/cogent/struct/annotation.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/struct copying build/lib.linux-i686-2.7/cogent/struct/knots.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/struct copying build/lib.linux-i686-2.7/cogent/struct/selection.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/struct copying build/lib.linux-i686-2.7/cogent/struct/_asa.so -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/struct creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/recalculation copying build/lib.linux-i686-2.7/cogent/recalculation/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/recalculation copying build/lib.linux-i686-2.7/cogent/recalculation/scope.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/recalculation copying build/lib.linux-i686-2.7/cogent/recalculation/setting.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/recalculation copying build/lib.linux-i686-2.7/cogent/recalculation/calculation.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/recalculation copying build/lib.linux-i686-2.7/cogent/recalculation/definition.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/recalculation creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/motif copying build/lib.linux-i686-2.7/cogent/motif/k_word.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/motif copying build/lib.linux-i686-2.7/cogent/motif/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/motif copying build/lib.linux-i686-2.7/cogent/motif/util.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/motif creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/cluster copying build/lib.linux-i686-2.7/cogent/cluster/goodness_of_fit.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/cluster copying build/lib.linux-i686-2.7/cogent/cluster/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/cluster copying build/lib.linux-i686-2.7/cogent/cluster/approximate_mds.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/cluster copying build/lib.linux-i686-2.7/cogent/cluster/procrustes.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/cluster copying build/lib.linux-i686-2.7/cogent/cluster/metric_scaling.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/cluster copying build/lib.linux-i686-2.7/cogent/cluster/nmds.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/cluster copying build/lib.linux-i686-2.7/cogent/cluster/UPGMA.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/cluster copying build/lib.linux-i686-2.7/cogent/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/draw copying build/lib.linux-i686-2.7/cogent/draw/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/draw copying build/lib.linux-i686-2.7/cogent/draw/linear.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/draw copying build/lib.linux-i686-2.7/cogent/draw/compatibility.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/draw copying build/lib.linux-i686-2.7/cogent/draw/arrow_rates.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/draw copying build/lib.linux-i686-2.7/cogent/draw/multivariate_plot.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/draw copying build/lib.linux-i686-2.7/cogent/draw/distribution_plots.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/draw copying build/lib.linux-i686-2.7/cogent/draw/codon_usage.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/draw copying build/lib.linux-i686-2.7/cogent/draw/util.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/draw copying build/lib.linux-i686-2.7/cogent/draw/dinuc.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/draw copying build/lib.linux-i686-2.7/cogent/draw/dotplot.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/draw copying build/lib.linux-i686-2.7/cogent/draw/legend.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/draw copying build/lib.linux-i686-2.7/cogent/draw/dendrogram.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/draw copying build/lib.linux-i686-2.7/cogent/draw/fancy_arrow.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/draw copying build/lib.linux-i686-2.7/cogent/draw/rlg2mpl.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/draw creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/mage.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/blast_xml.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/knetfold.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/rfam.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/kegg_pos.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/rna_fold.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/meme.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/ncbi_taxonomy.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/sequence.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/column.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/flowgram.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/agilent_microarray.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/tree_xml.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/ilm.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/greengenes.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/dialign.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/rnaalifold.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/unigene.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/dynalign.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/foldalign.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/cutg.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/locuslink.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/gcg.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/newick.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/stride.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/flowgram_parser.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/fastq.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/paml.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/kegg_ko.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/gibbs.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/flowgram_collection.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/cove.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/tinyseq.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/genbank.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/ct.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/mfold.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/macsim.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/binary_sff.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/psl.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/pdb.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/msms.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/rna_plot.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/pknotsrg.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/kegg_taxonomy.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/blast.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/nexus.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/infernal.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/sprinzl.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/table.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/contrafold.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/bpseq.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/carnac.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/gbseq.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/bowtie.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/clustal.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/kegg_fasta.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/aaindex.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/phylip.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/cut.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/tree.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/cmfinder.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/nupack.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/record.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/fasta.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/structure.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/comrna.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/dotur.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/mothur.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/sfold.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/rdb.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/stockholm.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/illumina_sequence.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/pfold.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/consan.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/ebi.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/rnashapes.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/record_finder.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/rnaview.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/gff.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/paml_matrix.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/unafold.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/cigar.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse copying build/lib.linux-i686-2.7/cogent/parse/rnaforester.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/parse creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/parsinsert.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/knetfold.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/mafft.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/rtax.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/gctmpca.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/formatdb.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/pplacer.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/ilm.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/dialign.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/usearch.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/rnaalifold.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/bwa.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/dynalign.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/foldalign.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/stride.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/cove.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/mfold.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/util.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/msms.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/pknotsrg.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/blast.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/rdp_classifier20.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/infernal.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/blat.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/contrafold.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/carnac.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/rdp_classifier.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/sfffile.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/muscle_v38.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/cmfinder.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/sffinfo.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/nupack.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/vienna_package.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/uclust.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/comrna.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/dotur.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/parameters.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/raxml.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/mothur.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/sfold.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/fasttree_v1.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/pfold.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/clearcut.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/consan.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/fasttree.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/rnashapes.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/muscle.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/clustalw.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/rnaview.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/cd_hit.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/raxml_v730.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/unafold.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/guppy.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app copying build/lib.linux-i686-2.7/cogent/app/rnaforester.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/app creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths copying build/lib.linux-i686-2.7/cogent/maths/scipy_optimize.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths copying build/lib.linux-i686-2.7/cogent/maths/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths copying build/lib.linux-i686-2.7/cogent/maths/matrix_logarithm.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths copying build/lib.linux-i686-2.7/cogent/maths/geometry.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/spatial copying build/lib.linux-i686-2.7/cogent/maths/spatial/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/spatial copying build/lib.linux-i686-2.7/cogent/maths/spatial/ckd3.so -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/spatial copying build/lib.linux-i686-2.7/cogent/maths/svd.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths copying build/lib.linux-i686-2.7/cogent/maths/_period.so -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths copying build/lib.linux-i686-2.7/cogent/maths/period.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/matrix copying build/lib.linux-i686-2.7/cogent/maths/matrix/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/matrix copying build/lib.linux-i686-2.7/cogent/maths/matrix/distance.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/matrix copying build/lib.linux-i686-2.7/cogent/maths/solve.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths copying build/lib.linux-i686-2.7/cogent/maths/scipy_optimisers.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/stats copying build/lib.linux-i686-2.7/cogent/maths/stats/rarefaction.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/stats copying build/lib.linux-i686-2.7/cogent/maths/stats/alpha_diversity.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/stats copying build/lib.linux-i686-2.7/cogent/maths/stats/jackknife.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/stats copying build/lib.linux-i686-2.7/cogent/maths/stats/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/stats copying build/lib.linux-i686-2.7/cogent/maths/stats/histogram.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/stats copying build/lib.linux-i686-2.7/cogent/maths/stats/test.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/stats copying build/lib.linux-i686-2.7/cogent/maths/stats/ks.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/stats copying build/lib.linux-i686-2.7/cogent/maths/stats/kendall.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/stats copying build/lib.linux-i686-2.7/cogent/maths/stats/period.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/stats copying build/lib.linux-i686-2.7/cogent/maths/stats/special.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/stats copying build/lib.linux-i686-2.7/cogent/maths/stats/util.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/stats copying build/lib.linux-i686-2.7/cogent/maths/stats/distribution.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/stats creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/stats/cai copying build/lib.linux-i686-2.7/cogent/maths/stats/cai/get_by_cai.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/stats/cai copying build/lib.linux-i686-2.7/cogent/maths/stats/cai/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/stats/cai copying build/lib.linux-i686-2.7/cogent/maths/stats/cai/adaptor.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/stats/cai copying build/lib.linux-i686-2.7/cogent/maths/stats/cai/util.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/stats/cai copying build/lib.linux-i686-2.7/cogent/maths/stats/information_criteria.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/stats copying build/lib.linux-i686-2.7/cogent/maths/optimisers.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths copying build/lib.linux-i686-2.7/cogent/maths/markov.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths copying build/lib.linux-i686-2.7/cogent/maths/fit_function.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths copying build/lib.linux-i686-2.7/cogent/maths/function_optimisation.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths copying build/lib.linux-i686-2.7/cogent/maths/distance_transform.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/unifrac copying build/lib.linux-i686-2.7/cogent/maths/unifrac/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/unifrac copying build/lib.linux-i686-2.7/cogent/maths/unifrac/fast_unifrac.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/unifrac copying build/lib.linux-i686-2.7/cogent/maths/unifrac/fast_tree.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths/unifrac copying build/lib.linux-i686-2.7/cogent/maths/simannealingoptimiser.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths copying build/lib.linux-i686-2.7/cogent/maths/matrix_exponentiation.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/maths creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/phylo copying build/lib.linux-i686-2.7/cogent/phylo/consensus.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/phylo copying build/lib.linux-i686-2.7/cogent/phylo/nj.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/phylo copying build/lib.linux-i686-2.7/cogent/phylo/maximum_likelihood.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/phylo copying build/lib.linux-i686-2.7/cogent/phylo/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/phylo copying build/lib.linux-i686-2.7/cogent/phylo/least_squares.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/phylo copying build/lib.linux-i686-2.7/cogent/phylo/util.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/phylo copying build/lib.linux-i686-2.7/cogent/phylo/tree_space.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/phylo copying build/lib.linux-i686-2.7/cogent/phylo/tree_collection.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/phylo copying build/lib.linux-i686-2.7/cogent/phylo/distance.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/phylo creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/seqsim copying build/lib.linux-i686-2.7/cogent/seqsim/microarray_normalize.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/seqsim copying build/lib.linux-i686-2.7/cogent/seqsim/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/seqsim copying build/lib.linux-i686-2.7/cogent/seqsim/randomization.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/seqsim copying build/lib.linux-i686-2.7/cogent/seqsim/analysis.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/seqsim copying build/lib.linux-i686-2.7/cogent/seqsim/usage.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/seqsim copying build/lib.linux-i686-2.7/cogent/seqsim/tree.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/seqsim copying build/lib.linux-i686-2.7/cogent/seqsim/searchpath.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/seqsim copying build/lib.linux-i686-2.7/cogent/seqsim/sequence_generators.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/seqsim copying build/lib.linux-i686-2.7/cogent/seqsim/birth_death.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/seqsim copying build/lib.linux-i686-2.7/cogent/seqsim/markov.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/seqsim copying build/lib.linux-i686-2.7/cogent/seqsim/microarray.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/seqsim creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/core copying build/lib.linux-i686-2.7/cogent/core/bitvector.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/core copying build/lib.linux-i686-2.7/cogent/core/sequence.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/core copying build/lib.linux-i686-2.7/cogent/core/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/core copying build/lib.linux-i686-2.7/cogent/core/info.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/core copying build/lib.linux-i686-2.7/cogent/core/entity.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/core copying build/lib.linux-i686-2.7/cogent/core/alphabet.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/core copying build/lib.linux-i686-2.7/cogent/core/alignment.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/core copying build/lib.linux-i686-2.7/cogent/core/usage.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/core copying build/lib.linux-i686-2.7/cogent/core/tree.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/core copying build/lib.linux-i686-2.7/cogent/core/genetic_code.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/core copying build/lib.linux-i686-2.7/cogent/core/annotation.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/core copying build/lib.linux-i686-2.7/cogent/core/moltype.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/core copying build/lib.linux-i686-2.7/cogent/core/profile.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/core copying build/lib.linux-i686-2.7/cogent/core/location.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/core creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/format copying build/lib.linux-i686-2.7/cogent/format/mage.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/format copying build/lib.linux-i686-2.7/cogent/format/pdb_color.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/format copying build/lib.linux-i686-2.7/cogent/format/xyzrn.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/format copying build/lib.linux-i686-2.7/cogent/format/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/format copying build/lib.linux-i686-2.7/cogent/format/text_tree.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/format copying build/lib.linux-i686-2.7/cogent/format/alignment.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/format copying build/lib.linux-i686-2.7/cogent/format/pdb.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/format copying build/lib.linux-i686-2.7/cogent/format/nexus.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/format copying build/lib.linux-i686-2.7/cogent/format/table.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/format copying build/lib.linux-i686-2.7/cogent/format/clustal.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/format copying build/lib.linux-i686-2.7/cogent/format/motif.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/format copying build/lib.linux-i686-2.7/cogent/format/phylip.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/format copying build/lib.linux-i686-2.7/cogent/format/fasta.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/format copying build/lib.linux-i686-2.7/cogent/format/structure.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/format copying build/lib.linux-i686-2.7/cogent/format/stockholm.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/format copying build/lib.linux-i686-2.7/cogent/format/rna_struct.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/format copying build/lib.linux-i686-2.7/cogent/format/bedgraph.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/format creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/align copying build/lib.linux-i686-2.7/cogent/align/indel_model.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/align copying build/lib.linux-i686-2.7/cogent/align/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/align copying build/lib.linux-i686-2.7/cogent/align/progressive.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/align copying build/lib.linux-i686-2.7/cogent/align/indel_positions.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/align copying build/lib.linux-i686-2.7/cogent/align/align.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/align copying build/lib.linux-i686-2.7/cogent/align/algorithm.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/align copying build/lib.linux-i686-2.7/cogent/align/traceback.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/align copying build/lib.linux-i686-2.7/cogent/align/_pairwise_seqs.so -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/align copying build/lib.linux-i686-2.7/cogent/align/_pairwise_pogs.so -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/align copying build/lib.linux-i686-2.7/cogent/align/pairwise.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/align copying build/lib.linux-i686-2.7/cogent/align/dp_calculation.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/align creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/align/weights copying build/lib.linux-i686-2.7/cogent/align/weights/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/align/weights copying build/lib.linux-i686-2.7/cogent/align/weights/util.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/align/weights copying build/lib.linux-i686-2.7/cogent/align/weights/methods.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/align/weights copying build/lib.linux-i686-2.7/cogent/align/_compare.so -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/align copying build/lib.linux-i686-2.7/cogent/align/pycompare.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/align creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/data copying build/lib.linux-i686-2.7/cogent/data/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/data copying build/lib.linux-i686-2.7/cogent/data/ligand_properties.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/data copying build/lib.linux-i686-2.7/cogent/data/energy_params.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/data copying build/lib.linux-i686-2.7/cogent/data/nucleic_properties.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/data copying build/lib.linux-i686-2.7/cogent/data/molecular_weight.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/data copying build/lib.linux-i686-2.7/cogent/data/protein_properties.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/data creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util copying build/lib.linux-i686-2.7/cogent/util/warning.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util copying build/lib.linux-i686-2.7/cogent/util/unit_test.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util copying build/lib.linux-i686-2.7/cogent/util/terminal.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util copying build/lib.linux-i686-2.7/cogent/util/progress_display.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util copying build/lib.linux-i686-2.7/cogent/util/organizer.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util copying build/lib.linux-i686-2.7/cogent/util/trie.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util copying build/lib.linux-i686-2.7/cogent/util/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util copying build/lib.linux-i686-2.7/cogent/util/dict2d.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util copying build/lib.linux-i686-2.7/cogent/util/datatypes.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util copying build/lib.linux-i686-2.7/cogent/util/array.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util copying build/lib.linux-i686-2.7/cogent/util/recode_alignment.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util copying build/lib.linux-i686-2.7/cogent/util/update_version.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util copying build/lib.linux-i686-2.7/cogent/util/table.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util copying build/lib.linux-i686-2.7/cogent/util/transform.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util copying build/lib.linux-i686-2.7/cogent/util/checkpointing.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util copying build/lib.linux-i686-2.7/cogent/util/misc.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util copying build/lib.linux-i686-2.7/cogent/util/modules.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util copying build/lib.linux-i686-2.7/cogent/util/parallel.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util copying build/lib.linux-i686-2.7/cogent/util/dict_array.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util copying build/lib.linux-i686-2.7/cogent/util/option_parsing.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/util creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/bootstrap.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/_pairwise_distance.so -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/_likelihood_tree.so -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/_solved_models.so -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/likelihood_tree.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/likelihood_calculation.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/predicate.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/substitution_model.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/simulate.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/discrete_markov.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/best_likelihood.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/solved_models.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/parameter_controller.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/motif_prob_model.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/models.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/likelihood_function.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/pairwise_distance.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/substitution_calculation.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/coevolution.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/evolve creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/db copying build/lib.linux-i686-2.7/cogent/db/rfam.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/db copying build/lib.linux-i686-2.7/cogent/db/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/db creating /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying build/lib.linux-i686-2.7/cogent/db/ensembl/name.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying build/lib.linux-i686-2.7/cogent/db/ensembl/database.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying build/lib.linux-i686-2.7/cogent/db/ensembl/sequence.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying build/lib.linux-i686-2.7/cogent/db/ensembl/host.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying build/lib.linux-i686-2.7/cogent/db/ensembl/__init__.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying build/lib.linux-i686-2.7/cogent/db/ensembl/genome.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying build/lib.linux-i686-2.7/cogent/db/ensembl/species.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying build/lib.linux-i686-2.7/cogent/db/ensembl/assembly.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying build/lib.linux-i686-2.7/cogent/db/ensembl/util.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying build/lib.linux-i686-2.7/cogent/db/ensembl/related_region.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying build/lib.linux-i686-2.7/cogent/db/ensembl/region.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying build/lib.linux-i686-2.7/cogent/db/ensembl/compara.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying build/lib.linux-i686-2.7/cogent/db/ensembl/feature_level.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying build/lib.linux-i686-2.7/cogent/db/util.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/db copying build/lib.linux-i686-2.7/cogent/db/pdb.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/db copying build/lib.linux-i686-2.7/cogent/db/ncbi.py -> /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent/db running install_egg_info Writing /build/buildd/python-cogent-1.5.3/debian/tmp/usr/lib/python2.7/dist-packages/cogent-1.5.3.egg-info dh_install debian/rules override_dh_installdocs make[1]: Entering directory `/build/buildd/python-cogent-1.5.3' dh_installdocs rm -rf debian/python-cogent/usr/share/doc/python-cogent/html/_sources make[1]: Leaving directory `/build/buildd/python-cogent-1.5.3' dh_installchangelogs dh_installexamples dh_installman dh_installcatalogs dh_installcron dh_installdebconf dh_installemacsen dh_installifupdown dh_installinfo dh_installinit dh_installmenu dh_installmime dh_installmodules dh_installlogcheck dh_installlogrotate dh_installpam dh_installppp dh_installudev dh_installwm dh_installxfonts dh_installgsettings dh_bugfiles dh_ucf dh_lintian dh_gconf dh_icons dh_perl dh_python2 dh_usrlocal dh_link debian/rules override_dh_compress make[1]: Entering directory `/build/buildd/python-cogent-1.5.3' dh_compress --exclude=.js --exclude=.fasta --exclude=.txt --exclude=.pdb make[1]: Leaving directory `/build/buildd/python-cogent-1.5.3' dh_fixperms debian/rules override_dh_strip make[1]: Entering directory `/build/buildd/python-cogent-1.5.3' dh_strip --dbg-package=python-cogent-dbg dh_strip debug symbol extraction: disabling for PPA build dh_strip debug symbol extraction: not doing anything since NO_PKG_MANGLE is given make[1]: Leaving directory `/build/buildd/python-cogent-1.5.3' dh_makeshlibs debian/rules override_dh_shlibdeps make[1]: Entering directory `/build/buildd/python-cogent-1.5.3' dh_shlibdeps dpkg-shlibdeps: warning: dependency on libpthread.so.0 could be avoided if "debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/_pairwise_pogs.so debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct/_asa.so debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/spatial/ckd3.so debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct/_contact.so debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/_solved_models.so debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/_likelihood_tree.so debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/_period.so debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/_compare.so debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/_pairwise_seqs.so debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/_pairwise_distance.so" were not uselessly linked against it (they use none of its symbols). dh_numpy make[1]: Leaving directory `/build/buildd/python-cogent-1.5.3' dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package python-cogent: unused substitution variable ${python:Versions} dpkg-gencontrol: warning: package python-cogent: unused substitution variable ${python:Provides} dpkg-gencontrol: warning: package python-cogent-dbg: unused substitution variable ${python:Depends} dpkg-gencontrol: warning: package python-cogent-doc: unused substitution variable ${python:Depends} dh_md5sums dh_builddeb INFO: pkgstriptranslations version 116 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build INFO: Disabling pkgstripfiles for PPA build dpkg-deb: building package `python-cogent' in `../python-cogent_1.5.3-1biolinux1_i386.deb'. INFO: pkgstriptranslations version 116 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build INFO: Disabling pkgstripfiles for PPA build dpkg-deb: building package `python-cogent-dbg' in `../python-cogent-dbg_1.5.3-1biolinux1_i386.deb'. INFO: pkgstriptranslations version 116 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build INFO: Disabling pkgstripfiles for PPA build dpkg-deb: building package `python-cogent-doc' in `../python-cogent-doc_1.5.3-1biolinux1_all.deb'. dpkg-genchanges -b -mUbuntu Build Daemon >../python-cogent_1.5.3-1biolinux1_i386.changes dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build python-cogent-1.5.3 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20131008-1600 chroot-autobuild/build/buildd/python-cogent_1.5.3-1biolinux1_i386.deb: new debian package, version 2.0. size 1223436 bytes: control archive= 11052 bytes. 954 bytes, 21 lines control 28269 bytes, 356 lines md5sums 163 bytes, 9 lines * postinst #!/bin/sh 263 bytes, 14 lines * prerm #!/bin/sh Package: python-cogent Version: 1.5.3-1biolinux1 Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 4799 Depends: libc6 (>= 2.4), python (<< 2.8), python (>= 2.7.1-0ubuntu2), python-numpy (>= 1:1.6.1), python-numpy-abi9, python2.7 Suggests: python-cogent-doc Section: python Priority: extra Homepage: http://pycogent.sourceforge.net/ Description: framework for genomic biology PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: * controlling third-party applications, * devising workflows; querying databases, * conducting novel probabilistic analyses of biological sequence evolution, and * generating publication quality graphics. It is distinguished by many unique built-in capabilities (such as true codon alignment) and the frequent addition of entirely new methods for the analysis of genomic data. chroot-autobuild/build/buildd/python-cogent-dbg_1.5.3-1biolinux1_i386.deb: new debian package, version 2.0. size 353496 bytes: control archive= 915 bytes. 465 bytes, 13 lines control 1252 bytes, 12 lines md5sums Package: python-cogent-dbg Source: python-cogent Version: 1.5.3-1biolinux1 Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 920 Depends: python-cogent (= 1.5.3-1biolinux1) Section: debug Priority: extra Homepage: http://pycogent.sourceforge.net/ Description: debug information for pycogent This package is needed to improve significantly the bug reports that users may feel inclined to send. chroot-autobuild/build/buildd/python-cogent-doc_1.5.3-1biolinux1_all.deb: new debian package, version 2.0. size 953588 bytes: control archive= 7892 bytes. 438 bytes, 13 lines control 26056 bytes, 249 lines md5sums Package: python-cogent-doc Source: python-cogent Version: 1.5.3-1biolinux1 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 4388 Depends: libjs-jquery, libjs-underscore Suggests: python-cogent (= 1.5.3-1biolinux1) Section: doc Priority: extra Homepage: http://pycogent.sourceforge.net/ Description: docs for python-cogent Documentation and examples for python-cogent chroot-autobuild/build/buildd/python-cogent_1.5.3-1biolinux1_i386.deb: drwxr-xr-x root/root 0 2013-10-08 15:59 ./ drwxr-xr-x root/root 0 2013-10-08 15:59 ./usr/ drwxr-xr-x root/root 0 2013-10-08 15:59 ./usr/lib/ drwxr-xr-x root/root 0 2013-10-08 15:59 ./usr/lib/pyshared/ drwxr-xr-x root/root 0 2013-10-08 15:59 ./usr/lib/pyshared/python2.7/ drwxr-xr-x root/root 0 2013-10-08 15:59 ./usr/lib/pyshared/python2.7/cogent/ drwxr-xr-x root/root 0 2013-10-08 15:59 ./usr/lib/pyshared/python2.7/cogent/struct/ drwxr-xr-x root/root 0 2013-10-08 15:59 ./usr/lib/pyshared/python2.7/cogent/maths/ drwxr-xr-x 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./usr/lib/pyshared/python2.7/cogent/evolve/_likelihood_tree.so -> ../../../../python2.7/dist-packages/cogent/evolve/_likelihood_tree.so lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/pyshared/python2.7/cogent/evolve/_solved_models.so -> ../../../../python2.7/dist-packages/cogent/evolve/_solved_models.so lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent-1.5.3.egg-info -> ../../../share/pyshared/cogent-1.5.3.egg-info lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/struct/__init__.py -> ../../../../../share/pyshared/cogent/struct/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/struct/asa.py -> ../../../../../share/pyshared/cogent/struct/asa.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/struct/rna2d.py -> ../../../../../share/pyshared/cogent/struct/rna2d.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/struct/manipulation.py -> ../../../../../share/pyshared/cogent/struct/manipulation.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/struct/contact.py -> ../../../../../share/pyshared/cogent/struct/contact.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/struct/dihedral.py -> ../../../../../share/pyshared/cogent/struct/dihedral.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/struct/pairs_util.py -> ../../../../../share/pyshared/cogent/struct/pairs_util.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/struct/annotation.py -> ../../../../../share/pyshared/cogent/struct/annotation.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/struct/knots.py -> ../../../../../share/pyshared/cogent/struct/knots.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/struct/selection.py -> ../../../../../share/pyshared/cogent/struct/selection.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/recalculation/__init__.py -> ../../../../../share/pyshared/cogent/recalculation/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/recalculation/scope.py -> ../../../../../share/pyshared/cogent/recalculation/scope.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/recalculation/setting.py -> ../../../../../share/pyshared/cogent/recalculation/setting.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/recalculation/calculation.py -> ../../../../../share/pyshared/cogent/recalculation/calculation.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/recalculation/definition.py -> ../../../../../share/pyshared/cogent/recalculation/definition.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/motif/k_word.py -> ../../../../../share/pyshared/cogent/motif/k_word.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/motif/__init__.py -> ../../../../../share/pyshared/cogent/motif/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/motif/util.py -> ../../../../../share/pyshared/cogent/motif/util.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/cluster/goodness_of_fit.py -> ../../../../../share/pyshared/cogent/cluster/goodness_of_fit.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/cluster/__init__.py -> ../../../../../share/pyshared/cogent/cluster/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/cluster/approximate_mds.py -> ../../../../../share/pyshared/cogent/cluster/approximate_mds.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/cluster/procrustes.py -> ../../../../../share/pyshared/cogent/cluster/procrustes.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/cluster/metric_scaling.py -> ../../../../../share/pyshared/cogent/cluster/metric_scaling.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/cluster/nmds.py -> ../../../../../share/pyshared/cogent/cluster/nmds.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/cluster/UPGMA.py -> ../../../../../share/pyshared/cogent/cluster/UPGMA.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/__init__.py -> ../../../../share/pyshared/cogent/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/draw/__init__.py -> ../../../../../share/pyshared/cogent/draw/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/draw/linear.py -> ../../../../../share/pyshared/cogent/draw/linear.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/draw/compatibility.py -> ../../../../../share/pyshared/cogent/draw/compatibility.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/draw/arrow_rates.py -> ../../../../../share/pyshared/cogent/draw/arrow_rates.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/draw/multivariate_plot.py -> ../../../../../share/pyshared/cogent/draw/multivariate_plot.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/draw/distribution_plots.py -> ../../../../../share/pyshared/cogent/draw/distribution_plots.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/draw/codon_usage.py -> ../../../../../share/pyshared/cogent/draw/codon_usage.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/draw/util.py -> ../../../../../share/pyshared/cogent/draw/util.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/draw/dinuc.py -> ../../../../../share/pyshared/cogent/draw/dinuc.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/draw/dotplot.py -> ../../../../../share/pyshared/cogent/draw/dotplot.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/draw/legend.py -> ../../../../../share/pyshared/cogent/draw/legend.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/draw/dendrogram.py -> ../../../../../share/pyshared/cogent/draw/dendrogram.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/draw/fancy_arrow.py -> ../../../../../share/pyshared/cogent/draw/fancy_arrow.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/draw/rlg2mpl.py -> ../../../../../share/pyshared/cogent/draw/rlg2mpl.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/mage.py -> ../../../../../share/pyshared/cogent/parse/mage.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/blast_xml.py -> ../../../../../share/pyshared/cogent/parse/blast_xml.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/knetfold.py -> ../../../../../share/pyshared/cogent/parse/knetfold.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/rfam.py -> ../../../../../share/pyshared/cogent/parse/rfam.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/kegg_pos.py -> ../../../../../share/pyshared/cogent/parse/kegg_pos.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/rna_fold.py -> ../../../../../share/pyshared/cogent/parse/rna_fold.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/meme.py -> ../../../../../share/pyshared/cogent/parse/meme.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/ncbi_taxonomy.py -> ../../../../../share/pyshared/cogent/parse/ncbi_taxonomy.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/sequence.py -> ../../../../../share/pyshared/cogent/parse/sequence.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/column.py -> ../../../../../share/pyshared/cogent/parse/column.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/flowgram.py -> ../../../../../share/pyshared/cogent/parse/flowgram.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/agilent_microarray.py -> ../../../../../share/pyshared/cogent/parse/agilent_microarray.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/__init__.py -> ../../../../../share/pyshared/cogent/parse/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/tree_xml.py -> ../../../../../share/pyshared/cogent/parse/tree_xml.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/ilm.py -> ../../../../../share/pyshared/cogent/parse/ilm.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/greengenes.py -> ../../../../../share/pyshared/cogent/parse/greengenes.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/dialign.py -> ../../../../../share/pyshared/cogent/parse/dialign.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/rnaalifold.py -> ../../../../../share/pyshared/cogent/parse/rnaalifold.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/unigene.py -> ../../../../../share/pyshared/cogent/parse/unigene.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/dynalign.py -> ../../../../../share/pyshared/cogent/parse/dynalign.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/foldalign.py -> ../../../../../share/pyshared/cogent/parse/foldalign.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/cutg.py -> ../../../../../share/pyshared/cogent/parse/cutg.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/locuslink.py -> ../../../../../share/pyshared/cogent/parse/locuslink.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/gcg.py -> ../../../../../share/pyshared/cogent/parse/gcg.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/newick.py -> ../../../../../share/pyshared/cogent/parse/newick.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/stride.py -> ../../../../../share/pyshared/cogent/parse/stride.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/flowgram_parser.py -> ../../../../../share/pyshared/cogent/parse/flowgram_parser.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/fastq.py -> ../../../../../share/pyshared/cogent/parse/fastq.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/paml.py -> ../../../../../share/pyshared/cogent/parse/paml.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/kegg_ko.py -> ../../../../../share/pyshared/cogent/parse/kegg_ko.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/gibbs.py -> ../../../../../share/pyshared/cogent/parse/gibbs.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/flowgram_collection.py -> ../../../../../share/pyshared/cogent/parse/flowgram_collection.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/cove.py -> ../../../../../share/pyshared/cogent/parse/cove.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/tinyseq.py -> ../../../../../share/pyshared/cogent/parse/tinyseq.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/genbank.py -> ../../../../../share/pyshared/cogent/parse/genbank.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/ct.py -> ../../../../../share/pyshared/cogent/parse/ct.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/mfold.py -> ../../../../../share/pyshared/cogent/parse/mfold.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/macsim.py -> ../../../../../share/pyshared/cogent/parse/macsim.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/binary_sff.py -> ../../../../../share/pyshared/cogent/parse/binary_sff.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/psl.py -> ../../../../../share/pyshared/cogent/parse/psl.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/pdb.py -> ../../../../../share/pyshared/cogent/parse/pdb.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/msms.py -> ../../../../../share/pyshared/cogent/parse/msms.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/rna_plot.py -> ../../../../../share/pyshared/cogent/parse/rna_plot.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/pknotsrg.py -> ../../../../../share/pyshared/cogent/parse/pknotsrg.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/kegg_taxonomy.py -> ../../../../../share/pyshared/cogent/parse/kegg_taxonomy.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/blast.py -> ../../../../../share/pyshared/cogent/parse/blast.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/nexus.py -> ../../../../../share/pyshared/cogent/parse/nexus.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/infernal.py -> ../../../../../share/pyshared/cogent/parse/infernal.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/sprinzl.py -> ../../../../../share/pyshared/cogent/parse/sprinzl.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/table.py -> ../../../../../share/pyshared/cogent/parse/table.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/contrafold.py -> ../../../../../share/pyshared/cogent/parse/contrafold.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/bpseq.py -> ../../../../../share/pyshared/cogent/parse/bpseq.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/carnac.py -> ../../../../../share/pyshared/cogent/parse/carnac.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/gbseq.py -> ../../../../../share/pyshared/cogent/parse/gbseq.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/bowtie.py -> ../../../../../share/pyshared/cogent/parse/bowtie.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/clustal.py -> ../../../../../share/pyshared/cogent/parse/clustal.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/kegg_fasta.py -> ../../../../../share/pyshared/cogent/parse/kegg_fasta.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/aaindex.py -> ../../../../../share/pyshared/cogent/parse/aaindex.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/phylip.py -> ../../../../../share/pyshared/cogent/parse/phylip.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/cut.py -> ../../../../../share/pyshared/cogent/parse/cut.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/tree.py -> ../../../../../share/pyshared/cogent/parse/tree.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/cmfinder.py -> ../../../../../share/pyshared/cogent/parse/cmfinder.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/nupack.py -> ../../../../../share/pyshared/cogent/parse/nupack.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/record.py -> ../../../../../share/pyshared/cogent/parse/record.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/fasta.py -> ../../../../../share/pyshared/cogent/parse/fasta.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/structure.py -> ../../../../../share/pyshared/cogent/parse/structure.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/comrna.py -> ../../../../../share/pyshared/cogent/parse/comrna.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/dotur.py -> ../../../../../share/pyshared/cogent/parse/dotur.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/mothur.py -> ../../../../../share/pyshared/cogent/parse/mothur.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/sfold.py -> ../../../../../share/pyshared/cogent/parse/sfold.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/rdb.py -> ../../../../../share/pyshared/cogent/parse/rdb.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/stockholm.py -> ../../../../../share/pyshared/cogent/parse/stockholm.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/illumina_sequence.py -> ../../../../../share/pyshared/cogent/parse/illumina_sequence.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/pfold.py -> ../../../../../share/pyshared/cogent/parse/pfold.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/consan.py -> ../../../../../share/pyshared/cogent/parse/consan.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/ebi.py -> ../../../../../share/pyshared/cogent/parse/ebi.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/rnashapes.py -> ../../../../../share/pyshared/cogent/parse/rnashapes.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/record_finder.py -> ../../../../../share/pyshared/cogent/parse/record_finder.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/rnaview.py -> ../../../../../share/pyshared/cogent/parse/rnaview.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/gff.py -> ../../../../../share/pyshared/cogent/parse/gff.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/paml_matrix.py -> ../../../../../share/pyshared/cogent/parse/paml_matrix.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/unafold.py -> ../../../../../share/pyshared/cogent/parse/unafold.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/cigar.py -> ../../../../../share/pyshared/cogent/parse/cigar.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/parse/rnaforester.py -> ../../../../../share/pyshared/cogent/parse/rnaforester.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/parsinsert.py -> ../../../../../share/pyshared/cogent/app/parsinsert.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/knetfold.py -> ../../../../../share/pyshared/cogent/app/knetfold.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/mafft.py -> ../../../../../share/pyshared/cogent/app/mafft.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/rtax.py -> ../../../../../share/pyshared/cogent/app/rtax.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/gctmpca.py -> ../../../../../share/pyshared/cogent/app/gctmpca.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/formatdb.py -> ../../../../../share/pyshared/cogent/app/formatdb.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/pplacer.py -> ../../../../../share/pyshared/cogent/app/pplacer.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/__init__.py -> ../../../../../share/pyshared/cogent/app/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/ilm.py -> ../../../../../share/pyshared/cogent/app/ilm.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/dialign.py -> ../../../../../share/pyshared/cogent/app/dialign.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/usearch.py -> ../../../../../share/pyshared/cogent/app/usearch.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/rnaalifold.py -> ../../../../../share/pyshared/cogent/app/rnaalifold.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/bwa.py -> ../../../../../share/pyshared/cogent/app/bwa.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/dynalign.py -> ../../../../../share/pyshared/cogent/app/dynalign.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/foldalign.py -> ../../../../../share/pyshared/cogent/app/foldalign.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/stride.py -> ../../../../../share/pyshared/cogent/app/stride.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/cove.py -> ../../../../../share/pyshared/cogent/app/cove.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/mfold.py -> ../../../../../share/pyshared/cogent/app/mfold.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/util.py -> ../../../../../share/pyshared/cogent/app/util.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/msms.py -> ../../../../../share/pyshared/cogent/app/msms.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/pknotsrg.py -> ../../../../../share/pyshared/cogent/app/pknotsrg.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/blast.py -> ../../../../../share/pyshared/cogent/app/blast.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/rdp_classifier20.py -> ../../../../../share/pyshared/cogent/app/rdp_classifier20.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/infernal.py -> ../../../../../share/pyshared/cogent/app/infernal.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/blat.py -> ../../../../../share/pyshared/cogent/app/blat.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/contrafold.py -> ../../../../../share/pyshared/cogent/app/contrafold.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/carnac.py -> ../../../../../share/pyshared/cogent/app/carnac.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/rdp_classifier.py -> ../../../../../share/pyshared/cogent/app/rdp_classifier.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/sfffile.py -> ../../../../../share/pyshared/cogent/app/sfffile.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/muscle_v38.py -> ../../../../../share/pyshared/cogent/app/muscle_v38.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/cmfinder.py -> ../../../../../share/pyshared/cogent/app/cmfinder.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/sffinfo.py -> ../../../../../share/pyshared/cogent/app/sffinfo.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/nupack.py -> ../../../../../share/pyshared/cogent/app/nupack.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/vienna_package.py -> ../../../../../share/pyshared/cogent/app/vienna_package.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/uclust.py -> ../../../../../share/pyshared/cogent/app/uclust.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/comrna.py -> ../../../../../share/pyshared/cogent/app/comrna.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/dotur.py -> ../../../../../share/pyshared/cogent/app/dotur.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/parameters.py -> ../../../../../share/pyshared/cogent/app/parameters.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/raxml.py -> ../../../../../share/pyshared/cogent/app/raxml.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/mothur.py -> ../../../../../share/pyshared/cogent/app/mothur.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/sfold.py -> ../../../../../share/pyshared/cogent/app/sfold.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/fasttree_v1.py -> ../../../../../share/pyshared/cogent/app/fasttree_v1.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/pfold.py -> ../../../../../share/pyshared/cogent/app/pfold.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/clearcut.py -> ../../../../../share/pyshared/cogent/app/clearcut.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/consan.py -> ../../../../../share/pyshared/cogent/app/consan.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/fasttree.py -> ../../../../../share/pyshared/cogent/app/fasttree.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/rnashapes.py -> ../../../../../share/pyshared/cogent/app/rnashapes.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/muscle.py -> ../../../../../share/pyshared/cogent/app/muscle.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/clustalw.py -> ../../../../../share/pyshared/cogent/app/clustalw.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/rnaview.py -> ../../../../../share/pyshared/cogent/app/rnaview.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/cd_hit.py -> ../../../../../share/pyshared/cogent/app/cd_hit.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/raxml_v730.py -> ../../../../../share/pyshared/cogent/app/raxml_v730.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/unafold.py -> ../../../../../share/pyshared/cogent/app/unafold.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/guppy.py -> ../../../../../share/pyshared/cogent/app/guppy.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/app/rnaforester.py -> ../../../../../share/pyshared/cogent/app/rnaforester.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/scipy_optimize.py -> ../../../../../share/pyshared/cogent/maths/scipy_optimize.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/__init__.py -> ../../../../../share/pyshared/cogent/maths/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/matrix_logarithm.py -> ../../../../../share/pyshared/cogent/maths/matrix_logarithm.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/geometry.py -> ../../../../../share/pyshared/cogent/maths/geometry.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/spatial/__init__.py -> ../../../../../../share/pyshared/cogent/maths/spatial/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/svd.py -> ../../../../../share/pyshared/cogent/maths/svd.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/period.py -> ../../../../../share/pyshared/cogent/maths/period.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/matrix/__init__.py -> ../../../../../../share/pyshared/cogent/maths/matrix/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/matrix/distance.py -> ../../../../../../share/pyshared/cogent/maths/matrix/distance.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/solve.py -> ../../../../../share/pyshared/cogent/maths/solve.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/scipy_optimisers.py -> ../../../../../share/pyshared/cogent/maths/scipy_optimisers.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/stats/rarefaction.py -> ../../../../../../share/pyshared/cogent/maths/stats/rarefaction.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/stats/alpha_diversity.py -> ../../../../../../share/pyshared/cogent/maths/stats/alpha_diversity.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/stats/jackknife.py -> ../../../../../../share/pyshared/cogent/maths/stats/jackknife.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/stats/__init__.py -> ../../../../../../share/pyshared/cogent/maths/stats/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/stats/histogram.py -> ../../../../../../share/pyshared/cogent/maths/stats/histogram.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/stats/test.py -> ../../../../../../share/pyshared/cogent/maths/stats/test.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/stats/ks.py -> ../../../../../../share/pyshared/cogent/maths/stats/ks.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/stats/kendall.py -> ../../../../../../share/pyshared/cogent/maths/stats/kendall.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/stats/period.py -> ../../../../../../share/pyshared/cogent/maths/stats/period.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/stats/special.py -> ../../../../../../share/pyshared/cogent/maths/stats/special.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/stats/util.py -> ../../../../../../share/pyshared/cogent/maths/stats/util.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/stats/distribution.py -> ../../../../../../share/pyshared/cogent/maths/stats/distribution.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/get_by_cai.py -> ../../../../../../../share/pyshared/cogent/maths/stats/cai/get_by_cai.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/__init__.py -> ../../../../../../../share/pyshared/cogent/maths/stats/cai/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/adaptor.py -> ../../../../../../../share/pyshared/cogent/maths/stats/cai/adaptor.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/util.py -> ../../../../../../../share/pyshared/cogent/maths/stats/cai/util.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/stats/information_criteria.py -> ../../../../../../share/pyshared/cogent/maths/stats/information_criteria.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/optimisers.py -> ../../../../../share/pyshared/cogent/maths/optimisers.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/markov.py -> ../../../../../share/pyshared/cogent/maths/markov.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/fit_function.py -> ../../../../../share/pyshared/cogent/maths/fit_function.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/function_optimisation.py -> ../../../../../share/pyshared/cogent/maths/function_optimisation.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/distance_transform.py -> ../../../../../share/pyshared/cogent/maths/distance_transform.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/unifrac/__init__.py -> ../../../../../../share/pyshared/cogent/maths/unifrac/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/unifrac/fast_unifrac.py -> ../../../../../../share/pyshared/cogent/maths/unifrac/fast_unifrac.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/unifrac/fast_tree.py -> ../../../../../../share/pyshared/cogent/maths/unifrac/fast_tree.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/simannealingoptimiser.py -> ../../../../../share/pyshared/cogent/maths/simannealingoptimiser.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/maths/matrix_exponentiation.py -> ../../../../../share/pyshared/cogent/maths/matrix_exponentiation.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/phylo/consensus.py -> ../../../../../share/pyshared/cogent/phylo/consensus.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/phylo/nj.py -> ../../../../../share/pyshared/cogent/phylo/nj.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/phylo/maximum_likelihood.py -> ../../../../../share/pyshared/cogent/phylo/maximum_likelihood.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/phylo/__init__.py -> ../../../../../share/pyshared/cogent/phylo/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/phylo/least_squares.py -> ../../../../../share/pyshared/cogent/phylo/least_squares.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/phylo/util.py -> ../../../../../share/pyshared/cogent/phylo/util.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/phylo/tree_space.py -> ../../../../../share/pyshared/cogent/phylo/tree_space.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/phylo/tree_collection.py -> ../../../../../share/pyshared/cogent/phylo/tree_collection.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/phylo/distance.py -> ../../../../../share/pyshared/cogent/phylo/distance.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/seqsim/microarray_normalize.py -> ../../../../../share/pyshared/cogent/seqsim/microarray_normalize.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/seqsim/__init__.py -> ../../../../../share/pyshared/cogent/seqsim/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/seqsim/randomization.py -> ../../../../../share/pyshared/cogent/seqsim/randomization.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py -> ../../../../../share/pyshared/cogent/seqsim/analysis.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/seqsim/usage.py -> ../../../../../share/pyshared/cogent/seqsim/usage.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/seqsim/tree.py -> ../../../../../share/pyshared/cogent/seqsim/tree.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/seqsim/searchpath.py -> ../../../../../share/pyshared/cogent/seqsim/searchpath.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/seqsim/sequence_generators.py -> ../../../../../share/pyshared/cogent/seqsim/sequence_generators.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/seqsim/birth_death.py -> ../../../../../share/pyshared/cogent/seqsim/birth_death.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/seqsim/markov.py -> ../../../../../share/pyshared/cogent/seqsim/markov.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/seqsim/microarray.py -> ../../../../../share/pyshared/cogent/seqsim/microarray.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/core/bitvector.py -> ../../../../../share/pyshared/cogent/core/bitvector.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/core/sequence.py -> ../../../../../share/pyshared/cogent/core/sequence.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/core/__init__.py -> ../../../../../share/pyshared/cogent/core/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/core/info.py -> ../../../../../share/pyshared/cogent/core/info.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/core/entity.py -> ../../../../../share/pyshared/cogent/core/entity.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/core/alphabet.py -> ../../../../../share/pyshared/cogent/core/alphabet.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/core/alignment.py -> ../../../../../share/pyshared/cogent/core/alignment.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/core/usage.py -> ../../../../../share/pyshared/cogent/core/usage.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/core/tree.py -> ../../../../../share/pyshared/cogent/core/tree.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/core/genetic_code.py -> ../../../../../share/pyshared/cogent/core/genetic_code.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/core/annotation.py -> ../../../../../share/pyshared/cogent/core/annotation.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/core/moltype.py -> ../../../../../share/pyshared/cogent/core/moltype.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/core/profile.py -> ../../../../../share/pyshared/cogent/core/profile.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/core/location.py -> ../../../../../share/pyshared/cogent/core/location.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/format/mage.py -> ../../../../../share/pyshared/cogent/format/mage.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/format/pdb_color.py -> ../../../../../share/pyshared/cogent/format/pdb_color.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/format/xyzrn.py -> ../../../../../share/pyshared/cogent/format/xyzrn.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/format/__init__.py -> ../../../../../share/pyshared/cogent/format/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/format/text_tree.py -> ../../../../../share/pyshared/cogent/format/text_tree.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/format/alignment.py -> ../../../../../share/pyshared/cogent/format/alignment.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/format/pdb.py -> ../../../../../share/pyshared/cogent/format/pdb.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/format/nexus.py -> ../../../../../share/pyshared/cogent/format/nexus.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/format/table.py -> ../../../../../share/pyshared/cogent/format/table.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/format/clustal.py -> ../../../../../share/pyshared/cogent/format/clustal.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/format/motif.py -> ../../../../../share/pyshared/cogent/format/motif.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/format/phylip.py -> ../../../../../share/pyshared/cogent/format/phylip.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/format/fasta.py -> ../../../../../share/pyshared/cogent/format/fasta.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/format/structure.py -> ../../../../../share/pyshared/cogent/format/structure.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/format/stockholm.py -> ../../../../../share/pyshared/cogent/format/stockholm.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/format/rna_struct.py -> ../../../../../share/pyshared/cogent/format/rna_struct.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/format/bedgraph.py -> ../../../../../share/pyshared/cogent/format/bedgraph.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/align/indel_model.py -> ../../../../../share/pyshared/cogent/align/indel_model.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/align/__init__.py -> ../../../../../share/pyshared/cogent/align/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/align/progressive.py -> ../../../../../share/pyshared/cogent/align/progressive.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/align/indel_positions.py -> ../../../../../share/pyshared/cogent/align/indel_positions.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/align/align.py -> ../../../../../share/pyshared/cogent/align/align.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/align/algorithm.py -> ../../../../../share/pyshared/cogent/align/algorithm.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/align/traceback.py -> ../../../../../share/pyshared/cogent/align/traceback.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/align/pairwise.py -> ../../../../../share/pyshared/cogent/align/pairwise.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/align/dp_calculation.py -> ../../../../../share/pyshared/cogent/align/dp_calculation.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/align/weights/__init__.py -> ../../../../../../share/pyshared/cogent/align/weights/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/align/weights/util.py -> ../../../../../../share/pyshared/cogent/align/weights/util.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/align/weights/methods.py -> ../../../../../../share/pyshared/cogent/align/weights/methods.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/align/pycompare.py -> ../../../../../share/pyshared/cogent/align/pycompare.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/data/__init__.py -> ../../../../../share/pyshared/cogent/data/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/data/ligand_properties.py -> ../../../../../share/pyshared/cogent/data/ligand_properties.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/data/energy_params.py -> ../../../../../share/pyshared/cogent/data/energy_params.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/data/nucleic_properties.py -> ../../../../../share/pyshared/cogent/data/nucleic_properties.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/data/molecular_weight.py -> ../../../../../share/pyshared/cogent/data/molecular_weight.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/data/protein_properties.py -> ../../../../../share/pyshared/cogent/data/protein_properties.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/util/warning.py -> ../../../../../share/pyshared/cogent/util/warning.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/util/unit_test.py -> ../../../../../share/pyshared/cogent/util/unit_test.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/util/terminal.py -> ../../../../../share/pyshared/cogent/util/terminal.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/util/progress_display.py -> ../../../../../share/pyshared/cogent/util/progress_display.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/util/organizer.py -> ../../../../../share/pyshared/cogent/util/organizer.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/util/trie.py -> ../../../../../share/pyshared/cogent/util/trie.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/util/__init__.py -> ../../../../../share/pyshared/cogent/util/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/util/dict2d.py -> ../../../../../share/pyshared/cogent/util/dict2d.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/util/datatypes.py -> ../../../../../share/pyshared/cogent/util/datatypes.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/util/array.py -> ../../../../../share/pyshared/cogent/util/array.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/util/recode_alignment.py -> ../../../../../share/pyshared/cogent/util/recode_alignment.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/util/update_version.py -> ../../../../../share/pyshared/cogent/util/update_version.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/util/table.py -> ../../../../../share/pyshared/cogent/util/table.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/util/transform.py -> ../../../../../share/pyshared/cogent/util/transform.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/util/checkpointing.py -> ../../../../../share/pyshared/cogent/util/checkpointing.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/util/misc.py -> ../../../../../share/pyshared/cogent/util/misc.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/util/modules.py -> ../../../../../share/pyshared/cogent/util/modules.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/util/parallel.py -> ../../../../../share/pyshared/cogent/util/parallel.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/util/dict_array.py -> ../../../../../share/pyshared/cogent/util/dict_array.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/util/option_parsing.py -> ../../../../../share/pyshared/cogent/util/option_parsing.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/evolve/bootstrap.py -> ../../../../../share/pyshared/cogent/evolve/bootstrap.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/evolve/__init__.py -> ../../../../../share/pyshared/cogent/evolve/__init__.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/evolve/likelihood_tree.py -> ../../../../../share/pyshared/cogent/evolve/likelihood_tree.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/evolve/likelihood_calculation.py -> ../../../../../share/pyshared/cogent/evolve/likelihood_calculation.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/evolve/predicate.py -> ../../../../../share/pyshared/cogent/evolve/predicate.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/evolve/substitution_model.py -> ../../../../../share/pyshared/cogent/evolve/substitution_model.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/evolve/simulate.py -> ../../../../../share/pyshared/cogent/evolve/simulate.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/evolve/discrete_markov.py -> ../../../../../share/pyshared/cogent/evolve/discrete_markov.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/evolve/best_likelihood.py -> ../../../../../share/pyshared/cogent/evolve/best_likelihood.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/evolve/solved_models.py -> ../../../../../share/pyshared/cogent/evolve/solved_models.py lrwxrwxrwx root/root 0 2013-10-08 15:59 ./usr/lib/python2.7/dist-packages/cogent/evolve/parameter_controller.py -> 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Format: 1.8 Date: Tue, 08 Oct 2013 16:11:50 +0100 Source: python-cogent Binary: python-cogent python-cogent-dbg python-cogent-doc Architecture: i386 all Version: 1.5.3-1biolinux1 Distribution: precise Urgency: low Maintainer: Ubuntu Build Daemon Changed-By: Tim Booth Description: python-cogent - framework for genomic biology python-cogent-dbg - debug information for pycogent python-cogent-doc - docs for python-cogent Changes: python-cogent (1.5.3-1biolinux1) precise; urgency=low . * Allow use of newer cd-hit that doesn't leave a tmp file Note - the tests still fail as output is different, but this is a quick fix. Checksums-Sha1: 1364f1ba33df6b8784d8846687bf1453eabd4216 1223436 python-cogent_1.5.3-1biolinux1_i386.deb 1f54cd7ed02ed29e88c085d4164fb698d57a6446 353496 python-cogent-dbg_1.5.3-1biolinux1_i386.deb e31db8935fec17d1d25dca64b1bae4a8506ae583 953588 python-cogent-doc_1.5.3-1biolinux1_all.deb Checksums-Sha256: 8de458bc2efbe5908983b75a1598331115099d0a697cf29aa3182b7340716ee3 1223436 python-cogent_1.5.3-1biolinux1_i386.deb 308e9d189ec75a180ca0fb8de18f434861287b91978134a72661ca0c5972f565 353496 python-cogent-dbg_1.5.3-1biolinux1_i386.deb 9383ea91163dcbc56cc51d175a8e843100aa1da5a59eeddd398129d88aedfd1c 953588 python-cogent-doc_1.5.3-1biolinux1_all.deb Files: a0e32177f799f2e73bd532572c0bcd63 1223436 python extra python-cogent_1.5.3-1biolinux1_i386.deb 6d947a2af54adc0169e6c4646b811939 353496 debug extra python-cogent-dbg_1.5.3-1biolinux1_i386.deb 27bd32b42e07aa50bac9ebcc5f8cf4a4 953588 doc extra python-cogent-doc_1.5.3-1biolinux1_all.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20131008-1600 Build needed 00:00:44, 54716k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-5085631'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-5085631/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-5085631'] Unmounting chroot for build PACKAGEBUILD-5085631... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-5085631'] Removing build PACKAGEBUILD-5085631