RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lcy01-05 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 Buildd toolchain package versions: launchpad-buildd_125 python-lpbuildd_125 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.04.1 bzr_2.6.0+bzr6593-1ubuntu1.1 dpkg-dev_1.17.5ubuntu5.3. Syncing the system clock with the buildd NTP service... 29 Aug 15:36:01 ntpdate[1424]: adjust time server 10.211.37.1 offset -0.152268 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-6309050', '/home/buildd/filecache-default/bcd5dc063ce51e1147d70d5a7a54c6f9cc3d3ea4'] Unpacking chroot for build PACKAGEBUILD-6309050 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-6309050'] Mounting chroot for build PACKAGEBUILD-6309050 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-6309050', 'deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty main', 'deb http://ppa.launchpad.net/marutter/rrutter/ubuntu trusty main', 'deb http://ftpmaster.internal/ubuntu trusty main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu trusty-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu trusty-updates main restricted universe multiverse'] Overriding sources.list in build-PACKAGEBUILD-6309050 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-6309050', 'amd64'] Updating debian chroot for build PACKAGEBUILD-6309050 Ign http://ppa.launchpad.net trusty InRelease Ign http://ftpmaster.internal trusty InRelease Ign http://ppa.launchpad.net trusty InRelease Ign http://ftpmaster.internal trusty-security InRelease Get:1 http://ppa.launchpad.net trusty Release.gpg [316 B] Ign http://ftpmaster.internal trusty-updates InRelease Get:2 http://ftpmaster.internal trusty Release.gpg [933 B] Get:3 http://ppa.launchpad.net trusty Release.gpg [316 B] Get:4 http://ftpmaster.internal trusty-security Release.gpg [933 B] Get:5 http://ftpmaster.internal trusty-updates Release.gpg [933 B] Get:6 http://ppa.launchpad.net trusty Release [14.0 kB] Get:7 http://ftpmaster.internal trusty Release [58.5 kB] Get:8 http://ftpmaster.internal trusty-security Release [59.7 kB] Get:9 http://ppa.launchpad.net trusty Release [14.0 kB] Get:10 http://ftpmaster.internal trusty-updates Release [59.7 kB] Ign http://ppa.launchpad.net trusty Release Get:11 http://ppa.launchpad.net trusty/main amd64 Packages [57.7 kB] Get:12 http://ftpmaster.internal trusty/main amd64 Packages [1350 kB] Ign http://ppa.launchpad.net trusty Release Ign http://ppa.launchpad.net trusty/main Translation-en Get:13 http://ppa.launchpad.net trusty/main amd64 Packages [11.2 kB] Ign http://ppa.launchpad.net trusty/main Translation-en Get:14 http://ftpmaster.internal trusty/restricted amd64 Packages [13.0 kB] Get:15 http://ftpmaster.internal trusty/universe amd64 Packages [5859 kB] Get:16 http://ftpmaster.internal trusty/multiverse amd64 Packages [132 kB] Get:17 http://ftpmaster.internal trusty/main Translation-en [762 kB] Get:18 http://ftpmaster.internal trusty/multiverse Translation-en [102 kB] Get:19 http://ftpmaster.internal trusty/restricted Translation-en [3457 B] Get:20 http://ftpmaster.internal trusty/universe Translation-en [4089 kB] Get:21 http://ftpmaster.internal trusty-security/main amd64 Packages [135 kB] Get:22 http://ftpmaster.internal trusty-security/restricted amd64 Packages [14 B] Get:23 http://ftpmaster.internal trusty-security/universe amd64 Packages [47.0 kB] Get:24 http://ftpmaster.internal trusty-security/multiverse amd64 Packages [1154 B] Get:25 http://ftpmaster.internal trusty-security/main Translation-en [65.5 kB] Get:26 http://ftpmaster.internal trusty-security/multiverse Translation-en [587 B] Get:27 http://ftpmaster.internal trusty-security/restricted Translation-en [14 B] Get:28 http://ftpmaster.internal trusty-security/universe Translation-en [26.8 kB] Get:29 http://ftpmaster.internal trusty-updates/main amd64 Packages [306 kB] Get:30 http://ftpmaster.internal trusty-updates/restricted amd64 Packages [5820 B] Get:31 http://ftpmaster.internal trusty-updates/universe amd64 Packages [190 kB] Get:32 http://ftpmaster.internal trusty-updates/multiverse amd64 Packages [8221 B] Get:33 http://ftpmaster.internal trusty-updates/main Translation-en [135 kB] Get:34 http://ftpmaster.internal trusty-updates/multiverse Translation-en [4599 B] Get:35 http://ftpmaster.internal trusty-updates/restricted Translation-en [1736 B] Get:36 http://ftpmaster.internal trusty-updates/universe Translation-en [93.5 kB] Fetched 13.6 MB in 9s (1405 kB/s) Reading package lists... W: GPG error: http://ppa.launchpad.net trusty 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 trusty 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 bsdutils dpkg dpkg-dev gnupg gpgv ifupdown initramfs-tools initramfs-tools-bin libapt-pkg4.12 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcgmanager0 libdbus-1-3 libdpkg-perl libgnutls26 libgssapi-krb5-2 libjson-c2 libjson0 libk5crypto3 libkrb5-3 libkrb5support0 libmount1 libselinux1 libssl1.0.0 libtasn1-6 libudev1 libuuid1 linux-libc-dev mount multiarch-support openssl patch tzdata udev upstart util-linux 43 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 19.3 MB of archives. After this operation, 53.2 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ trusty-updates/main base-files amd64 7.2ubuntu5.1 [70.2 kB] Get:2 http://ftpmaster.internal/ubuntu/ trusty-updates/main bash amd64 4.3-7ubuntu1 [575 kB] Get:3 http://ftpmaster.internal/ubuntu/ trusty-security/main dpkg amd64 1.17.5ubuntu5.3 [1954 kB] Get:4 http://ftpmaster.internal/ubuntu/ trusty-updates/main mount amd64 2.20.1-5.1ubuntu20.1 [115 kB] Get:5 http://ftpmaster.internal/ubuntu/ trusty-security/main tzdata all 2014e-0ubuntu0.14.04 [181 kB] Get:6 http://ftpmaster.internal/ubuntu/ trusty-updates/main util-linux amd64 2.20.1-5.1ubuntu20.1 [456 kB] Get:7 http://ftpmaster.internal/ubuntu/ trusty-security/main libdbus-1-3 amd64 1.6.18-0ubuntu4.1 [131 kB] Get:8 http://ftpmaster.internal/ubuntu/ trusty-security/main libjson-c2 amd64 0.11-3ubuntu1.2 [22.0 kB] Get:9 http://ftpmaster.internal/ubuntu/ trusty-updates/main libselinux1 amd64 2.2.2-1ubuntu0.1 [58.7 kB] Get:10 http://ftpmaster.internal/ubuntu/ trusty-updates/main libuuid1 amd64 2.20.1-5.1ubuntu20.1 [10.9 kB] Get:11 http://ftpmaster.internal/ubuntu/ trusty-updates/main libblkid1 amd64 2.20.1-5.1ubuntu20.1 [62.6 kB] Get:12 http://ftpmaster.internal/ubuntu/ trusty-updates/main libcgmanager0 amd64 0.24-0ubuntu7 [29.0 kB] Get:13 http://ftpmaster.internal/ubuntu/ trusty-updates/main udev amd64 204-5ubuntu20.4 [735 kB] Get:14 http://ftpmaster.internal/ubuntu/ trusty-updates/main libudev1 amd64 204-5ubuntu20.4 [33.2 kB] Get:15 http://ftpmaster.internal/ubuntu/ trusty-updates/main ifupdown amd64 0.7.47.2ubuntu4.1 [52.1 kB] Get:16 http://ftpmaster.internal/ubuntu/ trusty-security/main libjson0 amd64 0.11-3ubuntu1.2 [1080 B] Get:17 http://ftpmaster.internal/ubuntu/ trusty-updates/main upstart amd64 1.12.1-0ubuntu4.2 [390 kB] Get:18 http://ftpmaster.internal/ubuntu/ trusty-security/main libc6-dev amd64 2.19-0ubuntu6.3 [1910 kB] Get:19 http://ftpmaster.internal/ubuntu/ trusty-security/main libc-dev-bin amd64 2.19-0ubuntu6.3 [69.1 kB] Get:20 http://ftpmaster.internal/ubuntu/ trusty-security/main linux-libc-dev amd64 3.13.0-35.62 [793 kB] Get:21 http://ftpmaster.internal/ubuntu/ trusty-security/main libc-bin amd64 2.19-0ubuntu6.3 [1170 kB] Get:22 http://ftpmaster.internal/ubuntu/ trusty-security/main libc6 amd64 2.19-0ubuntu6.3 [4736 kB] Get:23 http://ftpmaster.internal/ubuntu/ trusty-security/main libapt-pkg4.12 amd64 1.0.1ubuntu2.1 [639 kB] Get:24 http://ftpmaster.internal/ubuntu/ trusty-security/main gpgv amd64 1.4.16-1ubuntu2.1 [160 kB] Get:25 http://ftpmaster.internal/ubuntu/ trusty-security/main gnupg amd64 1.4.16-1ubuntu2.1 [610 kB] Get:26 http://ftpmaster.internal/ubuntu/ trusty-security/main apt amd64 1.0.1ubuntu2.1 [952 kB] Get:27 http://ftpmaster.internal/ubuntu/ trusty-updates/main bsdutils amd64 1:2.20.1-5.1ubuntu20.1 [33.9 kB] Get:28 http://ftpmaster.internal/ubuntu/ trusty-updates/main libmount1 amd64 2.20.1-5.1ubuntu20.1 [60.1 kB] Get:29 http://ftpmaster.internal/ubuntu/ trusty-security/main libtasn1-6 amd64 3.4-3ubuntu0.1 [43.5 kB] Get:30 http://ftpmaster.internal/ubuntu/ trusty-security/main libgnutls26 amd64 2.12.23-12ubuntu2.1 [393 kB] Get:31 http://ftpmaster.internal/ubuntu/ trusty-security/main libssl1.0.0 amd64 1.0.1f-1ubuntu2.5 [826 kB] Get:32 http://ftpmaster.internal/ubuntu/ trusty-security/main libk5crypto3 amd64 1.12+dfsg-2ubuntu4.2 [79.8 kB] Get:33 http://ftpmaster.internal/ubuntu/ trusty-security/main libgssapi-krb5-2 amd64 1.12+dfsg-2ubuntu4.2 [113 kB] Get:34 http://ftpmaster.internal/ubuntu/ trusty-security/main libkrb5-3 amd64 1.12+dfsg-2ubuntu4.2 [262 kB] Get:35 http://ftpmaster.internal/ubuntu/ trusty-security/main libkrb5support0 amd64 1.12+dfsg-2ubuntu4.2 [29.8 kB] Get:36 http://ftpmaster.internal/ubuntu/ trusty-security/main multiarch-support amd64 2.19-0ubuntu6.3 [4484 B] Get:37 http://ftpmaster.internal/ubuntu/ trusty-updates/main initramfs-tools all 0.103ubuntu4.2 [44.3 kB] Get:38 http://ftpmaster.internal/ubuntu/ trusty-updates/main initramfs-tools-bin amd64 0.103ubuntu4.2 [8922 B] Get:39 http://ftpmaster.internal/ubuntu/ trusty-security/main apt-transport-https amd64 1.0.1ubuntu2.1 [25.1 kB] Get:40 http://ftpmaster.internal/ubuntu/ trusty-security/main openssl amd64 1.0.1f-1ubuntu2.5 [488 kB] Get:41 http://ftpmaster.internal/ubuntu/ trusty-security/main dpkg-dev all 1.17.5ubuntu5.3 [726 kB] Get:42 http://ftpmaster.internal/ubuntu/ trusty-security/main libdpkg-perl all 1.17.5ubuntu5.3 [179 kB] Get:43 http://ftpmaster.internal/ubuntu/ trusty-updates/main patch amd64 2.7.1-4ubuntu1 [84.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.3 MB in 1s (12.2 MB/s) (Reading database ... 11788 files and directories currently installed.) Preparing to unpack .../base-files_7.2ubuntu5.1_amd64.deb ... Unpacking base-files (7.2ubuntu5.1) over (7.2ubuntu5) ... Setting up base-files (7.2ubuntu5.1) ... 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 ... Installing new version of config file /etc/os-release ... (Reading database ... 11788 files and directories currently installed.) Preparing to unpack .../bash_4.3-7ubuntu1_amd64.deb ... Unpacking bash (4.3-7ubuntu1) over (4.3-6ubuntu1) ... Setting up bash (4.3-7ubuntu1) ... 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 ... 11788 files and directories currently installed.) Preparing to unpack .../dpkg_1.17.5ubuntu5.3_amd64.deb ... Unpacking dpkg (1.17.5ubuntu5.3) over (1.17.5ubuntu5) ... Setting up dpkg (1.17.5ubuntu5.3) ... 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Setting up apt (1.0.1ubuntu2.1) ... Processing triggers for libc-bin (2.19-0ubuntu6.3) ... (Reading database ... 11789 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.20.1-5.1ubuntu20.1_amd64.deb ... Unpacking bsdutils (1:2.20.1-5.1ubuntu20.1) over (1:2.20.1-5.1ubuntu20) ... Setting up bsdutils (1:2.20.1-5.1ubuntu20.1) ... (Reading database ... 11789 files and directories currently installed.) Preparing to unpack .../libmount1_2.20.1-5.1ubuntu20.1_amd64.deb ... Unpacking libmount1:amd64 (2.20.1-5.1ubuntu20.1) over (2.20.1-5.1ubuntu20) ... Setting up libmount1:amd64 (2.20.1-5.1ubuntu20.1) ... Processing triggers for libc-bin (2.19-0ubuntu6.3) ... (Reading database ... 11789 files and directories currently installed.) Preparing to unpack .../libtasn1-6_3.4-3ubuntu0.1_amd64.deb ... Unpacking libtasn1-6:amd64 (3.4-3ubuntu0.1) over (3.4-3) ... Preparing to unpack .../libgnutls26_2.12.23-12ubuntu2.1_amd64.deb ... Unpacking libgnutls26:amd64 (2.12.23-12ubuntu2.1) over (2.12.23-12ubuntu2) ... Preparing to unpack .../libssl1.0.0_1.0.1f-1ubuntu2.5_amd64.deb ... Unpacking libssl1.0.0:amd64 (1.0.1f-1ubuntu2.5) over (1.0.1f-1ubuntu2) ... Preparing to unpack .../libk5crypto3_1.12+dfsg-2ubuntu4.2_amd64.deb ... Unpacking libk5crypto3:amd64 (1.12+dfsg-2ubuntu4.2) over (1.12+dfsg-2ubuntu4) ... Preparing to unpack .../libgssapi-krb5-2_1.12+dfsg-2ubuntu4.2_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.12+dfsg-2ubuntu4.2) over (1.12+dfsg-2ubuntu4) ... Preparing to unpack .../libkrb5-3_1.12+dfsg-2ubuntu4.2_amd64.deb ... Unpacking libkrb5-3:amd64 (1.12+dfsg-2ubuntu4.2) over (1.12+dfsg-2ubuntu4) ... Preparing to unpack .../libkrb5support0_1.12+dfsg-2ubuntu4.2_amd64.deb ... Unpacking libkrb5support0:amd64 (1.12+dfsg-2ubuntu4.2) over (1.12+dfsg-2ubuntu4) ... Preparing to unpack .../multiarch-support_2.19-0ubuntu6.3_amd64.deb ... Unpacking multiarch-support (2.19-0ubuntu6.3) over (2.19-0ubuntu6) ... Setting up multiarch-support (2.19-0ubuntu6.3) ... (Reading database ... 11789 files and directories currently installed.) Preparing to unpack .../initramfs-tools_0.103ubuntu4.2_all.deb ... Unpacking initramfs-tools (0.103ubuntu4.2) over (0.103ubuntu4) ... Preparing to unpack .../initramfs-tools-bin_0.103ubuntu4.2_amd64.deb ... Unpacking initramfs-tools-bin (0.103ubuntu4.2) over (0.103ubuntu4) ... Preparing to unpack .../apt-transport-https_1.0.1ubuntu2.1_amd64.deb ... Unpacking apt-transport-https (1.0.1ubuntu2.1) over (1.0.1ubuntu2) ... Preparing to unpack .../openssl_1.0.1f-1ubuntu2.5_amd64.deb ... Unpacking openssl (1.0.1f-1ubuntu2.5) over (1.0.1f-1ubuntu2) ... Preparing to unpack .../dpkg-dev_1.17.5ubuntu5.3_all.deb ... Unpacking dpkg-dev (1.17.5ubuntu5.3) over (1.17.5ubuntu5) ... Preparing to unpack .../libdpkg-perl_1.17.5ubuntu5.3_all.deb ... Unpacking libdpkg-perl (1.17.5ubuntu5.3) over (1.17.5ubuntu5) ... Preparing to unpack .../patch_2.7.1-4ubuntu1_amd64.deb ... Unpacking patch (2.7.1-4ubuntu1) over (2.7.1-4) ... Setting up libdbus-1-3:amd64 (1.6.18-0ubuntu4.1) ... Setting up libjson-c2:amd64 (0.11-3ubuntu1.2) ... Setting up libcgmanager0:amd64 (0.24-0ubuntu7) ... Setting up libudev1:amd64 (204-5ubuntu20.4) ... Setting up udev (204-5ubuntu20.4) ... invoke-rc.d: policy-rc.d denied execution of restart. Removing 'diversion of /bin/udevadm to /bin/udevadm.upgrade by fake-udev' update-initramfs: deferring update (trigger activated) Setting up ifupdown (0.7.47.2ubuntu4.1) ... Installing new version of config file /etc/init/network-interface.conf ... Setting up libjson0:amd64 (0.11-3ubuntu1.2) ... Setting up upstart (1.12.1-0ubuntu4.2) ... Installing new version of config file /etc/cron.daily/upstart ... Setting up libc-dev-bin (2.19-0ubuntu6.3) ... Setting up linux-libc-dev:amd64 (3.13.0-35.62) ... Setting up libc6-dev:amd64 (2.19-0ubuntu6.3) ... Setting up libtasn1-6:amd64 (3.4-3ubuntu0.1) ... Setting up libgnutls26:amd64 (2.12.23-12ubuntu2.1) ... Setting up libssl1.0.0:amd64 (1.0.1f-1ubuntu2.5) ... Setting up libkrb5support0:amd64 (1.12+dfsg-2ubuntu4.2) ... Setting up libk5crypto3:amd64 (1.12+dfsg-2ubuntu4.2) ... Setting up libkrb5-3:amd64 (1.12+dfsg-2ubuntu4.2) ... Setting up libgssapi-krb5-2:amd64 (1.12+dfsg-2ubuntu4.2) ... Setting up initramfs-tools-bin (0.103ubuntu4.2) ... Setting up initramfs-tools (0.103ubuntu4.2) ... update-initramfs: deferring update (trigger activated) Setting up apt-transport-https (1.0.1ubuntu2.1) ... Setting up openssl (1.0.1f-1ubuntu2.5) ... Setting up libdpkg-perl (1.17.5ubuntu5.3) ... Setting up patch (2.7.1-4ubuntu1) ... Setting up dpkg-dev (1.17.5ubuntu5.3) ... Processing triggers for libc-bin (2.19-0ubuntu6.3) ... Processing triggers for initramfs-tools (0.103ubuntu4.2) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-6309050', 'amd64', 'trusty', '--nolog', '--batch', '--archive=ubuntu', '--dist=trusty', '--purpose=PPA', '--architecture=amd64', '--comp=main', 'khmer_1.1-0biolinux3.dsc'] Initiating build PACKAGEBUILD-6309050 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 Automatic build of khmer_1.1-0biolinux3 on lcy01-05 by sbuild/amd64 1.170.5 Build started at 20140829-1536 ****************************************************************************** khmer_1.1-0biolinux3.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 9), python, libpython-dev, zlib1g-dev, libbz2-dev, ruby-ronn (>= 0.7.3), python-pip, python-sphinx, python-markupsafe, python-nose, python-setuptools, python-screed, sphinxcontrib-autoprogram Checking for already installed source dependencies... debhelper: missing python: missing libpython-dev: missing zlib1g-dev: missing libbz2-dev: missing ruby-ronn: missing python-pip: missing python-sphinx: missing python-markupsafe: missing python-nose: missing python-setuptools: missing python-screed: missing sphinxcontrib-autoprogram: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper python libpython-dev zlib1g-dev libbz2-dev ruby-ronn python-pip python-sphinx python-markupsafe python-nose python-setuptools python-screed sphinxcontrib-autoprogram 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 intltool-debian libasprintf0c2 libcroco3 libexpat1 libexpat1-dev libglib2.0-0 libjs-jquery libjs-sphinxdoc libjs-underscore libmagic1 libpipeline1 libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libruby1.9.1 libunistring0 libxml2 libyaml-0-2 man-db mime-support po-debconf python-chardet python-colorama python-distlib python-docutils python-html5lib python-jinja2 python-minimal python-pkg-resources python-pygments python-requests python-roman python-six python-urllib3 python2.7 python2.7-minimal ruby ruby-fast-xs ruby-hpricot ruby-mustache ruby-rack ruby-rack-protection ruby-rdiscount ruby-sinatra ruby-tilt ruby1.9.1 sgml-base sphinx-common xml-core Suggested packages: wamerican wordlist whois vacation dh-make apparmor-easyprof gettext-doc groff javascript-common less www-browser libmail-box-perl python-doc python-tk texlive-latex-recommended texlive-latex-base texlive-lang-french fonts-linuxlibertine ttf-linux-libertine python-lxml python-genshi python-jinja2-doc python-coverage python-nose-doc python-distribute python-distribute-doc ttf-bitstream-vera jsmath libjs-mathjax dvipng texlive-latex-extra texlive-fonts-recommended python2.7-doc binfmt-support ri ruby-dev ruby1.9.1-examples ri1.9.1 graphviz ruby1.9.1-dev ruby-switch sgml-base-doc Recommended packages: curl wget lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info libmail-sendmail-perl python-pil libpaper-utils docutils-doc python-dev-all sphinx-doc The following NEW packages will be installed: bsdmainutils debhelper dh-apparmor docutils-common file gettext gettext-base groff-base intltool-debian libasprintf0c2 libbz2-dev libcroco3 libexpat1 libexpat1-dev libglib2.0-0 libjs-jquery libjs-sphinxdoc libjs-underscore libmagic1 libpipeline1 libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libruby1.9.1 libunistring0 libxml2 libyaml-0-2 man-db mime-support po-debconf python python-chardet python-colorama python-distlib python-docutils python-html5lib python-jinja2 python-markupsafe python-minimal python-nose python-pip python-pkg-resources python-pygments python-requests python-roman python-screed python-setuptools python-six python-sphinx python-urllib3 python2.7 python2.7-minimal ruby ruby-fast-xs ruby-hpricot ruby-mustache ruby-rack ruby-rack-protection ruby-rdiscount ruby-ronn ruby-sinatra ruby-tilt ruby1.9.1 sgml-base sphinx-common sphinxcontrib-autoprogram xml-core zlib1g-dev 0 upgraded, 71 newly installed, 0 to remove and 0 not upgraded. Need to get 39.6 MB of archives. After this operation, 107 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! python-screed sphinxcontrib-autoprogram Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ trusty/main libexpat1 amd64 2.1.0-4ubuntu1 [71.1 kB] Get:2 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main python-screed all 0.7.1-0biolinux1 [11.6 kB] Get:3 http://ftpmaster.internal/ubuntu/ trusty-security/main libmagic1 amd64 1:5.14-2ubuntu3.1 [184 kB] Get:4 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main sphinxcontrib-autoprogram all 0.1.1-0biolinux2 [5394 B] Get:5 http://ftpmaster.internal/ubuntu/ trusty-updates/main libasprintf0c2 amd64 0.18.3.1-1ubuntu3 [6712 B] Get:6 http://ftpmaster.internal/ubuntu/ trusty/main libglib2.0-0 amd64 2.40.0-2 [1057 kB] Get:7 http://ftpmaster.internal/ubuntu/ trusty/main libpipeline1 amd64 1.3.0-1 [24.0 kB] Get:8 http://ftpmaster.internal/ubuntu/ trusty-security/main libxml2 amd64 2.9.1+dfsg1-3ubuntu4.3 [571 kB] Get:9 http://ftpmaster.internal/ubuntu/ trusty/main groff-base amd64 1.22.2-5 [1053 kB] Get:10 http://ftpmaster.internal/ubuntu/ trusty/main bsdmainutils amd64 9.0.5ubuntu1 [203 kB] Get:11 http://ftpmaster.internal/ubuntu/ trusty/main man-db amd64 2.6.7.1-1 [858 kB] Get:12 http://ftpmaster.internal/ubuntu/ trusty/main sgml-base all 1.26+nmu4ubuntu1 [12.5 kB] Get:13 http://ftpmaster.internal/ubuntu/ trusty/main libcroco3 amd64 0.6.8-2ubuntu1 [82.4 kB] Get:14 http://ftpmaster.internal/ubuntu/ trusty/main libpython2.7-minimal amd64 2.7.6-8 [307 kB] Get:15 http://ftpmaster.internal/ubuntu/ trusty/main mime-support all 3.54ubuntu1 [31.7 kB] Get:16 http://ftpmaster.internal/ubuntu/ trusty/main libpython2.7-stdlib amd64 2.7.6-8 [1872 kB] Get:17 http://ftpmaster.internal/ubuntu/ trusty/main libpython2.7 amd64 2.7.6-8 [1044 kB] Get:18 http://ftpmaster.internal/ubuntu/ trusty/main libexpat1-dev amd64 2.1.0-4ubuntu1 [115 kB] Get:19 http://ftpmaster.internal/ubuntu/ trusty/main libpython2.7-dev amd64 2.7.6-8 [22.0 MB] Get:20 http://ftpmaster.internal/ubuntu/ trusty/main libunistring0 amd64 0.9.3-5ubuntu3 [271 kB] Get:21 http://ftpmaster.internal/ubuntu/ trusty/main libyaml-0-2 amd64 0.1.4-3ubuntu3 [48.2 kB] Get:22 http://ftpmaster.internal/ubuntu/ trusty/main python2.7-minimal amd64 2.7.6-8 [1190 kB] Get:23 http://ftpmaster.internal/ubuntu/ trusty-security/main file amd64 1:5.14-2ubuntu3.1 [18.8 kB] Get:24 http://ftpmaster.internal/ubuntu/ trusty-updates/main gettext-base amd64 0.18.3.1-1ubuntu3 [48.8 kB] Get:25 http://ftpmaster.internal/ubuntu/ trusty/main xml-core all 0.13+nmu2 [23.3 kB] Get:26 http://ftpmaster.internal/ubuntu/ trusty-updates/main gettext amd64 0.18.3.1-1ubuntu3 [829 kB] Get:27 http://ftpmaster.internal/ubuntu/ trusty/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:28 http://ftpmaster.internal/ubuntu/ trusty/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:29 http://ftpmaster.internal/ubuntu/ trusty/main dh-apparmor all 2.8.95~2430-0ubuntu5 [11.3 kB] Get:30 http://ftpmaster.internal/ubuntu/ trusty/main debhelper all 9.20131227ubuntu1 [604 kB] Get:31 http://ftpmaster.internal/ubuntu/ trusty/main docutils-common all 0.11-3 [143 kB] Get:32 http://ftpmaster.internal/ubuntu/ trusty/main libbz2-dev amd64 1.0.6-5 [33.2 kB] Get:33 http://ftpmaster.internal/ubuntu/ trusty/main libjs-jquery all 1.7.2+dfsg-2ubuntu1 [78.8 kB] Get:34 http://ftpmaster.internal/ubuntu/ trusty/main libjs-underscore all 1.4.4-2ubuntu1 [45.6 kB] Get:35 http://ftpmaster.internal/ubuntu/ trusty-updates/main libjs-sphinxdoc all 1.2.2+dfsg-1ubuntu1.1 [41.4 kB] Get:36 http://ftpmaster.internal/ubuntu/ trusty/main libpython-dev amd64 2.7.5-5ubuntu3 [7078 B] Get:37 http://ftpmaster.internal/ubuntu/ trusty/main libpython-stdlib amd64 2.7.5-5ubuntu3 [7012 B] Get:38 http://ftpmaster.internal/ubuntu/ trusty/main ruby all 1:1.9.3.4 [5334 B] Get:39 http://ftpmaster.internal/ubuntu/ trusty/main ruby1.9.1 amd64 1.9.3.484-2ubuntu1 [35.6 kB] Get:40 http://ftpmaster.internal/ubuntu/ trusty/main libruby1.9.1 amd64 1.9.3.484-2ubuntu1 [2667 kB] Get:41 http://ftpmaster.internal/ubuntu/ trusty/main python2.7 amd64 2.7.6-8 [197 kB] Get:42 http://ftpmaster.internal/ubuntu/ trusty/main python-minimal amd64 2.7.5-5ubuntu3 [27.5 kB] Get:43 http://ftpmaster.internal/ubuntu/ trusty/main python amd64 2.7.5-5ubuntu3 [134 kB] Get:44 http://ftpmaster.internal/ubuntu/ trusty/main python-chardet all 2.0.1-2build2 [106 kB] Get:45 http://ftpmaster.internal/ubuntu/ trusty/universe python-colorama all 0.2.5-0.1ubuntu1 [18.3 kB] Get:46 http://ftpmaster.internal/ubuntu/ trusty/universe python-distlib all 0.1.8-1 [113 kB] Get:47 http://ftpmaster.internal/ubuntu/ trusty/main python-roman all 2.0.0-1 [7758 B] Get:48 http://ftpmaster.internal/ubuntu/ trusty/main python-docutils all 0.11-3 [348 kB] Get:49 http://ftpmaster.internal/ubuntu/ trusty/main python-six all 1.5.2-1 [8060 B] Get:50 http://ftpmaster.internal/ubuntu/ trusty/main python-html5lib all 0.999-2 [83.2 kB] Get:51 http://ftpmaster.internal/ubuntu/ trusty/main python-markupsafe amd64 0.18-1build2 [14.3 kB] Get:52 http://ftpmaster.internal/ubuntu/ trusty/main python-jinja2 all 2.7.2-2 [161 kB] Get:53 http://ftpmaster.internal/ubuntu/ trusty/main python-pkg-resources all 3.3-1ubuntu1 [61.9 kB] Get:54 http://ftpmaster.internal/ubuntu/ trusty/main python-nose all 1.3.1-2 [119 kB] Get:55 http://ftpmaster.internal/ubuntu/ trusty/main python-setuptools all 3.3-1ubuntu1 [230 kB] Get:56 http://ftpmaster.internal/ubuntu/ trusty/main python-urllib3 all 1.7.1-1build1 [38.9 kB] Get:57 http://ftpmaster.internal/ubuntu/ trusty/main python-requests all 2.2.1-1 [42.5 kB] Get:58 http://ftpmaster.internal/ubuntu/ trusty/universe python-pip all 1.5.4-1 [97.7 kB] Get:59 http://ftpmaster.internal/ubuntu/ trusty/main python-pygments all 1.6+dfsg-1ubuntu1 [519 kB] Get:60 http://ftpmaster.internal/ubuntu/ trusty-updates/main sphinx-common all 1.2.2+dfsg-1ubuntu1.1 [392 kB] Get:61 http://ftpmaster.internal/ubuntu/ trusty-updates/main python-sphinx all 1.2.2+dfsg-1ubuntu1.1 [271 kB] Get:62 http://ftpmaster.internal/ubuntu/ trusty/universe ruby-fast-xs amd64 0.8.0-3build1 [8996 B] Get:63 http://ftpmaster.internal/ubuntu/ trusty/universe ruby-hpricot amd64 0.8.6-5ubuntu1 [79.9 kB] Get:64 http://ftpmaster.internal/ubuntu/ trusty/universe ruby-rack all 1.5.2-1 [95.8 kB] Get:65 http://ftpmaster.internal/ubuntu/ trusty/universe ruby-tilt all 2.0.0+really1.4.1-1 [20.9 kB] Get:66 http://ftpmaster.internal/ubuntu/ trusty/universe ruby-rack-protection all 1.5.1-1 [10.5 kB] Get:67 http://ftpmaster.internal/ubuntu/ trusty/universe ruby-sinatra all 1.4.3-2 [263 kB] Get:68 http://ftpmaster.internal/ubuntu/ trusty/universe ruby-mustache all 0.99.4-4 [28.7 kB] Get:69 http://ftpmaster.internal/ubuntu/ trusty/universe ruby-rdiscount amd64 1.6.8-3build1 [36.5 kB] Get:70 http://ftpmaster.internal/ubuntu/ trusty/universe ruby-ronn all 0.7.3-2 [29.4 kB] Get:71 http://ftpmaster.internal/ubuntu/ trusty/main zlib1g-dev amd64 1:1.2.8.dfsg-1ubuntu1 [183 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 39.6 MB in 3s (10.4 MB/s) Selecting previously unselected package libexpat1:amd64. (Reading database ... 11788 files and directories currently installed.) Preparing to unpack .../libexpat1_2.1.0-4ubuntu1_amd64.deb ... Unpacking libexpat1:amd64 (2.1.0-4ubuntu1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../libmagic1_1%3a5.14-2ubuntu3.1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.14-2ubuntu3.1) ... Selecting previously unselected package libasprintf0c2:amd64. Preparing to unpack .../libasprintf0c2_0.18.3.1-1ubuntu3_amd64.deb ... Unpacking libasprintf0c2:amd64 (0.18.3.1-1ubuntu3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../libglib2.0-0_2.40.0-2_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.40.0-2) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../libpipeline1_1.3.0-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.3.0-1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../libxml2_2.9.1+dfsg1-3ubuntu4.3_amd64.deb ... 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Preparing to unpack .../python-sphinx_1.2.2+dfsg-1ubuntu1.1_all.deb ... Unpacking python-sphinx (1.2.2+dfsg-1ubuntu1.1) ... Selecting previously unselected package ruby-fast-xs. Preparing to unpack .../ruby-fast-xs_0.8.0-3build1_amd64.deb ... Unpacking ruby-fast-xs (0.8.0-3build1) ... Selecting previously unselected package ruby-hpricot. Preparing to unpack .../ruby-hpricot_0.8.6-5ubuntu1_amd64.deb ... Unpacking ruby-hpricot (0.8.6-5ubuntu1) ... Selecting previously unselected package ruby-rack. Preparing to unpack .../ruby-rack_1.5.2-1_all.deb ... Unpacking ruby-rack (1.5.2-1) ... Selecting previously unselected package ruby-tilt. Preparing to unpack .../ruby-tilt_2.0.0+really1.4.1-1_all.deb ... Unpacking ruby-tilt (2.0.0+really1.4.1-1) ... Selecting previously unselected package ruby-rack-protection. Preparing to unpack .../ruby-rack-protection_1.5.1-1_all.deb ... Unpacking ruby-rack-protection (1.5.1-1) ... Selecting previously unselected package ruby-sinatra. Preparing to unpack .../ruby-sinatra_1.4.3-2_all.deb ... Unpacking ruby-sinatra (1.4.3-2) ... Selecting previously unselected package ruby-mustache. Preparing to unpack .../ruby-mustache_0.99.4-4_all.deb ... Unpacking ruby-mustache (0.99.4-4) ... Selecting previously unselected package ruby-rdiscount. Preparing to unpack .../ruby-rdiscount_1.6.8-3build1_amd64.deb ... Unpacking ruby-rdiscount (1.6.8-3build1) ... Selecting previously unselected package ruby-ronn. Preparing to unpack .../ruby-ronn_0.7.3-2_all.deb ... Unpacking ruby-ronn (0.7.3-2) ... Selecting previously unselected package sphinxcontrib-autoprogram. Preparing to unpack .../sphinxcontrib-autoprogram_0.1.1-0biolinux2_all.deb ... Unpacking sphinxcontrib-autoprogram (0.1.1-0biolinux2) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-1ubuntu1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-1ubuntu1) ... Setting up libexpat1:amd64 (2.1.0-4ubuntu1) ... Setting up libmagic1:amd64 (1:5.14-2ubuntu3.1) ... Setting up libasprintf0c2:amd64 (0.18.3.1-1ubuntu3) ... Setting up libglib2.0-0:amd64 (2.40.0-2) ... No schema files found: doing nothing. Setting up libpipeline1:amd64 (1.3.0-1) ... Setting up libxml2:amd64 (2.9.1+dfsg1-3ubuntu4.3) ... Setting up groff-base (1.22.2-5) ... Setting up bsdmainutils (9.0.5ubuntu1) ... 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 man-db (2.6.7.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up sgml-base (1.26+nmu4ubuntu1) ... Setting up libcroco3:amd64 (0.6.8-2ubuntu1) ... Setting up libpython2.7-minimal:amd64 (2.7.6-8) ... Setting up mime-support (3.54ubuntu1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode Setting up libpython2.7-stdlib:amd64 (2.7.6-8) ... Setting up libpython2.7:amd64 (2.7.6-8) ... Setting up libexpat1-dev:amd64 (2.1.0-4ubuntu1) ... Setting up libpython2.7-dev:amd64 (2.7.6-8) ... Setting up libunistring0:amd64 (0.9.3-5ubuntu3) ... Setting up libyaml-0-2:amd64 (0.1.4-3ubuntu3) ... Setting up python2.7-minimal (2.7.6-8) ... Linking and byte-compiling packages for runtime python2.7... Setting up file (1:5.14-2ubuntu3.1) ... Setting up gettext-base (0.18.3.1-1ubuntu3) ... Setting up xml-core (0.13+nmu2) ... Setting up gettext (0.18.3.1-1ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2ubuntu1) ... Setting up dh-apparmor (2.8.95~2430-0ubuntu5) ... Setting up debhelper (9.20131227ubuntu1) ... Setting up libbz2-dev:amd64 (1.0.6-5) ... Setting up libjs-jquery (1.7.2+dfsg-2ubuntu1) ... Setting up libjs-underscore (1.4.4-2ubuntu1) ... Setting up libjs-sphinxdoc (1.2.2+dfsg-1ubuntu1.1) ... Setting up libpython-dev:amd64 (2.7.5-5ubuntu3) ... Setting up libpython-stdlib:amd64 (2.7.5-5ubuntu3) ... Setting up python2.7 (2.7.6-8) ... Setting up python-minimal (2.7.5-5ubuntu3) ... Setting up python (2.7.5-5ubuntu3) ... Setting up python-chardet (2.0.1-2build2) ... Setting up python-colorama (0.2.5-0.1ubuntu1) ... Setting up python-distlib (0.1.8-1) ... Setting up python-roman (2.0.0-1) ... Setting up python-six (1.5.2-1) ... Setting up python-html5lib (0.999-2) ... Setting up python-markupsafe (0.18-1build2) ... Setting up python-jinja2 (2.7.2-2) ... Setting up python-pkg-resources (3.3-1ubuntu1) ... Setting up python-nose (1.3.1-2) ... Setting up python-setuptools (3.3-1ubuntu1) ... Setting up python-urllib3 (1.7.1-1build1) ... Setting up python-requests (2.2.1-1) ... Setting up python-pip (1.5.4-1) ... Setting up python-pygments (1.6+dfsg-1ubuntu1) ... Setting up python-screed (0.7.1-0biolinux1) ... Setting up sphinx-common (1.2.2+dfsg-1ubuntu1.1) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-1ubuntu1) ... Processing triggers for sgml-base (1.26+nmu4ubuntu1) ... Setting up docutils-common (0.11-3) ... Processing triggers for sgml-base (1.26+nmu4ubuntu1) ... Setting up python-docutils (0.11-3) ... 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-sphinx (1.2.2+dfsg-1ubuntu1.1) ... Setting up sphinxcontrib-autoprogram (0.1.1-0biolinux2) ... Setting up ruby (1:1.9.3.4) ... Setting up ruby1.9.1 (1.9.3.484-2ubuntu1) ... Setting up libruby1.9.1 (1.9.3.484-2ubuntu1) ... Setting up ruby-fast-xs (0.8.0-3build1) ... Setting up ruby-hpricot (0.8.6-5ubuntu1) ... Setting up ruby-rack (1.5.2-1) ... Setting up ruby-tilt (2.0.0+really1.4.1-1) ... Setting up ruby-rack-protection (1.5.1-1) ... Setting up ruby-sinatra (1.4.3-2) ... Setting up ruby-mustache (0.99.4-4) ... Setting up ruby-rdiscount (1.6.8-3build1) ... Setting up ruby-ronn (0.7.3-2) ... Processing triggers for libc-bin (2.19-0ubuntu6.3) ... Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.19-0ubuntu6.3 make_3.81-8.2ubuntu3 dpkg-dev_1.17.5ubuntu5.3 gcc-4.8_4.8.2-19ubuntu1 g++-4.8_4.8.2-19ubuntu1 binutils_2.24-5ubuntu3 libstdc++-4.8-dev_4.8.2-19ubuntu1 libstdc++6_4.8.2-19ubuntu1 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::Quilt gpgv: Signature made Fri Aug 29 15:23:15 2014 UTC using DSA key ID 113960C5 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./khmer_1.1-0biolinux3.dsc dpkg-source: info: extracting khmer in khmer-1.1 dpkg-source: info: unpacking khmer_1.1.orig.tar.gz dpkg-source: info: unpacking khmer_1.1-0biolinux3.debian.tar.gz dpkg-source: info: applying use_system_libs.patch dpkg-source: info: applying disable_google_analytics dpkg-source: info: applying makefile.patch dpkg-buildpackage: source package khmer dpkg-buildpackage: source version 1.1-0biolinux3 dpkg-buildpackage: source distribution trusty dpkg-source --before-build khmer-1.1 dpkg-buildpackage: host architecture amd64 /usr/bin/fakeroot debian/rules clean dh clean --with=python2 dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory `/build/buildd/khmer-1.1' dh_auto_clean make[2]: Entering directory `/build/buildd/khmer-1.1' cd lib && make clean || true make[3]: Entering directory `/build/buildd/khmer-1.1/lib' (cd ../third-party/zlib && make distclean) make[4]: Entering directory `/build/buildd/khmer-1.1/third-party/zlib' make[4]: *** No rule to make target `distclean'. Stop. make[4]: Leaving directory `/build/buildd/khmer-1.1/third-party/zlib' make[3]: [clean] Error 2 (ignored) (cd ../third-party/bzip2 && make -f Makefile-libbz2_so clean) make[4]: Entering directory `/build/buildd/khmer-1.1/third-party/bzip2' rm -f blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o bzip2.o libbz2.so.1.0.6 libbz2.so.1.0 bzip2-shared make[4]: Leaving directory `/build/buildd/khmer-1.1/third-party/bzip2' rm -f *.o zlib/Makefile make[3]: Leaving directory `/build/buildd/khmer-1.1/lib' cd tests && rm -rf khmertest_* || true rm -f khmer/_khmermodule.so || true rm khmer/*.pyc lib/*.pyc || true rm: cannot remove 'khmer/*.pyc': No such file or directory rm: cannot remove 'lib/*.pyc': No such file or directory ./setup.py clean --all || true running clean 'build/lib.linux-x86_64-2.7' does not exist -- can't clean it 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it rm coverage-debug || true rm: cannot remove 'coverage-debug': No such file or directory make[2]: Leaving directory `/build/buildd/khmer-1.1' rm -rf build find -name '*.pyc' -delete make[1]: Leaving directory `/build/buildd/khmer-1.1' debian/rules override_dh_clean make[1]: Entering directory `/build/buildd/khmer-1.1' dh_clean rm -rf _develop rm -rf *.egg-info rm -rf third-party rm -rf *.zip find -name '.git*' -delete rm -f debian/*.1 rm -rf l make[1]: Leaving directory `/build/buildd/khmer-1.1' debian/rules build-arch dh build-arch --with=python2 dh_testdir -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory `/build/buildd/khmer-1.1' dh_auto_build make[2]: Entering directory `/build/buildd/khmer-1.1' ./setup.py build_ext --inplace running build_ext building 'khmer._khmermodule' extension creating build creating build/temp.linux-x86_64-2.7 creating build/temp.linux-x86_64-2.7/khmer creating build/temp.linux-x86_64-2.7/lib x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c khmer/_khmermodule.cc -o build/temp.linux-x86_64-2.7/khmer/_khmermodule.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/khmer_config.cc -o build/temp.linux-x86_64-2.7/lib/khmer_config.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/thread_id_map.cc -o build/temp.linux-x86_64-2.7/lib/thread_id_map.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/trace_logger.cc -o build/temp.linux-x86_64-2.7/lib/trace_logger.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/perf_metrics.cc -o build/temp.linux-x86_64-2.7/lib/perf_metrics.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/read_parsers.cc -o build/temp.linux-x86_64-2.7/lib/read_parsers.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/kmer_hash.cc -o build/temp.linux-x86_64-2.7/lib/kmer_hash.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/hashtable.cc -o build/temp.linux-x86_64-2.7/lib/hashtable.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/hashbits.cc -o build/temp.linux-x86_64-2.7/lib/hashbits.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/labelhash.cc -o build/temp.linux-x86_64-2.7/lib/labelhash.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/counting.cc -o build/temp.linux-x86_64-2.7/lib/counting.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/subset.cc -o build/temp.linux-x86_64-2.7/lib/subset.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/aligner.cc -o build/temp.linux-x86_64-2.7/lib/aligner.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/scoringmatrix.cc -o build/temp.linux-x86_64-2.7/lib/scoringmatrix.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/node.cc -o build/temp.linux-x86_64-2.7/lib/node.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/kmer.cc -o build/temp.linux-x86_64-2.7/lib/kmer.o -O3 creating build/lib.linux-x86_64-2.7 creating build/lib.linux-x86_64-2.7/khmer c++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-2.7/khmer/_khmermodule.o build/temp.linux-x86_64-2.7/lib/khmer_config.o build/temp.linux-x86_64-2.7/lib/thread_id_map.o build/temp.linux-x86_64-2.7/lib/trace_logger.o build/temp.linux-x86_64-2.7/lib/perf_metrics.o build/temp.linux-x86_64-2.7/lib/read_parsers.o build/temp.linux-x86_64-2.7/lib/kmer_hash.o build/temp.linux-x86_64-2.7/lib/hashtable.o build/temp.linux-x86_64-2.7/lib/hashbits.o build/temp.linux-x86_64-2.7/lib/labelhash.o build/temp.linux-x86_64-2.7/lib/counting.o build/temp.linux-x86_64-2.7/lib/subset.o build/temp.linux-x86_64-2.7/lib/aligner.o build/temp.linux-x86_64-2.7/lib/scoringmatrix.o build/temp.linux-x86_64-2.7/lib/node.o build/temp.linux-x86_64-2.7/lib/kmer.o -lz -lbz2 -o build/lib.linux-x86_64-2.7/khmer/_khmermodule.so copying build/lib.linux-x86_64-2.7/khmer/_khmermodule.so -> khmer make[2]: Leaving directory `/build/buildd/khmer-1.1' #This is awkward... mkdir _develop env PYTHONPATH="`pwd`/_develop" python ./setup.py develop -d _develop running develop running egg_info creating khmer.egg-info writing requirements to khmer.egg-info/requires.txt writing khmer.egg-info/PKG-INFO writing top-level names to khmer.egg-info/top_level.txt writing dependency_links to khmer.egg-info/dependency_links.txt writing manifest file 'khmer.egg-info/SOURCES.txt' reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.cc' under directory 'third-party' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'README*' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching '*.c' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '[Mm]akefile*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching '*.h' under directory 'third-party' warning: no files found matching 'ChangeLog' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution writing manifest file 'khmer.egg-info/SOURCES.txt' running build_ext building 'khmer._khmermodule' extension x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c khmer/_khmermodule.cc -o build/temp.linux-x86_64-2.7/khmer/_khmermodule.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/khmer_config.cc -o build/temp.linux-x86_64-2.7/lib/khmer_config.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/thread_id_map.cc -o build/temp.linux-x86_64-2.7/lib/thread_id_map.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/trace_logger.cc -o build/temp.linux-x86_64-2.7/lib/trace_logger.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/perf_metrics.cc -o build/temp.linux-x86_64-2.7/lib/perf_metrics.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/read_parsers.cc -o build/temp.linux-x86_64-2.7/lib/read_parsers.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/kmer_hash.cc -o build/temp.linux-x86_64-2.7/lib/kmer_hash.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/hashtable.cc -o build/temp.linux-x86_64-2.7/lib/hashtable.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/hashbits.cc -o build/temp.linux-x86_64-2.7/lib/hashbits.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/labelhash.cc -o build/temp.linux-x86_64-2.7/lib/labelhash.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/counting.cc -o build/temp.linux-x86_64-2.7/lib/counting.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/subset.cc -o build/temp.linux-x86_64-2.7/lib/subset.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/aligner.cc -o build/temp.linux-x86_64-2.7/lib/aligner.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/scoringmatrix.cc -o build/temp.linux-x86_64-2.7/lib/scoringmatrix.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/node.cc -o build/temp.linux-x86_64-2.7/lib/node.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/kmer.cc -o build/temp.linux-x86_64-2.7/lib/kmer.o -O3 c++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-2.7/khmer/_khmermodule.o build/temp.linux-x86_64-2.7/lib/khmer_config.o build/temp.linux-x86_64-2.7/lib/thread_id_map.o build/temp.linux-x86_64-2.7/lib/trace_logger.o build/temp.linux-x86_64-2.7/lib/perf_metrics.o build/temp.linux-x86_64-2.7/lib/read_parsers.o build/temp.linux-x86_64-2.7/lib/kmer_hash.o build/temp.linux-x86_64-2.7/lib/hashtable.o build/temp.linux-x86_64-2.7/lib/hashbits.o build/temp.linux-x86_64-2.7/lib/labelhash.o build/temp.linux-x86_64-2.7/lib/counting.o build/temp.linux-x86_64-2.7/lib/subset.o build/temp.linux-x86_64-2.7/lib/aligner.o build/temp.linux-x86_64-2.7/lib/scoringmatrix.o build/temp.linux-x86_64-2.7/lib/node.o build/temp.linux-x86_64-2.7/lib/kmer.o -lz -lbz2 -o build/lib.linux-x86_64-2.7/khmer/_khmermodule.so copying build/lib.linux-x86_64-2.7/khmer/_khmermodule.so -> khmer Creating /build/buildd/khmer-1.1/_develop/site.py Creating /build/buildd/khmer-1.1/_develop/khmer.egg-link (link to .) Adding khmer 1.1 to easy-install.pth file Installing fastq-to-fasta.py script to _develop Installing abundance-dist.py script to _develop Installing merge-partitions.py script to _develop Installing filter-abund-single.py script to _develop Installing interleave-reads.py script to _develop Installing count-overlap.py script to _develop Installing filter-stoptags.py script to _develop Installing partition-graph.py script to _develop Installing abundance-dist-single.py script to _develop Installing extract-partitions.py script to _develop Installing count-median.py script to _develop Installing sample-reads-randomly.py script to _develop Installing split-paired-reads.py script to _develop Installing annotate-partitions.py script to _develop Installing find-knots.py script to _develop Installing do-partition.py script to _develop Installing extract-paired-reads.py script to _develop Installing load-into-counting.py script to _develop Installing load-graph.py script to _develop Installing make-initial-stoptags.py script to _develop Installing extract-long-sequences.py script to _develop Installing normalize-by-median.py script to _develop Installing filter-abund.py script to _develop Installed /build/buildd/khmer-1.1 Processing dependencies for khmer==1.1 Searching for screed==0.7.1 Best match: screed 0.7.1 Adding screed 0.7.1 to easy-install.pth file Using /usr/lib/python2.7/dist-packages Finished processing dependencies for khmer==1.1 make doc VERSION=1.1 make[2]: Entering directory `/build/buildd/khmer-1.1' pip2 install --user sphinx sphinxcontrib-autoprogram || pip2 install \ sphinx sphinxcontrib-autoprogram Requirement already satisfied (use --upgrade to upgrade): sphinx in /usr/lib/python2.7/dist-packages Requirement already satisfied (use --upgrade to upgrade): sphinxcontrib-autoprogram in /usr/lib/python2.7/dist-packages Requirement already satisfied (use --upgrade to upgrade): Pygments>=1.2 in /usr/lib/python2.7/dist-packages (from sphinx) Requirement already satisfied (use --upgrade to upgrade): docutils>=0.7 in /usr/lib/python2.7/dist-packages (from sphinx) Requirement already satisfied (use --upgrade to upgrade): Jinja2>=2.3 in /usr/lib/python2.7/dist-packages (from sphinx) Requirement already satisfied (use --upgrade to upgrade): markupsafe in /usr/lib/python2.7/dist-packages (from Jinja2>=2.3->sphinx) Cleaning up... ./setup.py build_sphinx --fresh-env running build_sphinx creating /build/buildd/khmer-1.1/build/sphinx creating /build/buildd/khmer-1.1/build/sphinx/doctrees creating /build/buildd/khmer-1.1/build/sphinx/html Running Sphinx v1.2.2 building [html]: targets for 20 source files that are out of date updating environment: 20 added, 0 changed, 0 removed reading sources... [ 5%] LICENSE reading sources... [ 10%] biblio reading sources... [ 15%] blog-posts reading sources... [ 20%] choosing-table-sizes reading sources... [ 25%] contributors reading sources... [ 30%] crazy-ideas reading sources... [ 35%] design reading sources... [ 40%] details reading sources... [ 45%] development reading sources... [ 50%] examples reading sources... [ 55%] galaxy reading sources... [ 60%] guide reading sources... [ 65%] index reading sources... [ 70%] install reading sources... [ 75%] introduction reading sources... [ 80%] known-issues reading sources... [ 85%] partitioning-big-data reading sources... [ 90%] release reading sources... [ 95%] requirements reading sources... [100%] scripts looking for now-outdated files... none found pickling environment... done checking consistency... /build/buildd/khmer-1.1/doc/requirements.txt:: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 5%] LICENSE writing output... [ 10%] biblio writing output... [ 15%] blog-posts writing output... [ 20%] choosing-table-sizes writing output... [ 25%] contributors writing output... [ 30%] crazy-ideas writing output... [ 35%] design writing output... [ 40%] details writing output... [ 45%] development writing output... [ 50%] examples writing output... [ 55%] galaxy writing output... [ 60%] guide writing output... [ 65%] index writing output... [ 70%] install writing output... [ 75%] introduction writing output... [ 80%] known-issues writing output... [ 85%] partitioning-big-data writing output... [ 90%] release writing output... [ 95%] requirements writing output... [100%] scripts writing additional files... genindex py-modindex search copying images... [ 50%] artifact-removal.png copying images... [100%] partitioning-workflow.png copying static files... done copying extra files... done dumping search index... done dumping object inventory... done build succeeded, 1 warning. --> docs in build/sphinx/html <-- make[2]: Leaving directory `/build/buildd/khmer-1.1' ronn -r --manual=khmer --organization='Michigan State University' debian/khmer.1.ronn roff: debian/khmer.1 mkdir l && ln -s /usr/lib/khmer/bin/ ./l/scripts make[1]: Leaving directory `/build/buildd/khmer-1.1' dh_auto_test -a make[1]: Entering directory `/build/buildd/khmer-1.1' pip2 install --user nose || pip2 install nose Requirement already satisfied (use --upgrade to upgrade): nose in /usr/lib/python2.7/dist-packages Cleaning up... ./setup.py nosetests running nosetests running egg_info writing requirements to khmer.egg-info/requires.txt writing khmer.egg-info/PKG-INFO writing top-level names to khmer.egg-info/top_level.txt writing dependency_links to khmer.egg-info/dependency_links.txt reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.cc' under directory 'third-party' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'README*' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching '*.c' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '[Mm]akefile*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching '*.h' under directory 'third-party' warning: no files found matching 'ChangeLog' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution writing manifest file 'khmer.egg-info/SOURCES.txt' running build_ext building 'khmer._khmermodule' extension x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c khmer/_khmermodule.cc -o build/temp.linux-x86_64-2.7/khmer/_khmermodule.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/khmer_config.cc -o build/temp.linux-x86_64-2.7/lib/khmer_config.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/thread_id_map.cc -o build/temp.linux-x86_64-2.7/lib/thread_id_map.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/trace_logger.cc -o build/temp.linux-x86_64-2.7/lib/trace_logger.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/perf_metrics.cc -o build/temp.linux-x86_64-2.7/lib/perf_metrics.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/read_parsers.cc -o build/temp.linux-x86_64-2.7/lib/read_parsers.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/kmer_hash.cc -o build/temp.linux-x86_64-2.7/lib/kmer_hash.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/hashtable.cc -o build/temp.linux-x86_64-2.7/lib/hashtable.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/hashbits.cc -o build/temp.linux-x86_64-2.7/lib/hashbits.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/labelhash.cc -o build/temp.linux-x86_64-2.7/lib/labelhash.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/counting.cc -o build/temp.linux-x86_64-2.7/lib/counting.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/subset.cc -o build/temp.linux-x86_64-2.7/lib/subset.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/aligner.cc -o build/temp.linux-x86_64-2.7/lib/aligner.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/scoringmatrix.cc -o build/temp.linux-x86_64-2.7/lib/scoringmatrix.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/node.cc -o build/temp.linux-x86_64-2.7/lib/node.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/kmer.cc -o build/temp.linux-x86_64-2.7/lib/kmer.o -O3 c++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-2.7/khmer/_khmermodule.o build/temp.linux-x86_64-2.7/lib/khmer_config.o build/temp.linux-x86_64-2.7/lib/thread_id_map.o build/temp.linux-x86_64-2.7/lib/trace_logger.o build/temp.linux-x86_64-2.7/lib/perf_metrics.o build/temp.linux-x86_64-2.7/lib/read_parsers.o build/temp.linux-x86_64-2.7/lib/kmer_hash.o build/temp.linux-x86_64-2.7/lib/hashtable.o build/temp.linux-x86_64-2.7/lib/hashbits.o build/temp.linux-x86_64-2.7/lib/labelhash.o build/temp.linux-x86_64-2.7/lib/counting.o build/temp.linux-x86_64-2.7/lib/subset.o build/temp.linux-x86_64-2.7/lib/aligner.o build/temp.linux-x86_64-2.7/lib/scoringmatrix.o build/temp.linux-x86_64-2.7/lib/node.o build/temp.linux-x86_64-2.7/lib/kmer.o -lz -lbz2 -o build/lib.linux-x86_64-2.7/khmer/_khmermodule.so copying build/lib.linux-x86_64-2.7/khmer/_khmermodule.so -> khmer tests.test_align.test_alignnocov ... ok tests.test_align.test_readalign ... ok tests.test_align.test_alignerrorregion ... ok tests.test_c_wrapper.test_raise_in_consume_fasta ... ok tests.test_counting_hash.Test_CountingHash.test_collision_1 ... ok tests.test_counting_hash.Test_CountingHash.test_collision_2 ... ok tests.test_counting_hash.Test_CountingHash.test_collision_3 ... ok tests.test_counting_hash.test_3_tables ... ok tests.test_counting_hash.test_simple_median ... ok tests.test_counting_hash.test_simple_kadian ... ok tests.test_counting_hash.test_simple_kadian_2 ... ok tests.test_counting_hash.test_2_kadian ... ok tests.test_counting_hash.test_save_load ... ok tests.test_counting_hash.test_load_gz ... ok tests.test_counting_hash.test_save_load_gz ... ok tests.test_counting_hash.test_trim_full ... ok tests.test_counting_hash.test_trim_short ... ok tests.test_counting_hash.test_maxcount ... ok tests.test_counting_hash.test_maxcount_with_bigcount ... ok tests.test_counting_hash.test_maxcount_with_bigcount_save ... ok tests.test_counting_hash.test_bigcount_save ... ok tests.test_counting_hash.test_nobigcount_save ... ok tests.test_counting_hash.test_bigcount_abund_dist ... ok tests.test_counting_hash.test_bigcount_abund_dist_2 ... ok tests.test_counting_hash.test_bigcount_overflow ... ok tests.test_counting_hash.test_get_ksize ... ok tests.test_counting_hash.test_get_hashsizes ... ok tests.test_counting_hash.test_consume_high_abund_kmers ... ok tests.test_counting_hash.test_load_notexist_should_fail ... ok tests.test_counting_hash.test_load_truncated_should_fail ... ok tests.test_counting_hash.test_load_gz_notexist_should_fail ... ok tests.test_counting_hash.test_load_gz_truncated_should_fail ... ok tests.test_counting_hash.test_counting_file_version_check ... ok tests.test_counting_hash.test_counting_gz_file_version_check ... ok tests.test_counting_hash.test_counting_file_type_check ... ok tests.test_counting_hash.test_counting_gz_file_type_check ... ok tests.test_counting_hash.test_counting_bad_primes_list ... ok tests.test_counting_hash.test_bad_use_bigcount ... ok tests.test_counting_hash.test_consume_absentfasta ... ok tests.test_counting_hash.test_consume_absentfasta_with_reads_parser ... ok tests.test_counting_hash.test_badconsume ... ok tests.test_counting_hash.test_badconsume_high_abund_kmers ... ok tests.test_counting_hash.test_get_badmin_count ... ok tests.test_counting_hash.test_get_badmax_count ... ok tests.test_counting_hash.test_get_badmedian_count ... ok tests.test_counting_hash.test_get_badkadian_count ... ok tests.test_counting_hash.test_badget ... ok tests.test_counting_hash.test_badtrim ... ok tests.test_counting_hash.test_badfasta_count_kmers_by_position ... ok tests.test_counting_hash.test_badload ... ok tests.test_counting_hash.test_badsave ... ok tests.test_counting_hash.test_badksize ... ok tests.test_counting_hash.test_badhashsizes ... ok tests.test_counting_hash.test_badconsume_and_tag ... ok tests.test_counting_hash.test_consume_fasta_and_tag ... ok tests.test_counting_single.Test_AbundanceDistribution.test_count_A ... ok tests.test_counting_single.Test_ConsumeString.test_abundance_by_pos ... ok tests.test_counting_single.Test_ConsumeString.test_abundance_by_pos_bigcount ... ok tests.test_counting_single.Test_ConsumeString.test_max_count ... ok tests.test_counting_single.Test_ConsumeString.test_min_count ... ok tests.test_counting_single.Test_ConsumeString.test_n_occupied ... ok tests.test_counting_single.Test_ConsumeString.test_n_occupied_args ... ok tests.test_counting_single.Test_ConsumeString.test_simple ... ok tests.test_counting_single.Test_ConsumeString.test_simple_2 ... ok tests.test_counting_single.Test_ConsumeString.test_simple_rc ... ok tests.test_counting_single.test_no_collision ... ok tests.test_counting_single.test_collision ... ok tests.test_counting_single.test_badcount ... ok tests.test_counting_single.test_hashtable_n_entries ... ok tests.test_counting_single.test_complete_no_collision ... ok tests.test_counting_single.test_complete_2_collision ... ok tests.test_counting_single.test_complete_4_collision ... ok tests.test_counting_single.test_maxcount ... ok tests.test_counting_single.test_maxcount_with_bigcount ... ok tests.test_counting_single.test_consume_uniqify_first ... ok tests.test_counting_single.test_maxcount_consume ... ok tests.test_counting_single.test_maxcount_consume_with_bigcount ... ok tests.test_counting_single.test_get_mincount ... ok tests.test_counting_single.test_get_maxcount ... ok tests.test_counting_single.test_get_maxcount_rc ... ok tests.test_counting_single.test_get_mincount_rc ... ok tests.test_counting_single.test_64bitshift ... ok tests.test_counting_single.test_64bitshift_2 ... ok tests.test_counting_single.test_very_short_read ... ok tests.test_filter.Test_Filter.test_abund ... ok tests.test_functions.test_forward_hash ... ok tests.test_functions.test_forward_hash_no_rc ... ok tests.test_functions.test_reverse_hash ... ok tests.test_functions.test_get_primes ... ok tests.test_functions.test_extract_countinghash_info ... ok tests.test_functions.test_extract_hashbits_info ... ok tests.test_graph.Test_ExactGraphFu.test_counts ... ok tests.test_graph.Test_ExactGraphFu.test_graph_links_next_a ... ok tests.test_graph.Test_ExactGraphFu.test_graph_links_next_c ... ok tests.test_graph.Test_ExactGraphFu.test_graph_links_next_g ... ok tests.test_graph.Test_ExactGraphFu.test_graph_links_next_t ... ok tests.test_graph.Test_ExactGraphFu.test_graph_links_prev_a ... ok tests.test_graph.Test_ExactGraphFu.test_graph_links_prev_c ... ok tests.test_graph.Test_ExactGraphFu.test_graph_links_prev_g ... ok tests.test_graph.Test_ExactGraphFu.test_graph_links_prev_t ... ok tests.test_graph.Test_InexactGraphFu.test_graph_links_next_a ... ok tests.test_graph.Test_InexactGraphFu.test_graph_links_next_c ... ok tests.test_graph.Test_InexactGraphFu.test_graph_links_next_g ... ok tests.test_graph.Test_InexactGraphFu.test_graph_links_next_t ... ok tests.test_graph.Test_InexactGraphFu.test_graph_links_prev_a ... ok tests.test_graph.Test_InexactGraphFu.test_graph_links_prev_c ... ok tests.test_graph.Test_InexactGraphFu.test_graph_links_prev_g ... ok tests.test_graph.Test_InexactGraphFu.test_graph_links_prev_t ... ok tests.test_graph.Test_Partitioning.test_connected_20_a ... ok tests.test_graph.Test_Partitioning.test_connected_20_b ... ok tests.test_graph.Test_Partitioning.test_connected_31_c ... ok tests.test_graph.Test_Partitioning.test_disconnected_20_a ... ok tests.test_graph.Test_Partitioning.test_disconnected_20_b ... ok tests.test_graph.Test_Partitioning.test_disconnected_31_c ... ok tests.test_graph.Test_Partitioning.test_not_output_unassigned ... ok tests.test_graph.Test_Partitioning.test_output_fq ... ok tests.test_graph.Test_Partitioning.test_output_unassigned ... ok tests.test_graph.Test_PythonAPI.test_ordered_connect ... ok tests.test_hashbits.test__get_set_tag_density ... ok tests.test_hashbits.test_n_occupied_1 ... ok tests.test_hashbits.test_bloom_python_1 ... ok tests.test_hashbits.test_bloom_c_1 ... ok tests.test_hashbits.test_n_occupied_2 ... ok tests.test_hashbits.test_bloom_c_2 ... ok tests.test_hashbits.test_filter_if_present ... ok tests.test_hashbits.test_combine_pe ... ok tests.test_hashbits.test_load_partitioned ... ok tests.test_hashbits.test_count_within_radius_simple ... ok tests.test_hashbits.test_count_within_radius_big ... ok tests.test_hashbits.test_count_kmer_degree ... ok tests.test_hashbits.test_find_radius_for_volume ... ok tests.test_hashbits.test_circumference ... ok tests.test_hashbits.test_save_load_tagset ... ok tests.test_hashbits.test_save_load_tagset_noclear ... ok tests.test_hashbits.test_stop_traverse ... ok tests.test_hashbits.test_tag_across_stoptraverse ... ok tests.test_hashbits.test_notag_across_stoptraverse ... ok tests.test_hashbits.test_find_stoptags ... ok tests.test_hashbits.test_find_stoptags2 ... ok tests.test_hashbits.test_get_ksize ... ok tests.test_hashbits.test_get_hashsizes ... ok tests.test_hashbits.test_extract_unique_paths_0 ... ok tests.test_hashbits.test_extract_unique_paths_1 ... ok tests.test_hashbits.test_extract_unique_paths_2 ... ok tests.test_hashbits.test_extract_unique_paths_3 ... ok tests.test_hashbits.test_extract_unique_paths_4 ... ok tests.test_hashbits.test_find_unpart ... ok tests.test_hashbits.test_find_unpart_notraverse ... ok tests.test_hashbits.test_find_unpart_fail ... ok tests.test_hashbits.test_simple_median ... ok tests.test_hashbits.test_load_notexist_should_fail ... ok tests.test_hashbits.test_load_truncated_should_fail ... ok tests.test_hashbits.test_save_load_tagset_notexist ... ok tests.test_hashbits.test_save_load_tagset_trunc ... ok tests.test_hashbits.test_hashbits_file_version_check ... ok tests.test_hashbits.test_hashbits_file_type_check ... ok tests.test_hashbits.test_stoptags_file_version_check ... ok tests.test_hashbits.test_stoptags_ksize_check ... ok tests.test_hashbits.test_stop_tags_filetype_check ... ok tests.test_hashbits.test_tagset_file_version_check ... ok tests.test_hashbits.test_tagset_ksize_check ... ok tests.test_hashbits.test_tagset_filetype_check ... ok tests.test_hashbits.test_bad_primes_list ... ok tests.test_hashbits.test_consume_absentfasta_with_reads_parser ... ok tests.test_hashbits_obj.test__get_set_tag_density ... ok tests.test_hashbits_obj.test_n_occupied_1 ... ok tests.test_hashbits_obj.test_bloom_python_1 ... ok tests.test_hashbits_obj.test_bloom_c_1 ... ok tests.test_hashbits_obj.test_n_occupied_2 ... ok tests.test_hashbits_obj.test_bloom_c_2 ... ok tests.test_hashbits_obj.test_filter_if_present ... ok tests.test_hashbits_obj.test_combine_pe ... ok tests.test_hashbits_obj.test_load_partitioned ... ok tests.test_hashbits_obj.test_count_within_radius_simple ... ok tests.test_hashbits_obj.test_count_within_radius_big ... ok tests.test_hashbits_obj.test_count_kmer_degree ... ok tests.test_hashbits_obj.test_find_radius_for_volume ... ok tests.test_hashbits_obj.test_circumference ... ok tests.test_hashbits_obj.test_save_load_tagset ... ok tests.test_hashbits_obj.test_save_load_tagset_noclear ... ok tests.test_hashbits_obj.test_stop_traverse ... ok tests.test_hashbits_obj.test_tag_across_stoptraverse ... ok tests.test_hashbits_obj.test_notag_across_stoptraverse ... ok tests.test_hashbits_obj.test_find_stoptags ... ok tests.test_hashbits_obj.test_find_stoptags2 ... ok tests.test_hashbits_obj.test_get_ksize ... ok tests.test_hashbits_obj.test_get_hashsizes ... ok tests.test_hashbits_obj.test_extract_unique_paths_0 ... ok tests.test_hashbits_obj.test_extract_unique_paths_1 ... ok tests.test_hashbits_obj.test_extract_unique_paths_2 ... ok tests.test_hashbits_obj.test_extract_unique_paths_3 ... ok tests.test_hashbits_obj.test_extract_unique_paths_4 ... ok tests.test_hashbits_obj.test_find_unpart ... ok tests.test_hashbits_obj.test_find_unpart_notraverse ... ok tests.test_hashbits_obj.test_find_unpart_fail ... ok tests.test_hashbits_obj.test_simple_median ... ok tests.test_hashbits_obj.test_bad_primes ... ok tests.test_hashbits_obj.test_consume_fasta_and_tag_with_badreads_parser ... ok Verify that 'has_extra_sanity_checks' exists. ... ok Verify that all of the various attributes exist. ... ok Verify that all of the various attributes exist. ... ok Verify that all of the various attributes exist. ... ok Verify that all of the various attributes exist. ... ok Verify that the number of threads set is what is reported. ... ok tests.test_khmer_config.test_WRONGETYPE_set_number_of_threads ... ok tests.test_khmer_config.test_WRONGTYPE_set_reads_input_buffer ... ok Verify that the reads file chunk size is what is reported. ... ok tests.test_labelhash.test_n_labels ... ok tests.test_labelhash.test_get_label_dict ... ok tests.test_labelhash.test_get_tag_labels ... ok tests.test_labelhash.test_consume_fasta_and_tag_with_labels ... ok tests.test_labelhash.test_consume_partitioned_fasta_and_tag_with_labels ... ok tests.test_labelhash.test_consume_sequence_and_tag_with_labels ... ok tests.test_labelhash.test_sweep_tag_neighborhood ... ok tests.test_labelhash.test_sweep_label_neighborhood ... ok tests.test_labelhash.test_label_tag_correctness ... ok tests.test_labelhash.test__get_set_tag_density ... ok tests.test_labelhash.test_n_occupied_1 ... ok tests.test_labelhash.test_bloom_python_1 ... ok tests.test_labelhash.test_bloom_c_1 ... ok tests.test_labelhash.test_n_occupied_2 ... ok tests.test_labelhash.test_bloom_c_2 ... ok tests.test_labelhash.test_filter_if_present ... ok tests.test_labelhash.test_combine_pe ... ok tests.test_labelhash.test_load_partitioned ... ok tests.test_labelhash.test_count_within_radius_simple ... ok tests.test_labelhash.test_count_within_radius_big ... ok tests.test_labelhash.test_count_kmer_degree ... ok tests.test_labelhash.test_find_radius_for_volume ... ok tests.test_labelhash.test_circumference ... ok tests.test_labelhash.test_save_load_tagset ... ok tests.test_labelhash.test_save_load_tagset_noclear ... ok tests.test_labelhash.test_stop_traverse ... ok tests.test_labelhash.test_tag_across_stoptraverse ... ok tests.test_labelhash.test_notag_across_stoptraverse ... ok tests.test_labelhash.test_find_stoptags ... ok tests.test_labelhash.test_find_stoptags2 ... ok tests.test_labelhash.test_get_ksize ... ok tests.test_labelhash.test_get_hashsizes ... ok tests.test_labelhash.test_extract_unique_paths_0 ... ok tests.test_labelhash.test_extract_unique_paths_1 ... ok tests.test_labelhash.test_extract_unique_paths_2 ... ok tests.test_labelhash.test_extract_unique_paths_3 ... ok tests.test_labelhash.test_extract_unique_paths_4 ... ok tests.test_labelhash.test_find_unpart ... ok tests.test_labelhash.test_find_unpart_notraverse ... ok tests.test_labelhash.test_find_unpart_fail ... ok tests.test_labelhash.test_simple_median ... ok tests.test_labelhash.test_bad_primes ... ok tests.test_lump.test_fakelump_together ... ok tests.test_lump.test_fakelump_stop ... ok tests.test_lump.test_fakelump_stop2 ... ok tests.test_lump.test_fakelump_repartitioning ... ok tests.test_lump.test_fakelump_load_stop_tags_trunc ... ok tests.test_lump.test_fakelump_load_stop_tags_notexist ... ok tests.test_read_parsers.test_read_properties ... ok tests.test_read_parsers.test_with_default_arguments ... ok tests.test_read_parsers.test_gzip_decompression ... ok tests.test_read_parsers.test_bzip2_decompression ... ok tests.test_read_parsers.test_badbzip2 ... ok tests.test_read_parsers.test_with_multiple_threads ... ok tests.test_read_parsers.test_old_illumina_pair_mating ... ok tests.test_read_parsers.test_casava_1_8_pair_mating ... ok tests.test_read_parsers.test_iterator_identities ... ok tests.test_read_parsers.test_read_pair_iterator_in_error_mode_xfail ... ok tests.test_read_parsers.test_constructor ... ok tests.test_read_parsers.test_iternext ... ok tests.test_sandbox_scripts.test_sweep_reads ... ok tests.test_sandbox_scripts.test_sweep_reads_fq ... ok tests.test_sandbox_scripts.test_sweep_reads_2 ... ok tests.test_sandbox_scripts.test_sweep_reads_3 ... ok tests.test_script_arguments.test_check_space ... ok tests.test_script_arguments.test_check_tablespace ... ok tests.test_scripts.test_check_space ... ok tests.test_scripts.test_load_into_counting ... ok tests.test_scripts.test_load_into_counting_fail ... ok tests.test_scripts.test_filter_abund_1 ... ok tests.test_scripts.test_filter_abund_2 ... ok tests.test_scripts.test_filter_abund_3_fq_retained ... ok tests.test_scripts.test_filter_abund_1_singlefile ... ok tests.test_scripts.test_filter_abund_4_retain_low_abund ... ok tests.test_scripts.test_filter_abund_5_trim_high_abund ... ok tests.test_scripts.test_filter_abund_6_trim_high_abund_Z ... ok tests.test_scripts.test_filter_stoptags ... ok tests.test_scripts.test_normalize_by_median ... ok tests.test_scripts.test_normalize_by_median_version ... ok tests.test_scripts.test_normalize_by_median_2 ... ok tests.test_scripts.test_normalize_by_median_paired ... ok tests.test_scripts.test_normalize_by_median_impaired ... ok tests.test_scripts.test_normalize_by_median_force ... ok tests.test_scripts.test_normalize_by_median_no_bigcount ... ok tests.test_scripts.test_normalize_by_median_dumpfrequency ... ok tests.test_scripts.test_normalize_by_median_empty ... ok tests.test_scripts.test_count_median ... ok tests.test_scripts.test_load_graph ... ok tests.test_scripts.test_load_graph_no_tags ... ok tests.test_scripts.test_load_graph_fail ... ok tests.test_scripts.test_partition_graph_1 ... ok tests.test_scripts.test_partition_graph_nojoin_k21 ... ok tests.test_scripts.test_partition_graph_nojoin_stoptags ... ok tests.test_scripts.test_partition_graph_big_traverse ... ok tests.test_scripts.test_partition_graph_no_big_traverse ... ok tests.test_scripts.test_annotate_partitions ... ok tests.test_scripts.test_annotate_partitions_2 ... ok tests.test_scripts.test_extract_partitions ... ok tests.test_scripts.test_extract_partitions_fq ... ok tests.test_scripts.test_extract_partitions_output_unassigned ... ok tests.test_scripts.test_extract_partitions_no_output_groups ... ok tests.test_scripts.test_extract_partitions_pid_0 ... ok tests.test_scripts.test_extract_partitions_multi_groups ... ok tests.test_scripts.test_extract_partitions_no_groups ... ok tests.test_scripts.test_abundance_dist ... ok tests.test_scripts.test_abundance_dist_nobigcount ... ok tests.test_scripts.test_abundance_dist_single ... ok tests.test_scripts.test_abundance_dist_single_nobigcount ... ok tests.test_scripts.test_do_partition ... ok tests.test_scripts.test_do_partition_2 ... ok tests.test_scripts.test_interleave_reads_1_fq ... ok tests.test_scripts.test_interleave_reads_2_fa ... ok tests.test_scripts.test_extract_paired_reads_1_fa ... ok tests.test_scripts.test_extract_paired_reads_2_fq ... ok tests.test_scripts.test_split_paired_reads_1_fa ... ok tests.test_scripts.test_split_paired_reads_2_fq ... ok tests.test_scripts.test_sample_reads_randomly ... ok tests.test_scripts.test_fastq_to_fasta ... ok tests.test_scripts.test_extract_long_sequences ... ok tests.test_scripts.test_sample_reads_randomly_S ... ok tests.test_scripts.test_count_overlap ... ok tests.test_subset_graph.Test_RandomData.test_3_merge_013 ... ok tests.test_subset_graph.Test_RandomData.test_3_merge_023 ... ok tests.test_subset_graph.Test_RandomData.test_5_merge_046 ... ok tests.test_subset_graph.Test_RandomData.test_random_20_a_succ ... ok tests.test_subset_graph.Test_RandomData.test_random_20_a_succ_II ... ok tests.test_subset_graph.Test_RandomData.test_random_20_a_succ_III ... ok tests.test_subset_graph.Test_RandomData.test_random_20_a_succ_IV ... ok tests.test_subset_graph.Test_RandomData.test_random_20_a_succ_IV_save ... ok tests.test_subset_graph.Test_SaveLoadPmap.test_merge_from_disk_file_bad_type ... ok tests.test_subset_graph.Test_SaveLoadPmap.test_merge_from_disk_file_version ... ok tests.test_subset_graph.Test_SaveLoadPmap.test_save_load_merge ... ok tests.test_subset_graph.Test_SaveLoadPmap.test_save_load_merge_2 ... ok tests.test_subset_graph.Test_SaveLoadPmap.test_save_load_merge_nexist ... ok tests.test_subset_graph.Test_SaveLoadPmap.test_save_merge_from_disk ... ok tests.test_subset_graph.Test_SaveLoadPmap.test_save_merge_from_disk_2 ... ok tests.test_subset_graph.Test_SaveLoadPmap.test_save_merge_from_disk_file_not_exist ... ok tests.test_subset_graph.Test_SaveLoadPmap.test_save_merge_from_disk_ksize ... ok tests.test_subset_graph.test_output_partitions ... ok tests.test_subset_graph.test_tiny_real_partitions ... ok tests.test_subset_graph.test_small_real_partitions ... ok tests.test_subset_graph.test_partition_on_abundance_1 ... ok tests.test_subset_graph.test_partition_on_abundance_2 ... ok tests.test_subset_graph.test_partition_on_abundance_3 ... ok tests.test_subset_graph.test_partition_overlap_1 ... ok tests.test_subset_graph.test_partition_overlap_2 ... ok tests.test_threaded_sequence_processor.test_basic ... ok tests.test_threaded_sequence_processor.test_basic_fastq_like ... ok tests.test_threaded_sequence_processor.test_odd ... ok tests.test_threaded_sequence_processor.test_basic_2thread ... ok tests.test_threaded_sequence_processor.test_paired_2thread ... ok tests.test_threaded_sequence_processor.test_paired_2thread_more_seq ... ok ---------------------------------------------------------------------- Ran 359 tests in 21.596s OK make[1]: Leaving directory `/build/buildd/khmer-1.1' /usr/bin/fakeroot debian/rules binary-arch dh binary-arch --with=python2 dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory `/build/buildd/khmer-1.1' python setup.py install --force --root=./debian/tmp --no-compile -O0 --install-layout=deb --install-scripts=/usr/lib/khmer/bin running install running build got version from expanded variable {'version': '1.1', 'full': '1fe98c92b5a9b3f46a5f4f05cd35d3229ce2ff0a'} running build_py copying khmer/__init__.py -> build/lib.linux-x86_64-2.7/khmer copying khmer/_version.py -> build/lib.linux-x86_64-2.7/khmer copying khmer/load_pe.py -> build/lib.linux-x86_64-2.7/khmer copying khmer/utils.py -> build/lib.linux-x86_64-2.7/khmer copying khmer/threading_args.py -> build/lib.linux-x86_64-2.7/khmer copying khmer/thread_utils.py -> build/lib.linux-x86_64-2.7/khmer copying khmer/file.py -> build/lib.linux-x86_64-2.7/khmer copying khmer/khmer_args.py -> build/lib.linux-x86_64-2.7/khmer creating build/lib.linux-x86_64-2.7/khmer/tests copying tests/__init__.py -> build/lib.linux-x86_64-2.7/khmer/tests copying tests/test_align.py -> build/lib.linux-x86_64-2.7/khmer/tests copying tests/test_c_wrapper.py -> build/lib.linux-x86_64-2.7/khmer/tests copying tests/test_graph.py -> build/lib.linux-x86_64-2.7/khmer/tests copying tests/test_filter.py -> build/lib.linux-x86_64-2.7/khmer/tests copying tests/test_hashbits_obj.py -> build/lib.linux-x86_64-2.7/khmer/tests copying tests/test_counting_single.py -> build/lib.linux-x86_64-2.7/khmer/tests copying tests/test_functions.py -> build/lib.linux-x86_64-2.7/khmer/tests copying tests/test_read_parsers.py -> build/lib.linux-x86_64-2.7/khmer/tests copying tests/test_counting_hash.py -> build/lib.linux-x86_64-2.7/khmer/tests copying tests/test_khmer_config.py -> build/lib.linux-x86_64-2.7/khmer/tests copying tests/test_lump.py -> build/lib.linux-x86_64-2.7/khmer/tests copying tests/test_subset_graph.py -> build/lib.linux-x86_64-2.7/khmer/tests copying tests/test_sandbox_scripts.py -> build/lib.linux-x86_64-2.7/khmer/tests copying tests/khmer_tst_utils.py -> build/lib.linux-x86_64-2.7/khmer/tests copying tests/test_script_arguments.py -> build/lib.linux-x86_64-2.7/khmer/tests copying tests/test_scripts.py -> build/lib.linux-x86_64-2.7/khmer/tests copying tests/test_hashbits.py -> build/lib.linux-x86_64-2.7/khmer/tests copying tests/test_threaded_sequence_processor.py -> build/lib.linux-x86_64-2.7/khmer/tests copying tests/test_labelhash.py -> build/lib.linux-x86_64-2.7/khmer/tests running egg_info writing requirements to khmer.egg-info/requires.txt writing khmer.egg-info/PKG-INFO writing top-level names to khmer.egg-info/top_level.txt writing dependency_links to khmer.egg-info/dependency_links.txt reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.cc' under directory 'third-party' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'README*' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching '*.c' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '[Mm]akefile*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching '*.h' under directory 'third-party' warning: no files found matching 'ChangeLog' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no previously-included files matching '*.orig' found anywhere in distribution writing manifest file 'khmer.egg-info/SOURCES.txt' copying khmer/_khmermodule.cc -> build/lib.linux-x86_64-2.7/khmer creating build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/100-reads.fq.bz2 -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/100-reads.fq.gz -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/all-A.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/badversion-k12.ht -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/badversion-k12.kh -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/badversion-k32.stoptags -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/badversion-k32.tagset -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/biglump-random-20-a.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/combine_parts_1.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/empty-file -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/fakelump.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/fakelump.fa.stoptags.txt -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/filter-test-A.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/filter-test-B.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/goodversion-k12.ht -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/goodversion-k12.ht.gz -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/goodversion-k32.stoptags -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/goodversion-k32.tagset -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/overlap.curve -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/overlap.out -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/paired-mixed.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/paired-mixed.fa.pe -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/paired-mixed.fa.se -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/paired-mixed.fq -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/paired-mixed.fq.pe -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/paired-mixed.fq.se -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/paired.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/paired.fa.1 -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/paired.fa.2 -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/paired.fq -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/paired.fq.1 -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/paired.fq.2 -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/random-20-X2.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/random-20-a.even.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/random-20-a.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/random-20-a.fa.part -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/random-20-a.fq -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/random-20-a.odd.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/random-20-b.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/random-31-c.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/real-partition-small.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/real-partition-tiny.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/simple_1.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/simple_2.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/simple_3.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/single-read.fq -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fq -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-abund-read-3.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-abund-read-impaired.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-abund-read-paired.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-abund-read.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-colors.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-empty.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-empty.fa.bz2 -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-error-reads.fq -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-est.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-fastq-n-reads.fq -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-fastq-reads.fq -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-graph.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-graph2.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-graph3.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-graph4.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-graph5.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-graph6.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-labels.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-output-partitions.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-overlap1.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-overlap2.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-reads.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-reads.fq.bz2 -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-short.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-sweep-contigs.fp -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-sweep-reads.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-sweep-reads.fq -> build/lib.linux-x86_64-2.7/khmer/tests/test-data copying tests/test-data/test-transcript.fa -> build/lib.linux-x86_64-2.7/khmer/tests/test-data running build_ext building 'khmer._khmermodule' extension x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c khmer/_khmermodule.cc -o build/temp.linux-x86_64-2.7/khmer/_khmermodule.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/khmer_config.cc -o build/temp.linux-x86_64-2.7/lib/khmer_config.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/thread_id_map.cc -o build/temp.linux-x86_64-2.7/lib/thread_id_map.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/trace_logger.cc -o build/temp.linux-x86_64-2.7/lib/trace_logger.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/perf_metrics.cc -o build/temp.linux-x86_64-2.7/lib/perf_metrics.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/read_parsers.cc -o build/temp.linux-x86_64-2.7/lib/read_parsers.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/kmer_hash.cc -o build/temp.linux-x86_64-2.7/lib/kmer_hash.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/hashtable.cc -o build/temp.linux-x86_64-2.7/lib/hashtable.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/hashbits.cc -o build/temp.linux-x86_64-2.7/lib/hashbits.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/labelhash.cc -o build/temp.linux-x86_64-2.7/lib/labelhash.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/counting.cc -o build/temp.linux-x86_64-2.7/lib/counting.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/subset.cc -o build/temp.linux-x86_64-2.7/lib/subset.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/aligner.cc -o build/temp.linux-x86_64-2.7/lib/aligner.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/scoringmatrix.cc -o build/temp.linux-x86_64-2.7/lib/scoringmatrix.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/node.cc -o build/temp.linux-x86_64-2.7/lib/node.o -O3 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python2.7 -c lib/kmer.cc -o build/temp.linux-x86_64-2.7/lib/kmer.o -O3 c++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-2.7/khmer/_khmermodule.o build/temp.linux-x86_64-2.7/lib/khmer_config.o build/temp.linux-x86_64-2.7/lib/thread_id_map.o build/temp.linux-x86_64-2.7/lib/trace_logger.o build/temp.linux-x86_64-2.7/lib/perf_metrics.o build/temp.linux-x86_64-2.7/lib/read_parsers.o build/temp.linux-x86_64-2.7/lib/kmer_hash.o build/temp.linux-x86_64-2.7/lib/hashtable.o build/temp.linux-x86_64-2.7/lib/hashbits.o build/temp.linux-x86_64-2.7/lib/labelhash.o build/temp.linux-x86_64-2.7/lib/counting.o build/temp.linux-x86_64-2.7/lib/subset.o build/temp.linux-x86_64-2.7/lib/aligner.o build/temp.linux-x86_64-2.7/lib/scoringmatrix.o build/temp.linux-x86_64-2.7/lib/node.o build/temp.linux-x86_64-2.7/lib/kmer.o -lz -lbz2 -o build/lib.linux-x86_64-2.7/khmer/_khmermodule.so running build_scripts creating build/scripts-2.7 copying and adjusting scripts/fastq-to-fasta.py -> build/scripts-2.7 copying and adjusting scripts/abundance-dist.py -> build/scripts-2.7 copying and adjusting scripts/merge-partitions.py -> build/scripts-2.7 copying and adjusting scripts/filter-abund-single.py -> build/scripts-2.7 copying and adjusting scripts/interleave-reads.py -> build/scripts-2.7 copying and adjusting scripts/count-overlap.py -> build/scripts-2.7 copying and adjusting scripts/filter-stoptags.py -> build/scripts-2.7 copying and adjusting scripts/partition-graph.py -> build/scripts-2.7 copying and adjusting scripts/abundance-dist-single.py -> build/scripts-2.7 copying and adjusting scripts/extract-partitions.py -> build/scripts-2.7 copying and adjusting scripts/count-median.py -> build/scripts-2.7 copying and adjusting scripts/sample-reads-randomly.py -> build/scripts-2.7 copying and adjusting scripts/split-paired-reads.py -> build/scripts-2.7 copying and adjusting scripts/annotate-partitions.py -> build/scripts-2.7 copying and adjusting scripts/find-knots.py -> build/scripts-2.7 copying and adjusting scripts/do-partition.py -> build/scripts-2.7 copying and adjusting scripts/extract-paired-reads.py -> build/scripts-2.7 copying and adjusting scripts/load-into-counting.py -> build/scripts-2.7 copying and adjusting scripts/load-graph.py -> build/scripts-2.7 copying and adjusting scripts/make-initial-stoptags.py -> build/scripts-2.7 copying and adjusting scripts/extract-long-sequences.py -> build/scripts-2.7 copying and adjusting scripts/normalize-by-median.py -> build/scripts-2.7 copying and adjusting scripts/filter-abund.py -> build/scripts-2.7 changing mode of build/scripts-2.7/fastq-to-fasta.py from 664 to 775 changing mode of build/scripts-2.7/abundance-dist.py from 664 to 775 changing mode of build/scripts-2.7/merge-partitions.py from 664 to 775 changing mode of build/scripts-2.7/filter-abund-single.py from 664 to 775 changing mode of build/scripts-2.7/interleave-reads.py from 664 to 775 changing mode of build/scripts-2.7/count-overlap.py from 664 to 775 changing mode of build/scripts-2.7/filter-stoptags.py from 664 to 775 changing mode of build/scripts-2.7/partition-graph.py from 664 to 775 changing mode of build/scripts-2.7/abundance-dist-single.py from 664 to 775 changing mode of build/scripts-2.7/extract-partitions.py from 664 to 775 changing mode of build/scripts-2.7/count-median.py from 664 to 775 changing mode of build/scripts-2.7/sample-reads-randomly.py from 664 to 775 changing mode of build/scripts-2.7/split-paired-reads.py from 664 to 775 changing mode of build/scripts-2.7/annotate-partitions.py from 664 to 775 changing mode of build/scripts-2.7/find-knots.py from 664 to 775 changing mode of build/scripts-2.7/do-partition.py from 664 to 775 changing mode of build/scripts-2.7/extract-paired-reads.py from 664 to 775 changing mode of build/scripts-2.7/load-into-counting.py from 664 to 775 changing mode of build/scripts-2.7/load-graph.py from 664 to 775 changing mode of build/scripts-2.7/make-initial-stoptags.py from 664 to 775 changing mode of build/scripts-2.7/extract-long-sequences.py from 664 to 775 changing mode of build/scripts-2.7/normalize-by-median.py from 664 to 775 changing mode of build/scripts-2.7/filter-abund.py from 664 to 775 UPDATING build/lib.linux-x86_64-2.7/khmer/_version.py running install_lib creating debian/tmp creating debian/tmp/usr creating debian/tmp/usr/lib creating debian/tmp/usr/lib/python2.7 creating debian/tmp/usr/lib/python2.7/dist-packages creating debian/tmp/usr/lib/python2.7/dist-packages/khmer copying build/lib.linux-x86_64-2.7/khmer/__init__.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer copying build/lib.linux-x86_64-2.7/khmer/_version.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer copying build/lib.linux-x86_64-2.7/khmer/load_pe.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer copying build/lib.linux-x86_64-2.7/khmer/utils.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer copying build/lib.linux-x86_64-2.7/khmer/_khmermodule.so -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer copying build/lib.linux-x86_64-2.7/khmer/threading_args.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer copying build/lib.linux-x86_64-2.7/khmer/thread_utils.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer creating debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests copying build/lib.linux-x86_64-2.7/khmer/tests/__init__.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests copying build/lib.linux-x86_64-2.7/khmer/tests/test_align.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests copying build/lib.linux-x86_64-2.7/khmer/tests/test_c_wrapper.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests copying build/lib.linux-x86_64-2.7/khmer/tests/test_graph.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests copying build/lib.linux-x86_64-2.7/khmer/tests/test_filter.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests copying build/lib.linux-x86_64-2.7/khmer/tests/test_hashbits_obj.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests copying build/lib.linux-x86_64-2.7/khmer/tests/test_counting_single.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests copying build/lib.linux-x86_64-2.7/khmer/tests/test_functions.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests copying build/lib.linux-x86_64-2.7/khmer/tests/test_read_parsers.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests copying build/lib.linux-x86_64-2.7/khmer/tests/test_counting_hash.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests copying build/lib.linux-x86_64-2.7/khmer/tests/test_khmer_config.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests copying build/lib.linux-x86_64-2.7/khmer/tests/test_lump.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests copying build/lib.linux-x86_64-2.7/khmer/tests/test_subset_graph.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests copying build/lib.linux-x86_64-2.7/khmer/tests/test_sandbox_scripts.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests copying build/lib.linux-x86_64-2.7/khmer/tests/khmer_tst_utils.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests copying build/lib.linux-x86_64-2.7/khmer/tests/test_script_arguments.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests copying build/lib.linux-x86_64-2.7/khmer/tests/test_scripts.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests copying build/lib.linux-x86_64-2.7/khmer/tests/test_hashbits.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests copying build/lib.linux-x86_64-2.7/khmer/tests/test_threaded_sequence_processor.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests copying build/lib.linux-x86_64-2.7/khmer/tests/test_labelhash.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests creating debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-graph3.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-graph4.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/paired-mixed.fa.pe -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/combine_parts_1.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-output-partitions.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/paired.fq.1 -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/single-read.fq -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/random-20-a.fa.part -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-abund-read-2.fq -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-abund-read-2.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/paired-mixed.fq -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/fakelump.fa.stoptags.txt -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/badversion-k12.ht -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-est.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-empty.fa.bz2 -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/goodversion-k12.ht -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-short.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/random-20-a.even.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-error-reads.fq -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/goodversion-k32.tagset -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-graph2.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-fastq-n-reads.fq -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/overlap.curve -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/paired-mixed.fq.se -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/paired-mixed.fa.se -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-abund-read-3.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/random-20-b.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-abund-read-impaired.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/biglump-random-20-a.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/random-20-X2.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/paired.fq -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/filter-test-B.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-fastq-reads.fq -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/paired-mixed.fq.pe -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/paired.fa.1 -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-colors.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/random-20-a.odd.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-sweep-reads.fq -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/goodversion-k12.ht.gz -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/real-partition-small.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/fakelump.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/all-A.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-overlap1.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-graph5.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-reads.fq.bz2 -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-graph.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/random-20-a.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-sweep-reads.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/paired.fq.2 -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/simple_3.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/paired.fa.2 -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/badversion-k32.stoptags -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/simple_1.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-abund-read-paired.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/filter-test-A.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/paired.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/overlap.out -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/random-31-c.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/badversion-k12.kh -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/simple_2.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-graph6.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/goodversion-k32.stoptags -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-transcript.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-empty.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-labels.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/empty-file -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-reads.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/100-reads.fq.bz2 -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/paired-mixed.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/random-20-a.fq -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/badversion-k32.tagset -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/real-partition-tiny.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-sweep-contigs.fp -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/100-reads.fq.gz -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-overlap2.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/tests/test-data/test-abund-read.fa -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer/tests/test-data copying build/lib.linux-x86_64-2.7/khmer/file.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer copying build/lib.linux-x86_64-2.7/khmer/_khmermodule.cc -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer copying build/lib.linux-x86_64-2.7/khmer/khmer_args.py -> ./debian/tmp/usr/lib/python2.7/dist-packages/khmer running install_egg_info Copying khmer.egg-info to ./debian/tmp/usr/lib/python2.7/dist-packages/khmer-1.1.egg-info running install_scripts creating debian/tmp/usr/lib/khmer creating debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/fastq-to-fasta.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/abundance-dist.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/merge-partitions.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/filter-abund-single.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/interleave-reads.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/count-overlap.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/filter-stoptags.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/partition-graph.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/abundance-dist-single.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/extract-partitions.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/count-median.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/sample-reads-randomly.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/split-paired-reads.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/annotate-partitions.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/find-knots.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/do-partition.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/extract-paired-reads.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/load-into-counting.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/load-graph.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/make-initial-stoptags.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/extract-long-sequences.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/normalize-by-median.py -> ./debian/tmp/usr/lib/khmer/bin copying build/scripts-2.7/filter-abund.py -> ./debian/tmp/usr/lib/khmer/bin changing mode of ./debian/tmp/usr/lib/khmer/bin/fastq-to-fasta.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/abundance-dist.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/merge-partitions.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/filter-abund-single.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/interleave-reads.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/count-overlap.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/filter-stoptags.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/partition-graph.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/abundance-dist-single.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/extract-partitions.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/count-median.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/sample-reads-randomly.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/split-paired-reads.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/annotate-partitions.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/find-knots.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/do-partition.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/extract-paired-reads.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/load-into-counting.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/load-graph.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/make-initial-stoptags.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/extract-long-sequences.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/normalize-by-median.py to 775 changing mode of ./debian/tmp/usr/lib/khmer/bin/filter-abund.py to 775 mv debian/tmp/usr/lib/python*/dist-packages/khmer/tests debian/tmp/usr/lib/khmer make[1]: Leaving directory `/build/buildd/khmer-1.1' dh_install -a dh_installdocs -a debian/rules override_dh_installchangelogs make[1]: Entering directory `/build/buildd/khmer-1.1' dh_installchangelogs ChangeLog make[1]: Leaving directory `/build/buildd/khmer-1.1' dh_installexamples -a dh_installman -a dh_python2 -a dh_perl -a debian/rules override_dh_link make[1]: Entering directory `/build/buildd/khmer-1.1' dh_link -Xscripts make[1]: Leaving directory `/build/buildd/khmer-1.1' dh_compress -a dh_fixperms -a dh_strip -a dh_strip debug symbol extraction: disabling for PPA build dh_strip debug symbol extraction: not enabling -a because /CurrentlyBuilding exists dh_strip debug symbol extraction: not doing anything since NO_PKG_MANGLE is given dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: package khmer: unused substitution variable ${python:Versions} dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 121 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build INFO: Disabling pkgstripfiles for PPA build dpkg-deb: building package `khmer' in `../khmer_1.1-0biolinux3_amd64.deb'. INFO: pkgstriptranslations version 121 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build INFO: Disabling pkgstripfiles for PPA build dpkg-deb: building package `khmer-test' in `../khmer-test_1.1-0biolinux3_amd64.deb'. INFO: pkgstriptranslations version 121 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build INFO: Disabling pkgstripfiles for PPA build dpkg-deb: building package `khmer-example' in `../khmer-example_1.1-0biolinux3_amd64.deb'. dpkg-genchanges -B -mUbuntu Build Daemon >../khmer_1.1-0biolinux3_amd64.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build khmer-1.1 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20140829-1542 chroot-autobuild/build/buildd/khmer_1.1-0biolinux3_amd64.deb: new debian package, version 2.0. size 408638 bytes: control archive=4554 bytes. 859 bytes, 18 lines control 9264 bytes, 119 lines md5sums 235 bytes, 13 lines * postinst #!/bin/sh 247 bytes, 14 lines * prerm #!/bin/sh Package: khmer Version: 1.1-0biolinux3 Architecture: amd64 Maintainer: Tim Booth Installed-Size: 1749 Depends: libbz2-1.0, libc6 (>= 2.14), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4), python (>= 2.7), python (<< 2.8), python:any (>= 2.7.1-0ubuntu2), python-screed Section: science Priority: optional Homepage: https://github.com/ged-lab/khmer Description: k-mer counting, filtering and graph traversal khmer is a library and suite of command line tools for working with DNA sequence. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform. khmer takes a k-mer-centric approach to sequence analysis, hence the name. . khmer is research software, so you should cite us when you use it in scientific publications! Please see the CITATION file for citation information. chroot-autobuild/build/buildd/khmer-test_1.1-0biolinux3_amd64.deb: new debian package, version 2.0. size 1858674 bytes: control archive=3273 bytes. 624 bytes, 17 lines control 7873 bytes, 99 lines md5sums Package: khmer-test Source: khmer Version: 1.1-0biolinux3 Architecture: amd64 Maintainer: Tim Booth Installed-Size: 6404 Depends: khmer (>= 1.1-0biolinux3) Section: science Priority: optional Homepage: https://github.com/ged-lab/khmer Description: k-mer counting, filtering and graph traversal khmer is a library and suite of command line tools for working with DNA sequence. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform. khmer takes a k-mer-centric approach to sequence analysis, hence the name. . This package installs the standard test data. chroot-autobuild/build/buildd/khmer-example_1.1-0biolinux3_amd64.deb: new debian package, version 2.0. size 15167244 bytes: control archive=6139 bytes. 643 bytes, 17 lines control 18164 bytes, 183 lines md5sums Package: khmer-example Source: khmer Version: 1.1-0biolinux3 Architecture: amd64 Maintainer: Tim Booth Installed-Size: 15165 Depends: khmer (>= 1.1-0biolinux3) Section: science Priority: optional Homepage: https://github.com/ged-lab/khmer Description: k-mer counting, filtering and graph traversal khmer is a library and suite of command line tools for working with DNA sequence. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform. khmer takes a k-mer-centric approach to sequence analysis, hence the name. . This package installs the example data used in the tutorial. chroot-autobuild/build/buildd/khmer_1.1-0biolinux3_amd64.deb: drwxr-xr-x root/root 0 2014-08-29 15:41 ./ drwxr-xr-x root/root 0 2014-08-29 15:41 ./usr/ drwxr-xr-x root/root 0 2014-08-29 15:41 ./usr/share/ drwxr-xr-x root/root 0 2014-08-29 15:41 ./usr/share/doc/ drwxr-xr-x root/root 0 2014-08-29 15:41 ./usr/share/doc/khmer/ -rw-r--r-- root/root 86 2014-06-17 15:18 ./usr/share/doc/khmer/CONTRIBUTING.md drwxr-xr-x root/root 0 2014-08-29 15:41 ./usr/share/doc/khmer/html/ -rw-r--r-- root/root 230 2014-08-29 15:39 ./usr/share/doc/khmer/html/.buildinfo -rw-r--r-- root/root 4793 2014-08-29 15:39 ./usr/share/doc/khmer/html/requirements.html drwxr-xr-x root/root 0 2014-08-29 15:41 ./usr/share/doc/khmer/html/_sources/ -rw-r--r-- root/root 3621 2014-06-17 15:18 ./usr/share/doc/khmer/html/_sources/introduction.txt -rw-r--r-- root/root 2063 2014-06-17 15:18 ./usr/share/doc/khmer/html/_sources/index.txt -rw-r--r-- root/root 2760 2014-06-17 15:18 ./usr/share/doc/khmer/html/_sources/install.txt -rw-r--r-- root/root 1971 2014-06-17 15:18 ./usr/share/doc/khmer/html/_sources/blog-posts.txt -rw-r--r-- root/root 208 2014-06-17 15:18 ./usr/share/doc/khmer/html/_sources/details.txt -rw-r--r-- root/root 8434 2014-06-17 15:18 ./usr/share/doc/khmer/html/_sources/guide.txt -rw-r--r-- root/root 3916 2014-06-17 15:18 ./usr/share/doc/khmer/html/_sources/scripts.txt -rw-r--r-- root/root 6591 2014-06-17 15:18 ./usr/share/doc/khmer/html/_sources/choosing-table-sizes.txt -rw-r--r-- root/root 1562 2014-06-17 15:18 ./usr/share/doc/khmer/html/_sources/galaxy.txt -rw-r--r-- root/root 7635 2014-06-17 15:18 ./usr/share/doc/khmer/html/_sources/development.txt -rw-r--r-- root/root 246 2014-06-17 15:18 ./usr/share/doc/khmer/html/_sources/crazy-ideas.txt -rw-r--r-- root/root 757 2014-06-17 15:18 ./usr/share/doc/khmer/html/_sources/biblio.txt -rw-r--r-- root/root 7441 2014-06-17 15:18 ./usr/share/doc/khmer/html/_sources/release.txt -rw-r--r-- root/root 1614 2014-06-17 15:18 ./usr/share/doc/khmer/html/_sources/LICENSE.txt -rw-r--r-- root/root 159 2014-06-17 15:18 ./usr/share/doc/khmer/html/_sources/requirements.txt -rw-r--r-- root/root 29095 2014-06-17 15:18 ./usr/share/doc/khmer/html/_sources/design.txt -rw-r--r-- root/root 970 2014-06-17 15:18 ./usr/share/doc/khmer/html/_sources/contributors.txt -rw-r--r-- root/root 1074 2014-06-17 15:18 ./usr/share/doc/khmer/html/_sources/examples.txt -rw-r--r-- root/root 5471 2014-06-17 15:18 ./usr/share/doc/khmer/html/_sources/partitioning-big-data.txt -rw-r--r-- root/root 1263 2014-06-17 15:18 ./usr/share/doc/khmer/html/_sources/known-issues.txt -rw-r--r-- root/root 10633 2014-08-29 15:39 ./usr/share/doc/khmer/html/introduction.html -rw-r--r-- root/root 93822 2014-08-29 15:39 ./usr/share/doc/khmer/html/scripts.html -rw-r--r-- root/root 17752 2014-08-29 15:39 ./usr/share/doc/khmer/html/release.html -rw-r--r-- root/root 11249 2014-08-29 15:39 ./usr/share/doc/khmer/html/install.html 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2014-08-29 15:39 ./usr/share/doc/khmer-example/examples/scripts -> /usr/lib/khmer/bin/ khmer_1.1-0biolinux3_amd64.changes: Format: 1.8 Date: Thu, 28 Aug 2014 13:12:55 +0100 Source: khmer Binary: khmer khmer-test khmer-example Architecture: amd64 Version: 1.1-0biolinux3 Distribution: trusty Urgency: low Maintainer: Ubuntu Build Daemon Changed-By: Tim Booth Description: khmer - k-mer counting, filtering and graph traversal khmer-example - k-mer counting, filtering and graph traversal khmer-test - k-mer counting, filtering and graph traversal Changes: khmer (1.1-0biolinux3) trusty; urgency=low . * Switch to 64-bit-only build as tests segfault on i386 * Add missing data files to -example and make the script vaguely work Checksums-Sha1: 17bb78d296c5ca7c8bcb7917c95a98362938d42e 408638 khmer_1.1-0biolinux3_amd64.deb 430a0319e080b8e35c8c394d8edfc8a5cf6b1edb 1858674 khmer-test_1.1-0biolinux3_amd64.deb 0583ed9d41d497f04dc6258d13a913db3886dc2e 15167244 khmer-example_1.1-0biolinux3_amd64.deb Checksums-Sha256: 63e20687099bfa91e4e6f18a18d2bc73aea78ec4c8d36827d6bc8333f6973ed9 408638 khmer_1.1-0biolinux3_amd64.deb 65b4e798826b024ee27b2cbae8a60c056a1b4b2171797e45f2d67964ce9e4a05 1858674 khmer-test_1.1-0biolinux3_amd64.deb 26c7db08da7c03ecfa41d3393e618b80c060330a2c0442330b784f7616ad2b25 15167244 khmer-example_1.1-0biolinux3_amd64.deb Files: b6123b9b4a0cce4d91043333c20ac92f 408638 science optional khmer_1.1-0biolinux3_amd64.deb 0ee0a3c849d6dc75e793f381240ff33e 1858674 science optional khmer-test_1.1-0biolinux3_amd64.deb 3f84fa80012fa02e5110756fba71a13a 15167244 science optional khmer-example_1.1-0biolinux3_amd64.deb ****************************************************************************** Built successfully NOTE: The package could have used binaries from the following packages (access time changed) without a source dependency: groff: /usr/bin/groff ****************************************************************************** Finished at 20140829-1542 Build needed 00:04:42, 135256k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-6309050'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-6309050/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-6309050'] Unmounting chroot for build PACKAGEBUILD-6309050... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-6309050'] Removing build PACKAGEBUILD-6309050