RUN: /bin/echo ['echo', 'Forking build subprocess...'] Forking build subprocess... RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', '616fc0356b960b4b25e1a728d7f0def169a5394e', '/home/buildd/filecache-default/7f84715a2487c0e25be20d612e2809c2352ed2ef'] Uncompressing the tarball... Synching the system clock with the buildd NTP service... 3 Dec 20:24:22 ntpdate[3401]: step time server 10.211.37.1 offset -473564.423145 sec Unpacking chroot for build 616fc0356b960b4b25e1a728d7f0def169a5394e RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', '616fc0356b960b4b25e1a728d7f0def169a5394e'] Mounting chroot for build 616fc0356b960b4b25e1a728d7f0def169a5394e RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', '616fc0356b960b4b25e1a728d7f0def169a5394e', 'deb http://ppa.launchpad.net/genomeinformatics/bioinformatics-software/ubuntu oneiric main', 'deb http://ftpmaster.internal/ubuntu oneiric main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu oneiric-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu oneiric-updates main restricted universe multiverse'] Overriding sources.list in build-616fc0356b960b4b25e1a728d7f0def169a5394e RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', '616fc0356b960b4b25e1a728d7f0def169a5394e', 'i386'] Updating debian chroot for build 616fc0356b960b4b25e1a728d7f0def169a5394e Ign http://ftpmaster.internal oneiric InRelease Ign http://ftpmaster.internal oneiric-security InRelease Ign http://ftpmaster.internal oneiric-updates InRelease Get:1 http://ftpmaster.internal oneiric Release.gpg [198 B] Get:2 http://ftpmaster.internal oneiric-security Release.gpg [198 B] Get:3 http://ftpmaster.internal oneiric-updates Release.gpg [198 B] Get:4 http://ftpmaster.internal oneiric Release [40.8 kB] Get:5 http://ftpmaster.internal oneiric-security Release [32.4 kB] Get:6 http://ftpmaster.internal oneiric-updates Release [32.4 kB] Ign http://ppa.launchpad.net oneiric InRelease Get:7 http://ppa.launchpad.net oneiric Release.gpg [316 B] Get:8 http://ppa.launchpad.net oneiric Release [9779 B] Get:9 http://ftpmaster.internal oneiric/main i386 Packages [1226 kB] Ign http://ppa.launchpad.net oneiric Release Get:10 http://ppa.launchpad.net oneiric/main i386 Packages [1110 B] Ign http://ppa.launchpad.net oneiric/main TranslationIndex Ign http://ppa.launchpad.net oneiric/main Translation-en Get:11 http://ftpmaster.internal oneiric/restricted i386 Packages [8216 B] Get:12 http://ftpmaster.internal oneiric/universe i386 Packages [4468 kB] Get:13 http://ftpmaster.internal oneiric/multiverse i386 Packages [119 kB] Get:14 http://ftpmaster.internal oneiric/main TranslationIndex [3289 B] Get:15 http://ftpmaster.internal oneiric/multiverse TranslationIndex [2265 B] Get:16 http://ftpmaster.internal oneiric/restricted TranslationIndex [2263 B] Get:17 http://ftpmaster.internal oneiric/universe TranslationIndex [2640 B] Get:18 http://ftpmaster.internal oneiric-security/main i386 Packages [46.0 kB] Get:19 http://ftpmaster.internal oneiric-security/restricted i386 Packages [14 B] Get:20 http://ftpmaster.internal oneiric-security/universe i386 Packages [14.1 kB] Get:21 http://ftpmaster.internal oneiric-security/multiverse i386 Packages [1653 B] Get:22 http://ftpmaster.internal oneiric-security/main TranslationIndex [73 B] Get:23 http://ftpmaster.internal oneiric-security/multiverse TranslationIndex [71 B] Get:24 http://ftpmaster.internal oneiric-security/restricted TranslationIndex [70 B] Get:25 http://ftpmaster.internal oneiric-security/universe TranslationIndex [73 B] Get:26 http://ftpmaster.internal oneiric-updates/main i386 Packages [205 kB] Get:27 http://ftpmaster.internal oneiric-updates/restricted i386 Packages [2935 B] Get:28 http://ftpmaster.internal oneiric-updates/universe i386 Packages [56.2 kB] Get:29 http://ftpmaster.internal oneiric-updates/multiverse i386 Packages [4396 B] Get:30 http://ftpmaster.internal oneiric-updates/main TranslationIndex [73 B] Get:31 http://ftpmaster.internal oneiric-updates/multiverse TranslationIndex [72 B] Get:32 http://ftpmaster.internal oneiric-updates/restricted TranslationIndex [71 B] Get:33 http://ftpmaster.internal oneiric-updates/universe TranslationIndex [73 B] Get:34 http://ftpmaster.internal oneiric/main Translation-en [701 kB] Get:35 http://ftpmaster.internal oneiric/multiverse Translation-en [92.6 kB] Get:36 http://ftpmaster.internal oneiric/restricted Translation-en [2229 B] Get:37 http://ftpmaster.internal oneiric/universe Translation-en [3165 kB] Get:38 http://ftpmaster.internal oneiric-security/main Translation-en [25.9 kB] Get:39 http://ftpmaster.internal oneiric-security/multiverse Translation-en [840 B] Get:40 http://ftpmaster.internal oneiric-security/restricted Translation-en [14 B] Get:41 http://ftpmaster.internal oneiric-security/universe Translation-en [10.0 kB] Get:42 http://ftpmaster.internal oneiric-updates/main Translation-en [95.6 kB] Get:43 http://ftpmaster.internal oneiric-updates/multiverse Translation-en [2419 B] Get:44 http://ftpmaster.internal oneiric-updates/restricted Translation-en [508 B] Get:45 http://ftpmaster.internal oneiric-updates/universe Translation-en [34.7 kB] Fetched 10.4 MB in 8s (1269 kB/s) Reading package lists... W: GPG error: http://ppa.launchpad.net oneiric Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 4CD7AA60FCDFFF54 Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: binutils initramfs-tools initramfs-tools-bin libgssapi-krb5-2 libk5crypto3 libkrb5-3 libkrb5support0 libldap-2.4-2 libpam-modules libpam-modules-bin libpam-runtime libpam0g linux-libc-dev tzdata upstart 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5196 kB of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpam0g libpam-modules-bin libpam-modules libk5crypto3 libgssapi-krb5-2 libkrb5-3 libkrb5support0 libldap-2.4-2 libpam-runtime tzdata initramfs-tools initramfs-tools-bin upstart binutils linux-libc-dev Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ oneiric-security/main libpam0g i386 1.1.3-2ubuntu2.1 [56.2 kB] Get:2 http://ftpmaster.internal/ubuntu/ oneiric-security/main libpam-modules-bin i386 1.1.3-2ubuntu2.1 [41.0 kB] Get:3 http://ftpmaster.internal/ubuntu/ oneiric-security/main libpam-modules i386 1.1.3-2ubuntu2.1 [270 kB] Get:4 http://ftpmaster.internal/ubuntu/ oneiric-updates/main libk5crypto3 i386 1.9.1+dfsg-1ubuntu2.1 [81.9 kB] Get:5 http://ftpmaster.internal/ubuntu/ oneiric-updates/main libgssapi-krb5-2 i386 1.9.1+dfsg-1ubuntu2.1 [120 kB] Get:6 http://ftpmaster.internal/ubuntu/ oneiric-updates/main libkrb5-3 i386 1.9.1+dfsg-1ubuntu2.1 [362 kB] Get:7 http://ftpmaster.internal/ubuntu/ oneiric-updates/main libkrb5support0 i386 1.9.1+dfsg-1ubuntu2.1 [24.1 kB] Get:8 http://ftpmaster.internal/ubuntu/ oneiric-security/main libldap-2.4-2 i386 2.4.25-1.1ubuntu4.1 [184 kB] Get:9 http://ftpmaster.internal/ubuntu/ oneiric-security/main libpam-runtime i386 1.1.3-2ubuntu2.1 [45.0 kB] Get:10 http://ftpmaster.internal/ubuntu/ oneiric-updates/main tzdata i386 2011n-0ubuntu0.11.10 [465 kB] Get:11 http://ftpmaster.internal/ubuntu/ oneiric-updates/main initramfs-tools all 0.99ubuntu8 [51.7 kB] Get:12 http://ftpmaster.internal/ubuntu/ oneiric-updates/main initramfs-tools-bin i386 0.99ubuntu8 [11.8 kB] Get:13 http://ftpmaster.internal/ubuntu/ oneiric-updates/main upstart i386 1.3-0ubuntu11 [289 kB] Get:14 http://ftpmaster.internal/ubuntu/ oneiric-updates/main binutils i386 2.21.53.20110810-0ubuntu5 [2383 kB] Get:15 http://ftpmaster.internal/ubuntu/ oneiric-security/main linux-libc-dev i386 3.0.0-13.22 [812 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 5196 kB in 0s (12.2 MB/s) (Reading database ... 14112 files and directories currently installed.) Preparing to replace libpam0g 1.1.3-2ubuntu1 (using .../libpam0g_1.1.3-2ubuntu2.1_i386.deb) ... Unpacking replacement libpam0g ... Setting up libpam0g (1.1.3-2ubuntu2.1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 14112 files and directories currently installed.) Preparing to replace libpam-modules-bin 1.1.3-2ubuntu1 (using .../libpam-modules-bin_1.1.3-2ubuntu2.1_i386.deb) ... Unpacking replacement libpam-modules-bin ... Setting up libpam-modules-bin (1.1.3-2ubuntu2.1) ... (Reading database ... 14112 files and directories currently installed.) Preparing to replace libpam-modules 1.1.3-2ubuntu1 (using .../libpam-modules_1.1.3-2ubuntu2.1_i386.deb) ... Unpacking replacement libpam-modules ... Setting up libpam-modules (1.1.3-2ubuntu2.1) ... (Reading database ... 14112 files and directories currently installed.) Preparing to replace libk5crypto3 1.9.1+dfsg-1ubuntu1 (using .../libk5crypto3_1.9.1+dfsg-1ubuntu2.1_i386.deb) ... Unpacking replacement libk5crypto3 ... Preparing to replace libgssapi-krb5-2 1.9.1+dfsg-1ubuntu1 (using .../libgssapi-krb5-2_1.9.1+dfsg-1ubuntu2.1_i386.deb) ... Unpacking replacement libgssapi-krb5-2 ... Preparing to replace libkrb5-3 1.9.1+dfsg-1ubuntu1 (using .../libkrb5-3_1.9.1+dfsg-1ubuntu2.1_i386.deb) ... Unpacking replacement libkrb5-3 ... Preparing to replace libkrb5support0 1.9.1+dfsg-1ubuntu1 (using .../libkrb5support0_1.9.1+dfsg-1ubuntu2.1_i386.deb) ... Unpacking replacement libkrb5support0 ... Preparing to replace libldap-2.4-2 2.4.25-1.1ubuntu4 (using .../libldap-2.4-2_2.4.25-1.1ubuntu4.1_i386.deb) ... Unpacking replacement libldap-2.4-2 ... Preparing to replace libpam-runtime 1.1.3-2ubuntu1 (using .../libpam-runtime_1.1.3-2ubuntu2.1_i386.deb) ... Unpacking replacement libpam-runtime ... Setting up libpam-runtime (1.1.3-2ubuntu2.1) ... (Reading database ... 14112 files and directories currently installed.) Preparing to replace tzdata 2011k-1 (using .../tzdata_2011n-0ubuntu0.11.10_i386.deb) ... Unpacking replacement tzdata ... Setting up tzdata (2011n-0ubuntu0.11.10) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Nov 28 08:52:50 UTC 2011. Universal Time is now: Mon Nov 28 08:52:50 UTC 2011. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 14112 files and directories currently installed.) Preparing to replace initramfs-tools 0.99ubuntu7 (using .../initramfs-tools_0.99ubuntu8_all.deb) ... Unpacking replacement initramfs-tools ... Preparing to replace initramfs-tools-bin 0.99ubuntu7 (using .../initramfs-tools-bin_0.99ubuntu8_i386.deb) ... Unpacking replacement initramfs-tools-bin ... Preparing to replace upstart 1.3-0ubuntu10 (using .../upstart_1.3-0ubuntu11_i386.deb) ... Unpacking replacement upstart ... Preparing to replace binutils 2.21.53.20110810-0ubuntu3 (using .../binutils_2.21.53.20110810-0ubuntu5_i386.deb) ... Unpacking replacement binutils ... Preparing to replace linux-libc-dev 3.0.0-12.20 (using .../linux-libc-dev_3.0.0-13.22_i386.deb) ... Unpacking replacement linux-libc-dev ... Setting up libkrb5support0 (1.9.1+dfsg-1ubuntu2.1) ... Setting up libk5crypto3 (1.9.1+dfsg-1ubuntu2.1) ... Setting up libkrb5-3 (1.9.1+dfsg-1ubuntu2.1) ... Setting up libgssapi-krb5-2 (1.9.1+dfsg-1ubuntu2.1) ... Setting up libldap-2.4-2 (2.4.25-1.1ubuntu4.1) ... Setting up initramfs-tools-bin (0.99ubuntu8) ... Setting up initramfs-tools (0.99ubuntu8) ... update-initramfs: deferring update (trigger activated) Setting up upstart (1.3-0ubuntu11) ... Installing new version of config file /etc/init/failsafe.conf ... Setting up binutils (2.21.53.20110810-0ubuntu5) ... Setting up linux-libc-dev (3.0.0-13.22) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Processing triggers for initramfs-tools ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', '616fc0356b960b4b25e1a728d7f0def169a5394e', 'i386', 'oneiric', '--nolog', '--batch', '--archive=ubuntu', '--dist=oneiric', '-A', '--purpose=PPA', '--architecture=i386', '--comp=main', 'cufflinks_1.1.0-3.dsc'] Initiating build 616fc0356b960b4b25e1a728d7f0def169a5394e with 2 processor cores. Automatic build of cufflinks_1.1.0-3 on kutjera by sbuild/i386 1.170.5 Build started at 20111128-0853 ****************************************************************************** cufflinks_1.1.0-3.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 8.0.0), autotools-dev, libboost-dev (>= 1.38.0), libboost-thread-dev, libbam-dev (>= 0.1.16), zlib1g-dev Checking for already installed source dependencies... debhelper: missing autotools-dev: missing libboost-dev: missing libboost-thread-dev: missing libbam-dev: missing zlib1g-dev: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper autotools-dev libboost-dev libboost-thread-dev libbam-dev zlib1g-dev Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils file gettext gettext-base groff-base html2text intltool-debian libboost-date-time1.46-dev libboost-date-time1.46.1 libboost-serialization1.46-dev libboost-serialization1.46.1 libboost-thread1.46-dev libboost-thread1.46.1 libboost1.46-dev libcroco3 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff libboost1.46-doc libboost-filesystem1.46-dev libboost-graph1.46-dev libboost-iostreams1.46-dev libboost-math1.46-dev libboost-program-options1.46-dev libboost-python1.46-dev libboost-random1.46-dev libboost-regex1.46-dev libboost-signals1.46-dev libboost-system1.46-dev libboost-test1.46-dev libboost-wave1.46-dev xsltproc doxygen docbook-xml docbook-xsl default-jdk fop less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur xml-core libmail-sendmail-perl The following NEW packages will be installed: autotools-dev bsdmainutils debhelper file gettext gettext-base groff-base html2text intltool-debian libbam-dev libboost-date-time1.46-dev libboost-date-time1.46.1 libboost-dev libboost-serialization1.46-dev libboost-serialization1.46.1 libboost-thread-dev libboost-thread1.46-dev libboost-thread1.46.1 libboost1.46-dev libcroco3 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. Need to get 14.0 MB of archives. After this operation, 101 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libmagic1 file bsdmainutils gettext-base groff-base libxml2 man-db autotools-dev html2text libcroco3 libunistring0 gettext intltool-debian po-debconf debhelper libbam-dev libboost1.46-dev libboost-date-time1.46.1 libboost-serialization1.46.1 libboost-serialization1.46-dev libboost-date-time1.46-dev libboost-dev libboost-thread1.46.1 libboost-thread1.46-dev libboost-thread-dev zlib1g-dev Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ oneiric/main libpipeline1 i386 1.2.0-3 [25.7 kB] Get:2 http://ftpmaster.internal/ubuntu/ oneiric/main libmagic1 i386 5.04-5ubuntu3 [205 kB] Get:3 http://ftpmaster.internal/ubuntu/ oneiric/main file i386 5.04-5ubuntu3 [19.8 kB] Get:4 http://ftpmaster.internal/ubuntu/ oneiric/main bsdmainutils i386 8.2.3 [196 kB] Get:5 http://ftpmaster.internal/ubuntu/ oneiric/main gettext-base i386 0.18.1.1-3ubuntu1 [56.6 kB] Get:6 http://ftpmaster.internal/ubuntu/ oneiric/main groff-base i386 1.21-6 [1024 kB] Get:7 http://ftpmaster.internal/ubuntu/ oneiric/main libxml2 i386 2.7.8.dfsg-4 [662 kB] Get:8 http://ftpmaster.internal/ubuntu/ oneiric/main man-db i386 2.6.0.2-2 [717 kB] Get:9 http://ftpmaster.internal/ubuntu/ oneiric/main autotools-dev all 20110511.1 [44.7 kB] Get:10 http://ftpmaster.internal/ubuntu/ oneiric/main html2text i386 1.3.2a-15 [101 kB] Get:11 http://ftpmaster.internal/ubuntu/ oneiric/main libcroco3 i386 0.6.2-1 [92.5 kB] Get:12 http://ftpmaster.internal/ubuntu/ oneiric/main libunistring0 i386 0.9.3-4 [431 kB] Get:13 http://ftpmaster.internal/ubuntu/ oneiric/main gettext i386 0.18.1.1-3ubuntu1 [1180 kB] Get:14 http://ftpmaster.internal/ubuntu/ oneiric/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:15 http://ftpmaster.internal/ubuntu/ oneiric/main po-debconf all 1.0.16+nmu1 [212 kB] Get:16 http://ftpmaster.internal/ubuntu/ oneiric/main debhelper all 8.9.0ubuntu1 [487 kB] Get:17 http://ftpmaster.internal/ubuntu/ oneiric/universe libbam-dev i386 0.1.17-1 [139 kB] Get:18 http://ftpmaster.internal/ubuntu/ oneiric/main libboost1.46-dev i386 1.46.1-5ubuntu2 [7643 kB] Get:19 http://ftpmaster.internal/ubuntu/ oneiric/universe libboost-date-time1.46.1 i386 1.46.1-5ubuntu2 [27.5 kB] Get:20 http://ftpmaster.internal/ubuntu/ oneiric/main libboost-serialization1.46.1 i386 1.46.1-5ubuntu2 [188 kB] Get:21 http://ftpmaster.internal/ubuntu/ oneiric/main libboost-serialization1.46-dev i386 1.46.1-5ubuntu2 [261 kB] Get:22 http://ftpmaster.internal/ubuntu/ oneiric/universe libboost-date-time1.46-dev i386 1.46.1-5ubuntu2 [24.7 kB] Get:23 http://ftpmaster.internal/ubuntu/ oneiric/main libboost-dev i386 1.46.1.1 [2652 B] Get:24 http://ftpmaster.internal/ubuntu/ oneiric/universe libboost-thread1.46.1 i386 1.46.1-5ubuntu2 [40.0 kB] Get:25 http://ftpmaster.internal/ubuntu/ oneiric/universe libboost-thread1.46-dev i386 1.46.1-5ubuntu2 [38.6 kB] Get:26 http://ftpmaster.internal/ubuntu/ oneiric/universe libboost-thread-dev i386 1.46.1.1 [2566 B] Get:27 http://ftpmaster.internal/ubuntu/ oneiric/main zlib1g-dev i386 1:1.2.3.4.dfsg-3ubuntu3 [160 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 14.0 MB in 1s (12.7 MB/s) Selecting previously deselected package libpipeline1. (Reading database ... 14112 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_i386.deb) ... Selecting previously deselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.04-5ubuntu3_i386.deb) ... Selecting previously deselected package file. Unpacking file (from .../file_5.04-5ubuntu3_i386.deb) ... Selecting previously deselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_i386.deb) ... Selecting previously deselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-3ubuntu1_i386.deb) ... Selecting previously deselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-6_i386.deb) ... Selecting previously deselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_i386.deb) ... Selecting previously deselected package man-db. Unpacking man-db (from .../man-db_2.6.0.2-2_i386.deb) ... Selecting previously deselected package autotools-dev. Unpacking autotools-dev (from .../autotools-dev_20110511.1_all.deb) ... Selecting previously deselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_i386.deb) ... Selecting previously deselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.2-1_i386.deb) ... Selecting previously deselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-4_i386.deb) ... Selecting previously deselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-3ubuntu1_i386.deb) ... Selecting previously deselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously deselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ... Selecting previously deselected package debhelper. Unpacking debhelper (from .../debhelper_8.9.0ubuntu1_all.deb) ... Selecting previously deselected package libbam-dev. Unpacking libbam-dev (from .../libbam-dev_0.1.17-1_i386.deb) ... Selecting previously deselected package libboost1.46-dev. Unpacking libboost1.46-dev (from .../libboost1.46-dev_1.46.1-5ubuntu2_i386.deb) ... Selecting previously deselected package libboost-date-time1.46.1. Unpacking libboost-date-time1.46.1 (from .../libboost-date-time1.46.1_1.46.1-5ubuntu2_i386.deb) ... Selecting previously deselected package libboost-serialization1.46.1. Unpacking libboost-serialization1.46.1 (from .../libboost-serialization1.46.1_1.46.1-5ubuntu2_i386.deb) ... Selecting previously deselected package libboost-serialization1.46-dev. Unpacking libboost-serialization1.46-dev (from .../libboost-serialization1.46-dev_1.46.1-5ubuntu2_i386.deb) ... Selecting previously deselected package libboost-date-time1.46-dev. Unpacking libboost-date-time1.46-dev (from .../libboost-date-time1.46-dev_1.46.1-5ubuntu2_i386.deb) ... Selecting previously deselected package libboost-dev. Unpacking libboost-dev (from .../libboost-dev_1.46.1.1_i386.deb) ... Selecting previously deselected package libboost-thread1.46.1. Unpacking libboost-thread1.46.1 (from .../libboost-thread1.46.1_1.46.1-5ubuntu2_i386.deb) ... Selecting previously deselected package libboost-thread1.46-dev. Unpacking libboost-thread1.46-dev (from .../libboost-thread1.46-dev_1.46.1-5ubuntu2_i386.deb) ... Selecting previously deselected package libboost-thread-dev. Unpacking libboost-thread-dev (from .../libboost-thread-dev_1.46.1.1_i386.deb) ... Selecting previously deselected package zlib1g-dev. Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3ubuntu3_i386.deb) ... Setting up libpipeline1 (1.2.0-3) ... Setting up libmagic1 (5.04-5ubuntu3) ... Setting up file (5.04-5ubuntu3) ... Setting up bsdmainutils (8.2.3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode. Setting up gettext-base (0.18.1.1-3ubuntu1) ... Setting up groff-base (1.21-6) ... Setting up libxml2 (2.7.8.dfsg-4) ... Setting up man-db (2.6.0.2-2) ... Building database of manual pages ... Setting up autotools-dev (20110511.1) ... Setting up html2text (1.3.2a-15) ... Setting up libcroco3 (0.6.2-1) ... Setting up libunistring0 (0.9.3-4) ... Setting up gettext (0.18.1.1-3ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu1) ... Setting up debhelper (8.9.0ubuntu1) ... Setting up libbam-dev (0.1.17-1) ... Setting up libboost1.46-dev (1.46.1-5ubuntu2) ... Setting up libboost-date-time1.46.1 (1.46.1-5ubuntu2) ... Setting up libboost-serialization1.46.1 (1.46.1-5ubuntu2) ... Setting up libboost-serialization1.46-dev (1.46.1-5ubuntu2) ... Setting up libboost-date-time1.46-dev (1.46.1-5ubuntu2) ... Setting up libboost-dev (1.46.1.1) ... Setting up libboost-thread1.46.1 (1.46.1-5ubuntu2) ... Setting up libboost-thread1.46-dev (1.46.1-5ubuntu2) ... Setting up libboost-thread-dev (1.46.1.1) ... Setting up zlib1g-dev (1:1.2.3.4.dfsg-3ubuntu3) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.13-20ubuntu5 make_3.81-8.1ubuntu1 dpkg-dev_1.16.0.3ubuntu5 gcc-4.6_4.6.1-9ubuntu3 g++-4.6_4.6.1-9ubuntu3 binutils_2.21.53.20110810-0ubuntu5 libstdc++6-4.6-dev_4.6.1-9ubuntu3 libstdc++6_4.6.1-9ubuntu3 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt gpgv: Signature made Mon Nov 28 08:49:43 2011 UTC using RSA key ID 7107D536 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./cufflinks_1.1.0-3.dsc dpkg-source: info: extracting cufflinks in cufflinks-1.1.0 dpkg-source: info: unpacking cufflinks_1.1.0.orig.tar.gz dpkg-source: info: unpacking cufflinks_1.1.0-3.debian.tar.gz dpkg-source: info: applying fix_includes_path.patch dpkg-source: info: applying fix_configure.patch dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): -Wl,-Bsymbolic-functions dpkg-buildpackage: source package cufflinks dpkg-buildpackage: source version 1.1.0-3 dpkg-source --before-build cufflinks-1.1.0 dpkg-buildpackage: host architecture i386 /usr/bin/fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean dh_clean debian/rules build dh build dh_testdir dh_auto_configure checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking for gawk... (cached) mawk checking for g++... g++ checking for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... none checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking dependency style of gcc... none checking whether make sets $(MAKE)... (cached) yes checking for ranlib... ranlib checking for a BSD-compatible install... /usr/bin/install -c checking for a Python interpreter with version >= 2.4... python checking for python... /usr/bin/python checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.7/site-packages checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-packages checking for boostlib >= 1.38.0... yes checking for bamlib... yes checking build system type... i686-pc-linux-gnu checking whether the Boost::Thread library is available... yes checking for exit in -lboost_thread-mt... yes checking how to run the C preprocessor... gcc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking if zlib is wanted... yes checking for inflateEnd in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for inflateEnd in -lz... (cached) yes checking zlib in /usr... ok checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for inline... inline checking for pid_t... yes checking for size_t... yes checking for ptrdiff_t... yes checking host system type... i686-pc-linux-gnu checking for struct sysinfo.totalram... yes checking whether sysctl is declared... yes checking whether CTL_HW is declared... no checking whether HW_PHYSMEM is declared... no checking how to create a pax tar archive... gnutar checking dependency style of gcc... (cached) none checking dependency style of g++... (cached) none configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands -- cufflinks 1.1.0 Configuration Results -- C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include GCC version: gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 Host System type: i686-pc-linux-gnu Install prefix: /usr Install eprefix: ${prefix} See config.h for further configuration information. Email with questions and bug reports. dh_auto_build make[1]: Entering directory `/build/buildd/cufflinks-1.1.0' make all-recursive make[2]: Entering directory `/build/buildd/cufflinks-1.1.0' Making all in src make[3]: Entering directory `/build/buildd/cufflinks-1.1.0/src' g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o clustering.o clustering.cpp g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o differential.o differential.cpp In file included from differential.h:29:0, from differential.cpp:18: replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&)': replicates.h:141:50: warning: unused variable 's2' [-Wunused-variable] differential.cpp: In member function 'void TestLauncher::perform_testing(std::vector >&)': differential.cpp:111:31: warning: unused variable 's2' [-Wunused-variable] differential.cpp: In function 'void sample_abundance_worker(const string&, SampleAbundances&, HitBundle*, bool, bool)': differential.cpp:671:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o common.o common.cpp In file included from common.cpp:28:0: replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&)': replicates.h:141:50: warning: unused variable 's2' [-Wunused-variable] g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o assemble.o assemble.cpp assemble.cpp: In function 'void create_reachability_bp_graph(DAG&, ReachGraph&, std::vector::BNode, std::allocator::BNode> >, DagToBp&, const boost::adjacency_list<>&, const std::vector&)': assemble.cpp:188:21: warning: variable 'a_for_b' set but not used [-Wunused-but-set-variable] assemble.cpp:123:17: warning: variable 'hits_for_node' set but not used [-Wunused-but-set-variable] assemble.cpp: In function 'void add_weights_to_reachability_bp_graph(ReachGraph&, const HitsForNodeMap&, const std::vector&, const std::vector&, lemon::BpUGraphExtender >::UEdgeMap&)': assemble.cpp:262:21: warning: variable 'a_for_b' set but not used [-Wunused-but-set-variable] g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o tokenize.o tokenize.cpp g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o abundances.o abundances.cpp In file included from abundances.cpp:35:0: replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&)': replicates.h:141:50: warning: unused variable 's2' [-Wunused-variable] abundances.cpp: In function 'void collapse_equivalent_hits(const std::vector&, std::vector >&, std::vector >&, std::vector&, std::vector&)': abundances.cpp:461:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] abundances.cpp: In function 'bool compute_fpkm_variance(long double&, double, double, double, double, double, double)': abundances.cpp:788:17: warning: variable 'bnb_mean' set but not used [-Wunused-but-set-variable] abundances.cpp: In member function 'void AbundanceGroup::calculate_FPKM_variance()': abundances.cpp:1093:18: warning: variable 'ok' set but not used [-Wunused-but-set-variable] abundances.cpp: In function 'void grad_ascent_step(int, int, const std::vector&, std::vector >&, const std::vector >&, const std::vector&, std::vector&, double&)': abundances.cpp:1689:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] abundances.cpp:1692:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] abundances.cpp:1697:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] abundances.cpp:1706:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] abundances.cpp: In function 'AbundanceStatus bootstrap_gamma_mle(const std::vector >&, const std::vector&, const std::vector&, boost::numeric::ublas::vector > >&, boost::numeric::ublas::matrix&, double&)': abundances.cpp:2617:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] abundances.cpp:2620:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] abundances.cpp:2633:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] abundances.cpp: In function 'AbundanceStatus gamma_mle(const std::vector >&, const std::vector&, const std::vector&, std::vector&, bool, std::vector*)': abundances.cpp:3101:10: warning: variable 'logL' set but not used [-Wunused-but-set-variable] g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o scaffolds.o scaffolds.cpp g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o hits.o hits.cpp hits.cpp: In member function 'virtual bool BAMHitFactory::inspect_header()': hits.cpp:618:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o genes.o genes.cpp g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o bundles.o bundles.cpp bundles.cpp:662:23: warning: integer constant is so large that it is unsigned [enabled by default] bundles.cpp:662:3: warning: this decimal constant is unsigned only in ISO C90 [enabled by default] bundles.cpp: In member function 'bool HitBundle::add_open_hit(boost::shared_ptr, const ReadHit*, bool)': bundles.cpp:294:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bundles.cpp: In member function 'double BundleFactory::next_valid_alignment(const ReadHit*&)': bundles.cpp:702:18: warning: variable 'found_scaff' set but not used [-Wunused-but-set-variable] bundles.cpp: In member function 'bool BundleFactory::next_bundle_ref_driven(HitBundle&)': bundles.cpp:801:8: warning: variable 'last_hit_ref_id_seen' set but not used [-Wunused-but-set-variable] bundles.cpp:802:6: warning: variable 'last_hit_pos_seen' set but not used [-Wunused-but-set-variable] g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o filters.o filters.cpp filters.cpp: In function 'void clip_by_3_prime_dropoff(std::vector&)': filters.cpp:820:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:822:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:869:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:795:20: warning: variable 'mean_to_keep' set but not used [-Wunused-but-set-variable] filters.cpp:796:20: warning: variable 'mean_to_trim' set but not used [-Wunused-but-set-variable] filters.cpp:922:20: warning: unused variable 'avg_cov' [-Wunused-variable] filters.cpp:926:36: warning: variable 'exon_3' set but not used [-Wunused-but-set-variable] filters.cpp:927:17: warning: variable 'mult' set but not used [-Wunused-but-set-variable] filters.cpp:928:17: warning: variable 'offset' set but not used [-Wunused-but-set-variable] g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o scaffold_graph.o scaffold_graph.cpp g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o matching_merge.o matching_merge.cpp g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o graph_optimize.o graph_optimize.cpp graph_optimize.cpp: In function 'bool collapse_contained_transfrags(std::vector&, uint32_t)': graph_optimize.cpp:264:30: warning: variable 'e' set but not used [-Wunused-but-set-variable] g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o biascorrection.o biascorrection.cpp gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o adap.o `test -f 'locfit/adap.c' || echo './'`locfit/adap.c locfit/adap.c: In function 'mmse': locfit/adap.c:29:17: warning: variable 'p' set but not used [-Wunused-but-set-variable] locfit/adap.c: In function 'aband3': locfit/adap.c:157:17: warning: variable 'n' set but not used [-Wunused-but-set-variable] locfit/adap.c:157:14: warning: variable 'd' set but not used [-Wunused-but-set-variable] gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o ar_funs.o `test -f 'locfit/ar_funs.c' || echo './'`locfit/ar_funs.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o arith.o `test -f 'locfit/arith.c' || echo './'`locfit/arith.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o band.o `test -f 'locfit/band.c' || echo './'`locfit/band.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o c_args.o `test -f 'locfit/c_args.c' || echo './'`locfit/c_args.c locfit/c_args.c: In function 'readilist': locfit/c_args.c:58:13: warning: variable 'nd' set but not used [-Wunused-but-set-variable] gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o c_plot.o `test -f 'locfit/c_plot.c' || echo './'`locfit/c_plot.c locfit/c_plot.c: In function 'plotfit': locfit/c_plot.c:228:13: warning: variable 'sd' set but not used [-Wunused-but-set-variable] locfit/c_plot.c:226:36: warning: variable 'sef' set but not used [-Wunused-but-set-variable] locfit/c_plot.c: In function 'setplot': locfit/c_plot.c:470:3: warning: passing argument 1 of 'setvarname' from incompatible pointer type [enabled by default] locfit/vari.hpp:23:10: note: expected 'struct vari *' but argument is of type 'char *' locfit/c_plot.c: In function 'plotfit': locfit/c_plot.c:364:45: warning: 'iy' may be used uninitialized in this function [-Wuninitialized] locfit/c_plot.c:361:43: warning: 'ix' may be used uninitialized in this function [-Wuninitialized] gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o cmd.o `test -f 'locfit/cmd.c' || echo './'`locfit/cmd.c locfit/cmd.c: In function 'ckap': locfit/cmd.c:101:10: warning: variable 'nd' set but not used [-Wunused-but-set-variable] locfit/cmd.c: In function 'predict': locfit/cmd.c:197:13: warning: variable 'data' set but not used [-Wunused-but-set-variable] locfit/cmd.c: In function 'setcolor': locfit/cmd.c:447:5: warning: 'return' with a value, in function returning void [enabled by default] locfit/cmd.c: In function 'cmdint': locfit/cmd.c:675:19: warning: variable 'nr' set but not used [-Wunused-but-set-variable] locfit/cmd.c: In function 'table': locfit/cmd.c:528:17: warning: 'ix' may be used uninitialized in this function [-Wuninitialized] gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o dens_haz.o `test -f 'locfit/dens_haz.c' || echo './'`locfit/dens_haz.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o dens_int.o `test -f 'locfit/dens_int.c' || echo './'`locfit/dens_int.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o dens_odi.o `test -f 'locfit/dens_odi.c' || echo './'`locfit/dens_odi.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o density.o `test -f 'locfit/density.c' || echo './'`locfit/density.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o dist.o `test -f 'locfit/dist.c' || echo './'`locfit/dist.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o ev_atree.o `test -f 'locfit/ev_atree.c' || echo './'`locfit/ev_atree.c locfit/ev_atree.c: In function 'atree_int': locfit/ev_atree.c:203:3: warning: 'nc' may be used uninitialized in this function [-Wuninitialized] gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o ev_interp.o `test -f 'locfit/ev_interp.c' || echo './'`locfit/ev_interp.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o ev_kdtre.o `test -f 'locfit/ev_kdtre.c' || echo './'`locfit/ev_kdtre.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o ev_main.o `test -f 'locfit/ev_main.c' || echo './'`locfit/ev_main.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o ev_trian.o `test -f 'locfit/ev_trian.c' || echo './'`locfit/ev_trian.c locfit/ev_trian.c: In function 'triang_grow': locfit/ev_trian.c:77:13: warning: 'jm' may be used uninitialized in this function [-Wuninitialized] locfit/ev_trian.c:76:13: warning: 'im' may be used uninitialized in this function [-Wuninitialized] locfit/ev_trian.c: In function 'triang_descend': locfit/ev_trian.c:121:38: warning: 'jm' may be used uninitialized in this function [-Wuninitialized] locfit/ev_trian.c:121:31: warning: 'im' may be used uninitialized in this function [-Wuninitialized] gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o family.o `test -f 'locfit/family.c' || echo './'`locfit/family.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o fitted.o `test -f 'locfit/fitted.c' || echo './'`locfit/fitted.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o frend.o `test -f 'locfit/frend.c' || echo './'`locfit/frend.c locfit/frend.c: In function 'procvvord': locfit/frend.c:205:39: warning: variable 'ip' set but not used [-Wunused-but-set-variable] locfit/frend.c:204:48: warning: variable 't2' set but not used [-Wunused-but-set-variable] gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o help.o `test -f 'locfit/help.c' || echo './'`locfit/help.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o lf_dercor.o `test -f 'locfit/lf_dercor.c' || echo './'`locfit/lf_dercor.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o lf_fitfun.o `test -f 'locfit/lf_fitfun.c' || echo './'`locfit/lf_fitfun.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o lf_robust.o `test -f 'locfit/lf_robust.c' || echo './'`locfit/lf_robust.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o lf_vari.o `test -f 'locfit/lf_vari.c' || echo './'`locfit/lf_vari.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o lfd.o `test -f 'locfit/lfd.c' || echo './'`locfit/lfd.c locfit/lfd.c: In function 'setfilename': locfit/lfd.c:60:7: warning: zero-length gnu_printf format string [-Wformat-zero-length] locfit/lfd.c: In function 'readchar': locfit/lfd.c:111:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] locfit/lfd.c: In function 'setfilename': locfit/lfd.c:77:17: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o lfstr.o `test -f 'locfit/lfstr.c' || echo './'`locfit/lfstr.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o linalg.o `test -f 'locfit/linalg.c' || echo './'`locfit/linalg.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o locfit.o `test -f 'locfit/locfit.c' || echo './'`locfit/locfit.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o m_chol.o `test -f 'locfit/m_chol.c' || echo './'`locfit/m_chol.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o m_eigen.o `test -f 'locfit/m_eigen.c' || echo './'`locfit/m_eigen.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o m_jacob.o `test -f 'locfit/m_jacob.c' || echo './'`locfit/m_jacob.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o m_max.o `test -f 'locfit/m_max.c' || echo './'`locfit/m_max.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o makecmd.o `test -f 'locfit/makecmd.c' || echo './'`locfit/makecmd.c locfit/makecmd.c: In function 'makefields': locfit/makecmd.c:88:5: warning: suggest parentheses around '&&' within '||' [-Wparentheses] locfit/makecmd.c: In function 'makecmd': locfit/makecmd.c:203:3: warning: format not a string literal and no format arguments [-Wformat-security] gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o math.o `test -f 'locfit/math.c' || echo './'`locfit/math.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o minmax.o `test -f 'locfit/minmax.c' || echo './'`locfit/minmax.c locfit/minmax.c: In function 'updatesd': locfit/minmax.c:94:21: warning: 'sd' may be used uninitialized in this function [-Wuninitialized] locfit/minmax.c: In function 'mmax': locfit/minmax.c:217:8: warning: 'sing' may be used uninitialized in this function [-Wuninitialized] gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o nbhd.o `test -f 'locfit/nbhd.c' || echo './'`locfit/nbhd.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o pcomp.o `test -f 'locfit/pcomp.c' || echo './'`locfit/pcomp.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o pout.o `test -f 'locfit/pout.c' || echo './'`locfit/pout.c locfit/pout.c: In function 'plotxwin': locfit/pout.c:447:38: warning: variable 'vz' set but not used [-Wunused-but-set-variable] locfit/pout.c:447:34: warning: variable 'vy' set but not used [-Wunused-but-set-variable] locfit/pout.c:447:30: warning: variable 'vx' set but not used [-Wunused-but-set-variable] gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o preplot.o `test -f 'locfit/preplot.c' || echo './'`locfit/preplot.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o random.o `test -f 'locfit/random.c' || echo './'`locfit/random.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o readfile.o `test -f 'locfit/readfile.c' || echo './'`locfit/readfile.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o scb.o `test -f 'locfit/scb.c' || echo './'`locfit/scb.c locfit/scb.c: In function 'cumulant': locfit/scb.c:61:10: warning: variable 'b2i' set but not used [-Wunused-but-set-variable] gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o scb_cons.o `test -f 'locfit/scb_cons.c' || echo './'`locfit/scb_cons.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o simul.o `test -f 'locfit/simul.c' || echo './'`locfit/simul.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o solve.o `test -f 'locfit/solve.c' || echo './'`locfit/solve.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o startlf.o `test -f 'locfit/startlf.c' || echo './'`locfit/startlf.c gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o strings.o `test -f 'locfit/strings.c' || echo './'`locfit/strings.c g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o vari.o `test -f 'locfit/vari.cpp' || echo './'`locfit/vari.cpp gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o wdiag.o `test -f 'locfit/wdiag.c' || echo './'`locfit/wdiag.c locfit/wdiag.c: In function 'wdiag': locfit/wdiag.c:109:18: warning: 'lxd' may be used uninitialized in this function [-Wuninitialized] gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -c -o weight.o `test -f 'locfit/weight.c' || echo './'`locfit/weight.c locfit/weight.c: In function 'weightdd': locfit/weight.c:162:10: warning: variable 'w' set but not used [-Wunused-but-set-variable] g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o replicates.o replicates.cpp In file included from replicates.cpp:15:0: replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&)': replicates.h:141:50: warning: unused variable 's2' [-Wunused-variable] replicates.cpp: In member function 'virtual double MassDispersionModel::scale_mass_variance(double) const': replicates.cpp:139:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] replicates.cpp:143:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] replicates.cpp: In function 'boost::shared_ptr fit_dispersion_model_helper(const string&, const std::vector&, const std::vector&)': replicates.cpp:253:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] replicates.cpp:307:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] replicates.cpp:322:30: warning: variable 'p' set but not used [-Wunused-but-set-variable] replicates.cpp: In function 'boost::shared_ptr fit_dispersion_model(const string&, const std::vector&, const std::vector&)': replicates.cpp:368:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o multireads.o multireads.cpp g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o jensen_shannon.o jensen_shannon.cpp rm -f libcufflinks.a ar cru libcufflinks.a clustering.o differential.o common.o assemble.o tokenize.o abundances.o scaffolds.o hits.o genes.o bundles.o filters.o scaffold_graph.o matching_merge.o graph_optimize.o biascorrection.o adap.o ar_funs.o arith.o band.o c_args.o c_plot.o cmd.o dens_haz.o dens_int.o dens_odi.o density.o dist.o ev_atree.o ev_interp.o ev_kdtre.o ev_main.o ev_trian.o family.o fitted.o frend.o help.o lf_dercor.o lf_fitfun.o lf_robust.o lf_vari.o lfd.o lfstr.o linalg.o locfit.o m_chol.o m_eigen.o m_jacob.o m_max.o makecmd.o math.o minmax.o nbhd.o pcomp.o pout.o preplot.o random.o readfile.o scb.o scb_cons.o simul.o solve.o startlf.o strings.o vari.o wdiag.o weight.o replicates.o multireads.o jensen_shannon.o ranlib libcufflinks.a g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o codons.o codons.cpp g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o GArgs.o GArgs.cpp g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o GBase.o GBase.cpp g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o gdna.o gdna.cpp g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o GStr.o GStr.cpp g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o GFaSeqGet.o GFaSeqGet.cpp g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o GFastaIndex.o GFastaIndex.cpp g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o gff.o gff.cpp g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o gff_utils.o gff_utils.cpp gff_utils.cpp: In function 'GffObj* redundantTranscripts(GffObj&, GffObj&, bool, bool)': gff_utils.cpp:206:6: warning: variable 'maxlen' set but not used [-Wunused-but-set-variable] gff_utils.cpp: In function 'void placeGf(GffObj*, GenomicSeqData*, bool, bool, bool, bool)': gff_utils.cpp:348:7: warning: variable 'tidx' set but not used [-Wunused-but-set-variable] g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o gtf_tracking.o gtf_tracking.cpp rm -f libgc.a ar cru libgc.a codons.o GArgs.o GBase.o gdna.o GStr.o GFaSeqGet.o GFastaIndex.o gff.o gff_utils.o gtf_tracking.o ranlib libgc.a g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o cufflinks.o cufflinks.cpp cufflinks.cpp: In function 'bool scaffolds_for_bundle(const HitBundle&, std::vector >&, std::vector >*, BundleStats*)': cufflinks.cpp:629:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cufflinks.cpp: In function 'void quantitate_transcript_cluster(AbundanceGroup&, double, std::vector&)': cufflinks.cpp:909:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cufflinks.cpp:917:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cufflinks.cpp: In function 'bool assemble_hits(BundleFactory&, BiasLearner*)': cufflinks.cpp:1410:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -o cufflinks -L/usr/lib cufflinks.o libcufflinks.a libgc.a -lboost_thread-mt -lbam -lz g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o cuffcompare.o cuffcompare.cpp cuffcompare.cpp: In function 'void printITrack(FILE*, GList&, int, int&)': cuffcompare.cpp:1831:12: warning: variable 'eqref' set but not used [-Wunused-but-set-variable] g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -o cuffcompare cuffcompare.o libgc.a -lz g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o cuffdiff.o cuffdiff.cpp In file included from differential.h:29:0, from cuffdiff.cpp:42: replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&)': replicates.h:141:50: warning: unused variable 's2' [-Wunused-variable] cuffdiff.cpp: In function 'void print_FPKM_tracking(FILE*, const FPKMTrackingTable&)': cuffdiff.cpp:457:25: warning: variable 'status' set but not used [-Wunused-but-set-variable] cuffdiff.cpp: In function 'void driver(FILE*, FILE*, std::vector >&, Outfiles&)': cuffdiff.cpp:866:10: warning: variable 'single_replicate_fac' set but not used [-Wunused-but-set-variable] cuffdiff.cpp: In function 'int main(int, char**)': cuffdiff.cpp:1386:35: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat] g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -o cuffdiff -L/usr/lib cuffdiff.o libcufflinks.a libgc.a -lboost_thread-mt -lbam -lz g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o gtf_to_sam.o gtf_to_sam.cpp gtf_to_sam.cpp: In function 'void print_scaff_as_sam(FILE*, const RefSequenceTable&, const Scaffold&)': gtf_to_sam.cpp:148:100: warning: format '%d' expects argument of type 'int', but argument 3 has type 'RefID {aka long long unsigned int}' [-Wformat] g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -o gtf_to_sam -L/usr/lib gtf_to_sam.o libcufflinks.a libgc.a -lboost_thread-mt -lbam -lz g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o compress_gtf.o compress_gtf.cpp g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -o compress_gtf -L/usr/lib compress_gtf.o libcufflinks.a libgc.a -lboost_thread-mt -lbam -lz g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -c -o gffread.o gffread.cpp g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -march=i686 -O3 -g -O2 -DNDEBUG -pthread -I/usr/include -o gffread gffread.o libgc.a -lz make[3]: Leaving directory `/build/buildd/cufflinks-1.1.0/src' make[3]: Entering directory `/build/buildd/cufflinks-1.1.0' make[3]: Nothing to be done for `all-am'. make[3]: Leaving directory `/build/buildd/cufflinks-1.1.0' make[2]: Leaving directory `/build/buildd/cufflinks-1.1.0' make[1]: Leaving directory `/build/buildd/cufflinks-1.1.0' dh_auto_test make[1]: Entering directory `/build/buildd/cufflinks-1.1.0' Making check in src make[2]: Entering directory `/build/buildd/cufflinks-1.1.0/src' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/cufflinks-1.1.0/src' make[2]: Entering directory `/build/buildd/cufflinks-1.1.0' make[2]: Nothing to be done for `check-am'. make[2]: Leaving directory `/build/buildd/cufflinks-1.1.0' make[1]: Leaving directory `/build/buildd/cufflinks-1.1.0' /usr/bin/fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_installdirs dh_auto_install make[1]: Entering directory `/build/buildd/cufflinks-1.1.0' Making install in src make[2]: Entering directory `/build/buildd/cufflinks-1.1.0/src' make[3]: Entering directory `/build/buildd/cufflinks-1.1.0/src' test -z "/usr/bin" || mkdir -p -- "/build/buildd/cufflinks-1.1.0/debian/cufflinks/usr/bin" /usr/bin/install -c 'cufflinks' '/build/buildd/cufflinks-1.1.0/debian/cufflinks/usr/bin/cufflinks' /usr/bin/install -c 'cuffcompare' '/build/buildd/cufflinks-1.1.0/debian/cufflinks/usr/bin/cuffcompare' /usr/bin/install -c 'cuffdiff' '/build/buildd/cufflinks-1.1.0/debian/cufflinks/usr/bin/cuffdiff' /usr/bin/install -c 'gtf_to_sam' '/build/buildd/cufflinks-1.1.0/debian/cufflinks/usr/bin/gtf_to_sam' /usr/bin/install -c 'compress_gtf' '/build/buildd/cufflinks-1.1.0/debian/cufflinks/usr/bin/compress_gtf' /usr/bin/install -c 'gffread' '/build/buildd/cufflinks-1.1.0/debian/cufflinks/usr/bin/gffread' test -z "/usr/bin" || mkdir -p -- "/build/buildd/cufflinks-1.1.0/debian/cufflinks/usr/bin" /usr/bin/install -c 'cuffmerge' '/build/buildd/cufflinks-1.1.0/debian/cufflinks/usr/bin/cuffmerge' make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/build/buildd/cufflinks-1.1.0/src' make[2]: Leaving directory `/build/buildd/cufflinks-1.1.0/src' make[2]: Entering directory `/build/buildd/cufflinks-1.1.0' make[3]: Entering directory `/build/buildd/cufflinks-1.1.0' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/build/buildd/cufflinks-1.1.0' make[2]: Leaving directory `/build/buildd/cufflinks-1.1.0' make[1]: Leaving directory `/build/buildd/cufflinks-1.1.0' dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_installcatalogs dh_installcron dh_installdebconf dh_installemacsen dh_installifupdown dh_installinfo dh_installinit dh_installmenu dh_installmime dh_installmodules dh_installlogcheck dh_installlogrotate dh_installpam dh_installppp dh_installudev dh_installwm dh_installxfonts dh_installgsettings dh_bugfiles dh_ucf dh_lintian dh_gconf dh_icons dh_perl dh_usrlocal dh_link dh_compress dh_fixperms dh_strip dh_strip debug symbol extraction: disabling for PPA build dh_strip debug symbol extraction: not doing anything since NO_PKG_MANGLE is given dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package cufflinks: unused substitution variable ${shlibs:Depends} dh_md5sums dh_builddeb INFO: pkgstriptranslations version 104 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build INFO: Disabling pkgstripfiles for PPA build dpkg-deb: building package `cufflinks' in `../cufflinks_1.1.0-3_i386.deb'. dpkg-genchanges -b -mUbuntu Build Daemon >../cufflinks_1.1.0-3_i386.changes dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build cufflinks-1.1.0 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20111128-0859 chroot-autobuild/build/buildd/cufflinks_1.1.0-3_i386.deb: new debian package, version 2.0. size 2299982 bytes: control archive= 718 bytes. 297 bytes, 9 lines control 650 bytes, 11 lines md5sums Package: cufflinks Version: 1.1.0-3 Architecture: i386 Maintainer: Johannes Koester Installed-Size: 5012 Section: science Priority: extra Homepage: http://cufflinks.cbcb.umd.edu Description: Calculate transcript abundances, and perform a differential expression. chroot-autobuild/build/buildd/cufflinks_1.1.0-3_i386.deb: drwxr-xr-x root/root 0 2011-11-28 08:59 ./ drwxr-xr-x root/root 0 2011-11-28 08:59 ./usr/ drwxr-xr-x root/root 0 2011-11-28 08:59 ./usr/share/ drwxr-xr-x root/root 0 2011-11-28 08:59 ./usr/share/doc/ drwxr-xr-x root/root 0 2011-11-28 08:59 ./usr/share/doc/cufflinks/ -rw-r--r-- root/root 200 2011-11-06 14:14 ./usr/share/doc/cufflinks/README.Debian -rw-r--r-- root/root 205 2011-11-28 08:49 ./usr/share/doc/cufflinks/changelog.Debian.gz -rw-r--r-- root/root 3536 2011-06-03 02:19 ./usr/share/doc/cufflinks/README -rw-r--r-- root/root 1508 2011-11-06 14:14 ./usr/share/doc/cufflinks/copyright drwxr-xr-x root/root 0 2011-11-28 08:59 ./usr/bin/ -rwxr-xr-x root/root 18983 2011-11-28 08:59 ./usr/bin/cuffmerge -rwxr-xr-x root/root 901720 2011-11-28 08:59 ./usr/bin/compress_gtf -rwxr-xr-x root/root 893496 2011-11-28 08:59 ./usr/bin/gtf_to_sam -rwxr-xr-x root/root 1414520 2011-11-28 08:59 ./usr/bin/cufflinks -rwxr-xr-x root/root 206472 2011-11-28 08:59 ./usr/bin/gffread -rwxr-xr-x root/root 1312024 2011-11-28 08:59 ./usr/bin/cuffdiff -rwxr-xr-x root/root 296640 2011-11-28 08:59 ./usr/bin/cuffcompare cufflinks_1.1.0-3_i386.changes: Format: 1.8 Date: Mon, 28 Nov 2011 09:49:15 +0100 Source: cufflinks Binary: cufflinks Architecture: i386 Version: 1.1.0-3 Distribution: oneiric Urgency: high Maintainer: Ubuntu Build Daemon Changed-By: Johannes Koester Description: cufflinks - Calculate transcript abundances, and perform a differential expre Changes: cufflinks (1.1.0-3) oneiric; urgency=high . * Fix architecture. Checksums-Sha1: dbf2665380d31b4112756b4bffdd0d050829b315 2299982 cufflinks_1.1.0-3_i386.deb Checksums-Sha256: a848bbf3f9d4404ac245e5d4b8622afbc4d95d135359a02bfa0efe275d5af26b 2299982 cufflinks_1.1.0-3_i386.deb Files: d2182c516c527e58bf115156ce76616f 2299982 science extra cufflinks_1.1.0-3_i386.deb ****************************************************************************** Built successfully Purging chroot-autobuild/build/buildd/cufflinks-1.1.0 ------------------------------------------------------------------------------ /usr/bin/sudo dpkg --purge intltool-debian groff-base libboost-date-time1.46-dev gettext file zlib1g-dev libboost1.46-dev html2text libboost-thread-dev gettext-base debhelper autotools-dev po-debconf libunistring0 libboost-serialization1.46.1 libboost-thread1.46-dev libcroco3 libmagic1 libpipeline1 libboost-date-time1.46.1 libbam-dev libboost-dev libboost-serialization1.46-dev libxml2 bsdmainutils man-db libboost-thread1.46.1 (Reading database ... 23919 files and directories currently installed.) Removing zlib1g-dev ... Removing libboost-thread-dev ... Removing debhelper ... Removing autotools-dev ... Removing po-debconf ... Removing libboost-thread1.46-dev ... Removing libbam-dev ... Removing libboost-dev ... Removing man-db ... Purging configuration files for man-db ... Removing catpages as well as /var/cache/man hierarchy. Removing libboost-thread1.46.1 ... Purging configuration files for libboost-thread1.46.1 ... Removing intltool-debian ... Removing groff-base ... Purging configuration files for groff-base ... Removing libboost-date-time1.46-dev ... Removing gettext ... Removing file ... Removing html2text ... Purging configuration files for html2text ... Removing gettext-base ... Removing libunistring0 ... Purging configuration files for libunistring0 ... Removing libcroco3 ... Purging configuration files for libcroco3 ... Removing libmagic1 ... Purging configuration files for libmagic1 ... Removing libpipeline1 ... Purging configuration files for libpipeline1 ... Removing libboost-date-time1.46.1 ... Purging configuration files for libboost-date-time1.46.1 ... Removing libboost-serialization1.46-dev ... Removing libxml2 ... Purging configuration files for libxml2 ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing libboost1.46-dev ... Removing libboost-serialization1.46.1 ... Purging configuration files for libboost-serialization1.46.1 ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place ****************************************************************************** Finished at 20111128-0900 Build needed 00:04:36, 136324k disk space Can't open average time db /var/debbuild/avg-build-times Can't open average space db /var/debbuild/avg-build-space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', '616fc0356b960b4b25e1a728d7f0def169a5394e'] Scanning for processes to kill in build /home/buildd/build-616fc0356b960b4b25e1a728d7f0def169a5394e/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', '616fc0356b960b4b25e1a728d7f0def169a5394e'] Unmounting chroot for build 616fc0356b960b4b25e1a728d7f0def169a5394e... none /home/buildd/build-616fc0356b960b4b25e1a728d7f0def169a5394e/chroot-autobuild/proc proc rw,relatime 0 0 none /home/buildd/build-616fc0356b960b4b25e1a728d7f0def169a5394e/chroot-autobuild/dev/pts devpts rw,relatime 0 0 none /home/buildd/build-616fc0356b960b4b25e1a728d7f0def169a5394e/chroot-autobuild/sys sysfs rw,relatime 0 0 none /home/buildd/build-616fc0356b960b4b25e1a728d7f0def169a5394e/chroot-autobuild/dev/shm tmpfs rw,relatime 0 0 RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', '616fc0356b960b4b25e1a728d7f0def169a5394e'] Removing build 616fc0356b960b4b25e1a728d7f0def169a5394e