RUN: /bin/echo ['echo', 'Forking build subprocess...'] Forking build subprocess... RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'f9ebd2fab1b4859cce3989cabf22edfbc04b01a4', '/home/buildd/filecache-default/7f84715a2487c0e25be20d612e2809c2352ed2ef'] Uncompressing the tarball... Synching the system clock with the buildd NTP service... 9 Nov 23:41:18 ntpdate[3397]: step time server 10.211.37.1 offset -38647.366203 sec Unpacking chroot for build f9ebd2fab1b4859cce3989cabf22edfbc04b01a4 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'f9ebd2fab1b4859cce3989cabf22edfbc04b01a4'] Mounting chroot for build f9ebd2fab1b4859cce3989cabf22edfbc04b01a4 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'f9ebd2fab1b4859cce3989cabf22edfbc04b01a4', '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-f9ebd2fab1b4859cce3989cabf22edfbc04b01a4 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'f9ebd2fab1b4859cce3989cabf22edfbc04b01a4', 'i386'] Updating debian chroot for build f9ebd2fab1b4859cce3989cabf22edfbc04b01a4 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 [28.2 kB] Get:6 http://ftpmaster.internal oneiric-updates Release [32.4 kB] Get:7 http://ftpmaster.internal oneiric/main i386 Packages [1226 kB] Get:8 http://ftpmaster.internal oneiric/restricted i386 Packages [8216 B] Get:9 http://ftpmaster.internal oneiric/universe i386 Packages [4468 kB] Get:10 http://ftpmaster.internal oneiric/multiverse i386 Packages [119 kB] Get:11 http://ftpmaster.internal oneiric/main TranslationIndex [3289 B] Get:12 http://ftpmaster.internal oneiric/multiverse TranslationIndex [2265 B] Get:13 http://ftpmaster.internal oneiric/restricted TranslationIndex [2263 B] Get:14 http://ftpmaster.internal oneiric/universe TranslationIndex [2640 B] Get:15 http://ftpmaster.internal oneiric-security/main i386 Packages [15.7 kB] Get:16 http://ftpmaster.internal oneiric-security/restricted i386 Packages [14 B] Get:17 http://ftpmaster.internal oneiric-security/universe i386 Packages [5467 B] Get:18 http://ftpmaster.internal oneiric-security/multiverse i386 Packages [14 B] Get:19 http://ftpmaster.internal oneiric-security/main TranslationIndex [72 B] Get:20 http://ftpmaster.internal oneiric-security/multiverse TranslationIndex [70 B] Get:21 http://ftpmaster.internal oneiric-security/restricted TranslationIndex [70 B] Get:22 http://ftpmaster.internal oneiric-security/universe TranslationIndex [72 B] Get:23 http://ftpmaster.internal oneiric-updates/main i386 Packages [128 kB] Get:24 http://ftpmaster.internal oneiric-updates/restricted i386 Packages [2878 B] Get:25 http://ftpmaster.internal oneiric-updates/universe i386 Packages [37.2 kB] Get:26 http://ftpmaster.internal oneiric-updates/multiverse i386 Packages [2703 B] Get:27 http://ftpmaster.internal oneiric-updates/main TranslationIndex [73 B] Get:28 http://ftpmaster.internal oneiric-updates/multiverse TranslationIndex [72 B] Get:29 http://ftpmaster.internal oneiric-updates/restricted TranslationIndex [71 B] Get:30 http://ftpmaster.internal oneiric-updates/universe TranslationIndex [73 B] Get:31 http://ftpmaster.internal oneiric/main Translation-en [701 kB] Get:32 http://ftpmaster.internal oneiric/multiverse Translation-en [92.6 kB] Get:33 http://ftpmaster.internal oneiric/restricted Translation-en [2229 B] Get:34 http://ftpmaster.internal oneiric/universe Translation-en [3165 kB] Get:35 http://ftpmaster.internal oneiric-security/main Translation-en [9986 B] Get:36 http://ftpmaster.internal oneiric-security/multiverse Translation-en [14 B] Get:37 http://ftpmaster.internal oneiric-security/restricted Translation-en [14 B] Get:38 http://ftpmaster.internal oneiric-security/universe Translation-en [4479 B] Get:39 http://ftpmaster.internal oneiric-updates/main Translation-en [67.3 kB] Get:40 http://ftpmaster.internal oneiric-updates/multiverse Translation-en [1190 B] Get:41 http://ftpmaster.internal oneiric-updates/restricted Translation-en [508 B] Get:42 http://ftpmaster.internal oneiric-updates/universe Translation-en [23.0 kB] Fetched 10.2 MB in 7s (1316 kB/s) Reading package lists... 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 libpam-modules libpam-modules-bin libpam-runtime libpam0g tzdata upstart 13 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 4200 kB of archives. After this operation, 4096 B disk space will be freed. WARNING: The following packages cannot be authenticated! libpam0g libpam-modules-bin libpam-modules libk5crypto3 libgssapi-krb5-2 libkrb5-3 libkrb5support0 libpam-runtime tzdata initramfs-tools initramfs-tools-bin upstart binutils 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 libpam-runtime i386 1.1.3-2ubuntu2.1 [45.0 kB] Get:9 http://ftpmaster.internal/ubuntu/ oneiric-updates/main tzdata i386 2011n-0ubuntu0.11.10 [465 kB] Get:10 http://ftpmaster.internal/ubuntu/ oneiric-updates/main initramfs-tools all 0.99ubuntu8 [51.7 kB] Get:11 http://ftpmaster.internal/ubuntu/ oneiric-updates/main initramfs-tools-bin i386 0.99ubuntu8 [11.8 kB] Get:12 http://ftpmaster.internal/ubuntu/ oneiric-updates/main upstart i386 1.3-0ubuntu11 [289 kB] Get:13 http://ftpmaster.internal/ubuntu/ oneiric-updates/main binutils i386 2.21.53.20110810-0ubuntu5 [2383 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 4200 kB in 0s (14.3 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 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: Wed Nov 9 12:58:21 UTC 2011. Universal Time is now: Wed Nov 9 12:58:21 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 ... 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 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) ... 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', 'f9ebd2fab1b4859cce3989cabf22edfbc04b01a4', 'i386', 'oneiric', '--nolog', '--batch', '--archive=ubuntu', '--dist=oneiric', '-A', '--purpose=PPA', '--architecture=i386', '--comp=main', 'pysam_0.5-1.dsc'] Initiating build f9ebd2fab1b4859cce3989cabf22edfbc04b01a4 with 2 processor cores. Automatic build of pysam_0.5-1 on thallium by sbuild/i386 1.170.5 Build started at 20111109-1258 ****************************************************************************** pysam_0.5-1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: python-setuptools (>= 0.6b3), python-all-dev (>= 2.6.6-3), debhelper (>= 7), cython (>= 0.12) Checking for already installed source dependencies... python-setuptools: missing python-all-dev: missing debhelper: missing cython: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install python-setuptools python-all-dev debhelper cython 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 libcroco3 libdb4.8 libexpat1 libexpat1-dev libmagic1 libpipeline1 libpython2.6 libpython2.7 libsqlite3-0 libssl-dev libunistring0 libxml2 man-db mime-support po-debconf python python-all python-dev python-pkg-resources python-support python2.6 python2.6-dev python2.6-minimal python2.7 python2.7-dev zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser libmail-box-perl python-doc python-tk python-distribute python-distribute-doc python2.6-doc binfmt-support python2.7-doc Recommended packages: curl wget lynx-cur libssl-doc xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils cython debhelper file gettext gettext-base groff-base html2text intltool-debian libcroco3 libdb4.8 libexpat1 libexpat1-dev libmagic1 libpipeline1 libpython2.6 libpython2.7 libsqlite3-0 libssl-dev libunistring0 libxml2 man-db mime-support po-debconf python python-all python-all-dev python-dev python-pkg-resources python-setuptools python-support python2.6 python2.6-dev python2.6-minimal python2.7 python2.7-dev zlib1g-dev 0 upgraded, 37 newly installed, 0 to remove and 0 not upgraded. Need to get 28.5 MB of archives. After this operation, 91.1 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libdb4.8 libexpat1 libsqlite3-0 libpipeline1 libmagic1 file mime-support python2.7 python bsdmainutils gettext-base groff-base libxml2 man-db python-support cython html2text libcroco3 libunistring0 gettext intltool-debian po-debconf debhelper libexpat1-dev python2.6-minimal python2.6 libpython2.6 libpython2.7 zlib1g-dev libssl-dev python-all python2.7-dev python-dev python2.6-dev python-all-dev python-pkg-resources python-setuptools Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ oneiric/main libdb4.8 i386 4.8.30-9ubuntu1 [711 kB] Get:2 http://ftpmaster.internal/ubuntu/ oneiric/main libexpat1 i386 2.0.1-7ubuntu3 [135 kB] Get:3 http://ftpmaster.internal/ubuntu/ oneiric/main libsqlite3-0 i386 3.7.7-2ubuntu2 [346 kB] Get:4 http://ftpmaster.internal/ubuntu/ oneiric/main libpipeline1 i386 1.2.0-3 [25.7 kB] Get:5 http://ftpmaster.internal/ubuntu/ oneiric/main libmagic1 i386 5.04-5ubuntu3 [205 kB] Get:6 http://ftpmaster.internal/ubuntu/ oneiric/main file i386 5.04-5ubuntu3 [19.8 kB] Get:7 http://ftpmaster.internal/ubuntu/ oneiric/main mime-support all 3.51-1ubuntu1 [30.7 kB] Get:8 http://ftpmaster.internal/ubuntu/ oneiric/main python2.7 i386 2.7.2-5ubuntu1 [2569 kB] Get:9 http://ftpmaster.internal/ubuntu/ oneiric/main python all 2.7.2-7ubuntu2 [166 kB] Get:10 http://ftpmaster.internal/ubuntu/ oneiric/main bsdmainutils i386 8.2.3 [196 kB] Get:11 http://ftpmaster.internal/ubuntu/ oneiric/main gettext-base i386 0.18.1.1-3ubuntu1 [56.6 kB] Get:12 http://ftpmaster.internal/ubuntu/ oneiric/main groff-base i386 1.21-6 [1024 kB] Get:13 http://ftpmaster.internal/ubuntu/ oneiric/main libxml2 i386 2.7.8.dfsg-4 [662 kB] Get:14 http://ftpmaster.internal/ubuntu/ oneiric/main man-db i386 2.6.0.2-2 [717 kB] Get:15 http://ftpmaster.internal/ubuntu/ oneiric/main python-support all 1.0.13ubuntu1 [26.6 kB] Get:16 http://ftpmaster.internal/ubuntu/ oneiric/universe cython i386 0.14.1-6 [1500 kB] Get:17 http://ftpmaster.internal/ubuntu/ oneiric/main html2text i386 1.3.2a-15 [101 kB] Get:18 http://ftpmaster.internal/ubuntu/ oneiric/main libcroco3 i386 0.6.2-1 [92.5 kB] Get:19 http://ftpmaster.internal/ubuntu/ oneiric/main libunistring0 i386 0.9.3-4 [431 kB] Get:20 http://ftpmaster.internal/ubuntu/ oneiric/main gettext i386 0.18.1.1-3ubuntu1 [1180 kB] Get:21 http://ftpmaster.internal/ubuntu/ oneiric/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:22 http://ftpmaster.internal/ubuntu/ oneiric/main po-debconf all 1.0.16+nmu1 [212 kB] Get:23 http://ftpmaster.internal/ubuntu/ oneiric/main debhelper all 8.9.0ubuntu1 [487 kB] Get:24 http://ftpmaster.internal/ubuntu/ oneiric/main libexpat1-dev i386 2.0.1-7ubuntu3 [211 kB] Get:25 http://ftpmaster.internal/ubuntu/ oneiric/main python2.6-minimal i386 2.6.7-4ubuntu1 [1438 kB] Get:26 http://ftpmaster.internal/ubuntu/ oneiric/main python2.6 i386 2.6.7-4ubuntu1 [2408 kB] Get:27 http://ftpmaster.internal/ubuntu/ oneiric/main libpython2.6 i386 2.6.7-4ubuntu1 [1049 kB] Get:28 http://ftpmaster.internal/ubuntu/ oneiric/main libpython2.7 i386 2.7.2-5ubuntu1 [1134 kB] Get:29 http://ftpmaster.internal/ubuntu/ oneiric/main zlib1g-dev i386 1:1.2.3.4.dfsg-3ubuntu3 [160 kB] Get:30 http://ftpmaster.internal/ubuntu/ oneiric/main libssl-dev i386 1.0.0e-2ubuntu4 [1398 kB] Get:31 http://ftpmaster.internal/ubuntu/ oneiric/main python-all all 2.7.2-7ubuntu2 [922 B] Get:32 http://ftpmaster.internal/ubuntu/ oneiric/main python2.7-dev i386 2.7.2-5ubuntu1 [4893 kB] Get:33 http://ftpmaster.internal/ubuntu/ oneiric/main python-dev all 2.7.2-7ubuntu2 [1008 B] Get:34 http://ftpmaster.internal/ubuntu/ oneiric/main python2.6-dev i386 2.6.7-4ubuntu1 [4623 kB] Get:35 http://ftpmaster.internal/ubuntu/ oneiric/main python-all-dev all 2.7.2-7ubuntu2 [938 B] Get:36 http://ftpmaster.internal/ubuntu/ oneiric/main python-pkg-resources all 0.6.16-1 [62.6 kB] Get:37 http://ftpmaster.internal/ubuntu/ oneiric/main python-setuptools all 0.6.16-1 [212 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 28.5 MB in 2s (13.3 MB/s) Selecting previously deselected package libdb4.8. (Reading database ... 14112 files and directories currently installed.) Unpacking libdb4.8 (from .../libdb4.8_4.8.30-9ubuntu1_i386.deb) ... Selecting previously deselected package libexpat1. Unpacking libexpat1 (from .../libexpat1_2.0.1-7ubuntu3_i386.deb) ... Selecting previously deselected package libsqlite3-0. Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.7-2ubuntu2_i386.deb) ... Selecting previously deselected package libpipeline1. 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 mime-support. Unpacking mime-support (from .../mime-support_3.51-1ubuntu1_all.deb) ... Selecting previously deselected package python2.7. Unpacking python2.7 (from .../python2.7_2.7.2-5ubuntu1_i386.deb) ... Selecting previously deselected package python. Unpacking python (from .../python_2.7.2-7ubuntu2_all.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 python-support. Unpacking python-support (from .../python-support_1.0.13ubuntu1_all.deb) ... Selecting previously deselected package cython. Unpacking cython (from .../cython_0.14.1-6_i386.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 libexpat1-dev. Unpacking libexpat1-dev (from .../libexpat1-dev_2.0.1-7ubuntu3_i386.deb) ... Selecting previously deselected package python2.6-minimal. Unpacking python2.6-minimal (from .../python2.6-minimal_2.6.7-4ubuntu1_i386.deb) ... Selecting previously deselected package python2.6. Unpacking python2.6 (from .../python2.6_2.6.7-4ubuntu1_i386.deb) ... Selecting previously deselected package libpython2.6. Unpacking libpython2.6 (from .../libpython2.6_2.6.7-4ubuntu1_i386.deb) ... Selecting previously deselected package libpython2.7. Unpacking libpython2.7 (from .../libpython2.7_2.7.2-5ubuntu1_i386.deb) ... Selecting previously deselected package zlib1g-dev. Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3ubuntu3_i386.deb) ... Selecting previously deselected package libssl-dev. Unpacking libssl-dev (from .../libssl-dev_1.0.0e-2ubuntu4_i386.deb) ... Selecting previously deselected package python-all. Unpacking python-all (from .../python-all_2.7.2-7ubuntu2_all.deb) ... Selecting previously deselected package python2.7-dev. Unpacking python2.7-dev (from .../python2.7-dev_2.7.2-5ubuntu1_i386.deb) ... Selecting previously deselected package python-dev. Unpacking python-dev (from .../python-dev_2.7.2-7ubuntu2_all.deb) ... Selecting previously deselected package python2.6-dev. Unpacking python2.6-dev (from .../python2.6-dev_2.6.7-4ubuntu1_i386.deb) ... Selecting previously deselected package python-all-dev. Unpacking python-all-dev (from .../python-all-dev_2.7.2-7ubuntu2_all.deb) ... Selecting previously deselected package python-pkg-resources. Unpacking python-pkg-resources (from .../python-pkg-resources_0.6.16-1_all.deb) ... Selecting previously deselected package python-setuptools. Unpacking python-setuptools (from .../python-setuptools_0.6.16-1_all.deb) ... Setting up libdb4.8 (4.8.30-9ubuntu1) ... Setting up libexpat1 (2.0.1-7ubuntu3) ... Setting up libsqlite3-0 (3.7.7-2ubuntu2) ... Setting up libpipeline1 (1.2.0-3) ... Setting up libmagic1 (5.04-5ubuntu3) ... Setting up file (5.04-5ubuntu3) ... Setting up mime-support (3.51-1ubuntu1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode. Setting up python2.7 (2.7.2-5ubuntu1) ... Setting up python (2.7.2-7ubuntu2) ... 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 python-support (1.0.13ubuntu1) ... Setting up cython (0.14.1-6) ... 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 libexpat1-dev (2.0.1-7ubuntu3) ... Setting up python2.6-minimal (2.6.7-4ubuntu1) ... Linking and byte-compiling packages for runtime python2.6... Setting up python2.6 (2.6.7-4ubuntu1) ... Setting up libpython2.6 (2.6.7-4ubuntu1) ... Setting up libpython2.7 (2.7.2-5ubuntu1) ... Setting up zlib1g-dev (1:1.2.3.4.dfsg-3ubuntu3) ... Setting up libssl-dev (1.0.0e-2ubuntu4) ... Setting up python-all (2.7.2-7ubuntu2) ... Setting up python2.7-dev (2.7.2-5ubuntu1) ... Setting up python-dev (2.7.2-7ubuntu2) ... Setting up python2.6-dev (2.6.7-4ubuntu1) ... Setting up python-all-dev (2.7.2-7ubuntu2) ... Setting up python-pkg-resources (0.6.16-1) ... Setting up python-setuptools (0.6.16-1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Processing triggers for python-support ... Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.13-20ubuntu5 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 7 14:53:33 2011 UTC using RSA key ID 7107D536 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./pysam_0.5-1.dsc dpkg-source: info: extracting pysam in pysam-0.5 dpkg-source: info: unpacking pysam_0.5.orig.tar.gz dpkg-source: info: unpacking pysam_0.5-1.debian.tar.gz 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 pysam dpkg-buildpackage: source version 0.5-1 dpkg-source --before-build pysam-0.5 dpkg-buildpackage: host architecture i386 /usr/bin/fakeroot debian/rules clean dh clean --with python2 --buildsystem=python_distutils dh_testdir -O--buildsystem=python_distutils dh_auto_clean -O--buildsystem=python_distutils running clean 'build/lib.linux-i686-2.6' does not exist -- can't clean it 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-2.6' does not exist -- can't clean it running clean 'build/lib.linux-i686-2.7' does not exist -- can't clean it 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it dh_clean -O--buildsystem=python_distutils debian/rules build dh build --with python2 --buildsystem=python_distutils dh_testdir -O--buildsystem=python_distutils dh_auto_configure -O--buildsystem=python_distutils dh_auto_build -O--buildsystem=python_distutils running build running build_py creating build creating build/lib.linux-i686-2.6 creating build/lib.linux-i686-2.6/pysam copying pysam/__init__.py -> build/lib.linux-i686-2.6/pysam copying pysam/Pileup.py -> build/lib.linux-i686-2.6/pysam copying pysam/namedtuple.py -> build/lib.linux-i686-2.6/pysam copying pysam/version.py -> build/lib.linux-i686-2.6/pysam running build_ext cythoning pysam/csamtools.pyx to pysam/csamtools.c building 'csamtools' extension creating build/temp.linux-i686-2.6 creating build/temp.linux-i686-2.6/pysam creating build/temp.linux-i686-2.6/samtools creating build/temp.linux-i686-2.6/samtools/misc creating build/temp.linux-i686-2.6/samtools/bcftools gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c pysam/csamtools.c -o build/temp.linux-i686-2.6/pysam/csamtools.o In file included from pysam/csamtools.c:232:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from pysam/csamtools.c:234:0: samtools/glf.h:43:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from pysam/csamtools.c:235:0: samtools/bam_maqcns.h:44:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_maqcns.h:52:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] pysam/csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_9fetch': pysam/csamtools.c:8415:124: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type [enabled by default] samtools/bam.h:621:6: note: expected 'bam_fetch_f' but argument is of type 'int (*)(struct bam1_t *, void *)' pysam/csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_10mate': pysam/csamtools.c:8806:318: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type [enabled by default] samtools/bam.h:621:6: note: expected 'bam_fetch_f' but argument is of type 'int (*)(struct bam1_t *, void *)' pysam/csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_11count': pysam/csamtools.c:9293:95: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type [enabled by default] samtools/bam.h:621:6: note: expected 'bam_fetch_f' but argument is of type 'int (*)(struct bam1_t *, void *)' pysam/csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_12pileup': pysam/csamtools.c:9730:97: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type [enabled by default] samtools/bam.h:621:6: note: expected 'bam_fetch_f' but argument is of type 'int (*)(struct bam1_t *, void *)' pysam/csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_17__exit__': pysam/csamtools.c:10206:13: warning: variable '__pyx_v_traceback' set but not used [-Wunused-but-set-variable] pysam/csamtools.c:10205:13: warning: variable '__pyx_v_exc_value' set but not used [-Wunused-but-set-variable] pysam/csamtools.c:10204:13: warning: variable '__pyx_v_exc_type' set but not used [-Wunused-but-set-variable] pysam/csamtools.c: In function '__pyx_f_9csamtools___advance_snpcalls': pysam/csamtools.c:15024:7: warning: implicit declaration of function 'bam_prob_realn' [-Wimplicit-function-declaration] pysam/csamtools.c:15052:7: warning: implicit declaration of function 'bam_cap_mapQ' [-Wimplicit-function-declaration] pysam/csamtools.c: In function '__pyx_f_9csamtools_13SNPCallerBase___dump': pysam/csamtools.c:26979:3: warning: format not a string literal and no format arguments [-Wformat-security] pysam/csamtools.c: In function '__pyx_pf_9csamtools_16IteratorSNPCalls_2__next__': pysam/csamtools.c:27355:5: warning: this decimal constant is unsigned only in ISO C90 [enabled by default] pysam/csamtools.c: In function '__pyx_pf_9csamtools_9SNPCaller_1call': pysam/csamtools.c:27878:5: warning: this decimal constant is unsigned only in ISO C90 [enabled by default] pysam/csamtools.c: In function '__pyx_pf_9csamtools_15IndelCallerBase_2_call': pysam/csamtools.c:29327:15: warning: assignment discards 'const' qualifier from pointer target type [enabled by default] pysam/csamtools.c: In function '__Pyx_InitGlobals': pysam/csamtools.c:36689:3: warning: this decimal constant is unsigned only in ISO C90 [enabled by default] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c pysam/pysam_util.c -o build/temp.linux-i686-2.6/pysam/pysam_util.o In file included from pysam/pysam_util.c:3:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from pysam/pysam_util.c:6:0: samtools/bam_endian.h:6:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from pysam/pysam_util.h:52:0, from pysam/pysam_util.c:8: samtools/glf.h:43:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from pysam/pysam_util.h:55:0, from pysam/pysam_util.c:8: samtools/bam_maqcns.h:44:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_maqcns.h:52:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] pysam/pysam_util.c:49:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] pysam/pysam_util.c:50:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] pysam/pysam_util.c:81:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] pysam/pysam_util.c: In function 'pysam_pileup_next': pysam/pysam_util.c:178:8: warning: assignment discards 'const' qualifier from pointer target type [enabled by default] pysam/pysam_util.c: At top level: pysam/pysam_util.c:81:19: warning: 'mp_init' defined but not used [-Wunused-function] pysam/pysam_util.c:87:13: warning: 'mp_destroy' defined but not used [-Wunused-function] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/sam.c.pysam.c -o build/temp.linux-i686-2.6/samtools/sam.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/sam.c.pysam.c:6: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/kprobaln.c.pysam.c -o build/temp.linux-i686-2.6/samtools/kprobaln.c.pysam.o samtools/kprobaln.c.pysam.c: In function 'kpa_glocal': samtools/kprobaln.c.pysam.c:80:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/kstring.c.pysam.c -o build/temp.linux-i686-2.6/samtools/kstring.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/phase.c.pysam.c -o build/temp.linux-i686-2.6/samtools/phase.c.pysam.o In file included from samtools/phase.c.pysam.c:9:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/phase.c.pysam.c:47:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/phase.c.pysam.c:48:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam2bcf_indel.c.pysam.o In file included from samtools/bam2bcf_indel.c.pysam.c:6:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam2bcf.h:6:0, from samtools/bam2bcf_indel.c.pysam.c:7: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam2bcf_indel.c.pysam.c:12:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam2bcf.c.pysam.o In file included from samtools/bam2bcf.c.pysam.c:5:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam2bcf.h:6:0, from samtools/bam2bcf.c.pysam.c:7: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_aux.c.pysam.o In file included from samtools/bam_aux.c.pysam.c:4:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_aux.c.pysam.c:7:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_aux.c.pysam.c:8:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_lpileup.c.pysam.o In file included from samtools/bam_lpileup.c.pysam.c:6:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_lpileup.c.pysam.c:25:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_pileup.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_pileup.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/bam_pileup.c.pysam.c:7: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_pileup.c.pysam.c:29:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_pileup.c.pysam.c: In function 'resolve_cigar2': samtools/bam_pileup.c.pysam.c:77:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_index.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_index.c.pysam.o In file included from samtools/bam_index.c.pysam.c:5:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam_index.c.pysam.c:8:0: samtools/bam_endian.h:6:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_index.c.pysam.c:66:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_index.c.pysam.c: In function 'bam_index_load_core': samtools/bam_index.c.pysam.c:328:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:348:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:351:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:355:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:359:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:369:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:373:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/sam_header.c.pysam.c -o build/temp.linux-i686-2.6/samtools/sam_header.c.pysam.o samtools/sam_header.c.pysam.c:11:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/glf.c.pysam.c -o build/temp.linux-i686-2.6/samtools/glf.c.pysam.o In file included from samtools/glf.c.pysam.c:5:0: samtools/glf.h:43:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/glf.c.pysam.c:24:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/glf.c.pysam.c:30:16: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_md.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_md.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/bam_md.c.pysam.c:9: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_rmdupse.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/bam_rmdupse.c.pysam.c:4: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdupse.c.pysam.c:17:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdupse.c.pysam.c:17:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdupse.c.pysam.c:20:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdupse.c.pysam.c:27:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/sam_view.c.pysam.c -o build/temp.linux-i686-2.6/samtools/sam_view.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/sam_view.c.pysam.c:9: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/sam_view.c.pysam.c:13:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_cat.c.pysam.o In file included from samtools/bam_cat.c.pysam.c:65:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bgzf.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bgzf.c.pysam.o samtools/bgzf.c.pysam.c:46:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bgzf.c.pysam.c:142:14: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bgzf.c.pysam.c: In function 'bgzf_close': samtools/bgzf.c.pysam.c:632:8: warning: variable 'count' set but not used [-Wunused-but-set-variable] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_stat.c.pysam.o In file included from samtools/bam_stat.c.pysam.c:5:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_rmdup.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/bam_rmdup.c.pysam.c:8: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdup.c.pysam.c:13:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdup.c.pysam.c:14:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdup.c.pysam.c:22:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/cut_target.c.pysam.c -o build/temp.linux-i686-2.6/samtools/cut_target.c.pysam.o In file included from samtools/cut_target.c.pysam.c:6:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/cut_target.c.pysam.c: In function 'main_cut_target': samtools/cut_target.c.pysam.c:139:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/kaln.c.pysam.c -o build/temp.linux-i686-2.6/samtools/kaln.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/razf.c.pysam.c -o build/temp.linux-i686-2.6/samtools/razf.c.pysam.o samtools/razf.c.pysam.c:76:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/razf.c.pysam.c: In function 'razf_close': samtools/razf.c.pysam.c:806:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:807:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:812:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c: In function 'razf_end_flush': samtools/razf.c.pysam.c:260:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c: In function '_razf_write': samtools/razf.c.pysam.c:203:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c: In function 'save_zindex': samtools/razf.c.pysam.c:98:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:101:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:108:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:109:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c: In function 'razf_flush': samtools/razf.c.pysam.c:223:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:236:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bedidx.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bedidx.c.pysam.o samtools/bedidx.c.pysam.c:22:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/knetfile.c.pysam.c -o build/temp.linux-i686-2.6/samtools/knetfile.c.pysam.o samtools/knetfile.c.pysam.c: In function 'khttp_connect_file': samtools/knetfile.c.pysam.c:417:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/knetfile.c.pysam.c: In function 'kftp_send_cmd': samtools/knetfile.c.pysam.c:238:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_tview.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_tview.c.pysam.o samtools/bam_tview.c.pysam.c:420:2: warning: #warning "No curses library is available; tview is disabled." [-Wcpp] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_color.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_color.c.pysam.o In file included from samtools/bam_color.c.pysam.c:4:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_mate.c.pysam.o In file included from samtools/bam_mate.c.pysam.c:5:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam2depth.c.pysam.o In file included from samtools/bam2depth.c.pysam.c:13:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_sort.c.pysam.o In file included from samtools/bam_sort.c.pysam.c:10:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/sample.c.pysam.c -o build/temp.linux-i686-2.6/samtools/sample.c.pysam.o samtools/sample.c.pysam.c:7:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_import.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_import.c.pysam.o In file included from samtools/bam_import.c.pysam.c:14:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_import.c.pysam.c:20:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_import.c.pysam.c: In function 'append_text': samtools/bam_import.c.pysam.c:181:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat] samtools/bam_import.c.pysam.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat] samtools/bam_import.c.pysam.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat] samtools/bam_import.c.pysam.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat] samtools/bam_import.c.pysam.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/faidx.c.pysam.c -o build/temp.linux-i686-2.6/samtools/faidx.c.pysam.o samtools/faidx.c.pysam.c:15:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam.c.pysam.o In file included from samtools/bam.c.pysam.c:7:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam.c.pysam.c:8:0: samtools/bam_endian.h:6:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.c.pysam.c:47:15: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_maqcns.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_maqcns.c.pysam.o In file included from samtools/bam_maqcns.c.pysam.c:5:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam_maqcns.h:4:0, from samtools/bam_maqcns.c.pysam.c:6: samtools/glf.h:43:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam_maqcns.c.pysam.c:6:0: samtools/bam_maqcns.h:44:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_maqcns.h:52:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_maqcns.c.pysam.c:107:15: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_maqcns.c.pysam.c:322:21: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/errmod.c.pysam.c -o build/temp.linux-i686-2.6/samtools/errmod.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_plcmd.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/bam_plcmd.c.pysam.c:9: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam_maqcns.h:4:0, from samtools/bam_plcmd.c.pysam.c:11: samtools/glf.h:43:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam_plcmd.c.pysam.c:11:0: samtools/bam_maqcns.h:44:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_maqcns.h:52:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_plcmd.c.pysam.c:17:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam2bcf.h:6:0, from samtools/bam_plcmd.c.pysam.c:529: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/misc/md5.c.pysam.c -o build/temp.linux-i686-2.6/samtools/misc/md5.c.pysam.o samtools/misc/md5.c.pysam.c:33:6: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/prob1.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/prob1.c.pysam.o In file included from samtools/bcftools/prob1.h:4:0, from samtools/bcftools/prob1.c.pysam.c:9: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/fet.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/fet.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/kmin.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/kmin.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/index.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/index.c.pysam.o In file included from samtools/bcftools/index.c.pysam.c:6:0: samtools/bam_endian.h:6:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bcftools/index.c.pysam.c:8:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/vcf.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/vcf.c.pysam.o In file included from samtools/bcftools/vcf.c.pysam.c:7:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/call1.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/call1.c.pysam.o In file included from samtools/bcftools/call1.c.pysam.c:8:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/bcfutils.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/bcfutils.c.pysam.o In file included from samtools/bcftools/bcfutils.c.pysam.c:5:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bcftools/bcfutils.c.pysam.c:8:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bcftools/bcfutils.c.pysam.c:23:7: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/kfunc.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/kfunc.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/em.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/em.c.pysam.o In file included from samtools/bcftools/em.c.pysam.c:6:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bcftools/em.c.pysam.c: In function 'bcf_em1': samtools/bcftools/em.c.pysam.c:176:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/bcf2qcall.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/bcf2qcall.c.pysam.o In file included from samtools/bcftools/bcf2qcall.c.pysam.c:7:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/bcf.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/bcf.c.pysam.o In file included from samtools/bcftools/bcf.c.pysam.c:7:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -O2 build/temp.linux-i686-2.6/pysam/csamtools.o build/temp.linux-i686-2.6/pysam/pysam_util.o build/temp.linux-i686-2.6/samtools/sam.c.pysam.o build/temp.linux-i686-2.6/samtools/kprobaln.c.pysam.o build/temp.linux-i686-2.6/samtools/kstring.c.pysam.o build/temp.linux-i686-2.6/samtools/phase.c.pysam.o build/temp.linux-i686-2.6/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-i686-2.6/samtools/bam2bcf.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_aux.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_lpileup.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_pileup.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_index.c.pysam.o build/temp.linux-i686-2.6/samtools/sam_header.c.pysam.o build/temp.linux-i686-2.6/samtools/glf.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_md.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_rmdupse.c.pysam.o build/temp.linux-i686-2.6/samtools/sam_view.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_cat.c.pysam.o build/temp.linux-i686-2.6/samtools/bgzf.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_stat.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_rmdup.c.pysam.o build/temp.linux-i686-2.6/samtools/cut_target.c.pysam.o build/temp.linux-i686-2.6/samtools/kaln.c.pysam.o build/temp.linux-i686-2.6/samtools/razf.c.pysam.o build/temp.linux-i686-2.6/samtools/bedidx.c.pysam.o build/temp.linux-i686-2.6/samtools/knetfile.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_tview.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_color.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_mate.c.pysam.o build/temp.linux-i686-2.6/samtools/bam2depth.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_sort.c.pysam.o build/temp.linux-i686-2.6/samtools/sample.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_import.c.pysam.o build/temp.linux-i686-2.6/samtools/faidx.c.pysam.o build/temp.linux-i686-2.6/samtools/bam.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_maqcns.c.pysam.o build/temp.linux-i686-2.6/samtools/errmod.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_plcmd.c.pysam.o build/temp.linux-i686-2.6/samtools/misc/md5.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/prob1.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/fet.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/kmin.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/index.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/vcf.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/call1.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/bcfutils.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/kfunc.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/em.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/bcf2qcall.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/bcf.c.pysam.o -lz -o build/lib.linux-i686-2.6/csamtools.so cythoning pysam/ctabix.pyx to pysam/ctabix.c building 'ctabix' extension creating build/temp.linux-i686-2.6/tabix gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.6 -c pysam/ctabix.c -o build/temp.linux-i686-2.6/pysam/ctabix.o pysam/ctabix.c: In function '__pyx_pf_6ctabix_9Tabixfile_7contigs___get__': pysam/ctabix.c:2760:21: warning: assignment from incompatible pointer type [enabled by default] pysam/ctabix.c: In function '__pyx_pf_6ctabix_13TabixIterator_2__next__': pysam/ctabix.c:3084:15: warning: assignment discards 'const' qualifier from pointer target type [enabled by default] pysam/ctabix.c: In function '__pyx_pf_6ctabix_19TabixHeaderIterator_2__next__': pysam/ctabix.c:3366:13: warning: assignment discards 'const' qualifier from pointer target type [enabled by default] pysam/ctabix.c: In function '__pyx_pf_6ctabix_19TabixIteratorParsed_2__next__': pysam/ctabix.c:4178:15: warning: assignment discards 'const' qualifier from pointer target type [enabled by default] pysam/ctabix.c: In function '__pyx_pf_6ctabix_tabix_compress': pysam/ctabix.c:4553:8: warning: '__pyx_v_c' may be used uninitialized in this function [-Wuninitialized] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.6 -c pysam/tabix_util.c -o build/temp.linux-i686-2.6/pysam/tabix_util.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.6 -c tabix/kstring.c.pysam.c -o build/temp.linux-i686-2.6/tabix/kstring.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.6 -c tabix/bgzip.c.pysam.c -o build/temp.linux-i686-2.6/tabix/bgzip.c.pysam.o tabix/bgzip.c.pysam.c:38:12: warning: function declaration isn't a prototype [-Wstrict-prototypes] tabix/bgzip.c.pysam.c: In function 'main': tabix/bgzip.c.pysam.c:200:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] tabix/bgzip.c.pysam.c: In function 'write_open': tabix/bgzip.c.pysam.c:59:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.6 -c tabix/index.c.pysam.c -o build/temp.linux-i686-2.6/tabix/index.c.pysam.o In file included from tabix/index.c.pysam.c:9:0: tabix/bam_endian.h:6:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] tabix/index.c.pysam.c:36:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] tabix/index.c.pysam.c:37:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.6 -c tabix/bgzf.c.pysam.c -o build/temp.linux-i686-2.6/tabix/bgzf.c.pysam.o tabix/bgzf.c.pysam.c:46:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] tabix/bgzf.c.pysam.c:142:14: warning: function declaration isn't a prototype [-Wstrict-prototypes] tabix/bgzf.c.pysam.c: In function 'bgzf_close': tabix/bgzf.c.pysam.c:632:8: warning: variable 'count' set but not used [-Wunused-but-set-variable] tabix/bgzf.c.pysam.c: In function 'bgzf_check_EOF': tabix/bgzf.c.pysam.c:683:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.6 -c tabix/bedidx.c.pysam.c -o build/temp.linux-i686-2.6/tabix/bedidx.c.pysam.o tabix/bedidx.c.pysam.c:22:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.6 -c tabix/knetfile.c.pysam.c -o build/temp.linux-i686-2.6/tabix/knetfile.c.pysam.o tabix/knetfile.c.pysam.c: In function 'khttp_connect_file': tabix/knetfile.c.pysam.c:420:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] tabix/knetfile.c.pysam.c: In function 'kftp_send_cmd': tabix/knetfile.c.pysam.c:241:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -O2 build/temp.linux-i686-2.6/pysam/ctabix.o build/temp.linux-i686-2.6/pysam/tabix_util.o build/temp.linux-i686-2.6/tabix/kstring.c.pysam.o build/temp.linux-i686-2.6/tabix/bgzip.c.pysam.o build/temp.linux-i686-2.6/tabix/index.c.pysam.o build/temp.linux-i686-2.6/tabix/bgzf.c.pysam.o build/temp.linux-i686-2.6/tabix/bedidx.c.pysam.o build/temp.linux-i686-2.6/tabix/knetfile.c.pysam.o -lz -o build/lib.linux-i686-2.6/ctabix.so cythoning pysam/TabProxies.pyx to pysam/TabProxies.c building 'TabProxies' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -I/usr/include/python2.6 -c pysam/TabProxies.c -o build/temp.linux-i686-2.6/pysam/TabProxies.o gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -O2 build/temp.linux-i686-2.6/pysam/TabProxies.o -lz -o build/lib.linux-i686-2.6/TabProxies.so cythoning pysam/cvcf.pyx to pysam/cvcf.c building 'cvcf' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -I/usr/include/python2.6 -c pysam/cvcf.c -o build/temp.linux-i686-2.6/pysam/cvcf.o pysam/cvcf.c: In function '__pyx_pf_4cvcf_3VCF_13convertGTback': pysam/cvcf.c:10949:13: warning: variable '__pyx_v_self' set but not used [-Wunused-but-set-variable] pysam/cvcf.c: In function '__pyx_pf_4cvcf_3VCF_38compare_calls': pysam/cvcf.c:19319:13: warning: variable '__pyx_v_self' set but not used [-Wunused-but-set-variable] pysam/cvcf.c: In function '__pyx_pf_4cvcf_3VCF_16parse_data': pysam/cvcf.c:16269:33: warning: '__pyx_v_qual' may be used uninitialized in this function [-Wuninitialized] gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -O2 build/temp.linux-i686-2.6/pysam/cvcf.o -lz -o build/lib.linux-i686-2.6/cvcf.so running build running build_py creating build/lib.linux-i686-2.7 creating build/lib.linux-i686-2.7/pysam copying pysam/__init__.py -> build/lib.linux-i686-2.7/pysam copying pysam/Pileup.py -> build/lib.linux-i686-2.7/pysam copying pysam/namedtuple.py -> build/lib.linux-i686-2.7/pysam copying pysam/version.py -> build/lib.linux-i686-2.7/pysam running build_ext cythoning pysam/csamtools.pyx to pysam/csamtools.c building 'csamtools' extension creating build/temp.linux-i686-2.7 creating build/temp.linux-i686-2.7/pysam creating build/temp.linux-i686-2.7/samtools creating build/temp.linux-i686-2.7/samtools/misc creating build/temp.linux-i686-2.7/samtools/bcftools gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c pysam/csamtools.c -o build/temp.linux-i686-2.7/pysam/csamtools.o In file included from pysam/csamtools.c:232:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from pysam/csamtools.c:234:0: samtools/glf.h:43:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from pysam/csamtools.c:235:0: samtools/bam_maqcns.h:44:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_maqcns.h:52:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] pysam/csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_9fetch': pysam/csamtools.c:8415:124: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type [enabled by default] samtools/bam.h:621:6: note: expected 'bam_fetch_f' but argument is of type 'int (*)(struct bam1_t *, void *)' pysam/csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_10mate': pysam/csamtools.c:8806:318: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type [enabled by default] samtools/bam.h:621:6: note: expected 'bam_fetch_f' but argument is of type 'int (*)(struct bam1_t *, void *)' pysam/csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_11count': pysam/csamtools.c:9293:95: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type [enabled by default] samtools/bam.h:621:6: note: expected 'bam_fetch_f' but argument is of type 'int (*)(struct bam1_t *, void *)' pysam/csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_12pileup': pysam/csamtools.c:9730:97: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type [enabled by default] samtools/bam.h:621:6: note: expected 'bam_fetch_f' but argument is of type 'int (*)(struct bam1_t *, void *)' pysam/csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_17__exit__': pysam/csamtools.c:10206:13: warning: variable '__pyx_v_traceback' set but not used [-Wunused-but-set-variable] pysam/csamtools.c:10205:13: warning: variable '__pyx_v_exc_value' set but not used [-Wunused-but-set-variable] pysam/csamtools.c:10204:13: warning: variable '__pyx_v_exc_type' set but not used [-Wunused-but-set-variable] pysam/csamtools.c: In function '__pyx_f_9csamtools___advance_snpcalls': pysam/csamtools.c:15024:7: warning: implicit declaration of function 'bam_prob_realn' [-Wimplicit-function-declaration] pysam/csamtools.c:15052:7: warning: implicit declaration of function 'bam_cap_mapQ' [-Wimplicit-function-declaration] pysam/csamtools.c: In function '__pyx_f_9csamtools_13SNPCallerBase___dump': pysam/csamtools.c:26979:3: warning: format not a string literal and no format arguments [-Wformat-security] pysam/csamtools.c: In function '__pyx_pf_9csamtools_16IteratorSNPCalls_2__next__': pysam/csamtools.c:27355:5: warning: this decimal constant is unsigned only in ISO C90 [enabled by default] pysam/csamtools.c: In function '__pyx_pf_9csamtools_9SNPCaller_1call': pysam/csamtools.c:27878:5: warning: this decimal constant is unsigned only in ISO C90 [enabled by default] pysam/csamtools.c: In function '__pyx_pf_9csamtools_15IndelCallerBase_2_call': pysam/csamtools.c:29327:15: warning: assignment discards 'const' qualifier from pointer target type [enabled by default] pysam/csamtools.c: In function '__Pyx_InitGlobals': pysam/csamtools.c:36689:3: warning: this decimal constant is unsigned only in ISO C90 [enabled by default] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-i686-2.7/pysam/pysam_util.o In file included from pysam/pysam_util.c:3:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from pysam/pysam_util.c:6:0: samtools/bam_endian.h:6:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from pysam/pysam_util.h:52:0, from pysam/pysam_util.c:8: samtools/glf.h:43:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from pysam/pysam_util.h:55:0, from pysam/pysam_util.c:8: samtools/bam_maqcns.h:44:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_maqcns.h:52:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] pysam/pysam_util.c:49:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] pysam/pysam_util.c:50:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] pysam/pysam_util.c:81:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] pysam/pysam_util.c: In function 'pysam_pileup_next': pysam/pysam_util.c:178:8: warning: assignment discards 'const' qualifier from pointer target type [enabled by default] pysam/pysam_util.c: At top level: pysam/pysam_util.c:81:19: warning: 'mp_init' defined but not used [-Wunused-function] pysam/pysam_util.c:87:13: warning: 'mp_destroy' defined but not used [-Wunused-function] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-i686-2.7/samtools/sam.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/sam.c.pysam.c:6: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/kprobaln.c.pysam.c -o build/temp.linux-i686-2.7/samtools/kprobaln.c.pysam.o samtools/kprobaln.c.pysam.c: In function 'kpa_glocal': samtools/kprobaln.c.pysam.c:80:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/kstring.c.pysam.c -o build/temp.linux-i686-2.7/samtools/kstring.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-i686-2.7/samtools/phase.c.pysam.o In file included from samtools/phase.c.pysam.c:9:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/phase.c.pysam.c:47:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/phase.c.pysam.c:48:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bam2bcf_indel.c.pysam.o In file included from samtools/bam2bcf_indel.c.pysam.c:6:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam2bcf.h:6:0, from samtools/bam2bcf_indel.c.pysam.c:7: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam2bcf_indel.c.pysam.c:12:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bam2bcf.c.pysam.o In file included from samtools/bam2bcf.c.pysam.c:5:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam2bcf.h:6:0, from samtools/bam2bcf.c.pysam.c:7: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bam_aux.c.pysam.o In file included from samtools/bam_aux.c.pysam.c:4:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_aux.c.pysam.c:7:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_aux.c.pysam.c:8:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bam_lpileup.c.pysam.o In file included from samtools/bam_lpileup.c.pysam.c:6:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_lpileup.c.pysam.c:25:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_pileup.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bam_pileup.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/bam_pileup.c.pysam.c:7: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_pileup.c.pysam.c:29:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_pileup.c.pysam.c: In function 'resolve_cigar2': samtools/bam_pileup.c.pysam.c:77:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bam_index.c.pysam.o In file included from samtools/bam_index.c.pysam.c:5:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam_index.c.pysam.c:8:0: samtools/bam_endian.h:6:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_index.c.pysam.c:66:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_index.c.pysam.c: In function 'bam_index_load_core': samtools/bam_index.c.pysam.c:328:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:348:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:351:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:355:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:359:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:369:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:373:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.linux-i686-2.7/samtools/sam_header.c.pysam.o samtools/sam_header.c.pysam.c:11:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/glf.c.pysam.c -o build/temp.linux-i686-2.7/samtools/glf.c.pysam.o In file included from samtools/glf.c.pysam.c:5:0: samtools/glf.h:43:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/glf.c.pysam.c:24:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/glf.c.pysam.c:30:16: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bam_md.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/bam_md.c.pysam.c:9: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bam_rmdupse.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/bam_rmdupse.c.pysam.c:4: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdupse.c.pysam.c:17:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdupse.c.pysam.c:17:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdupse.c.pysam.c:20:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdupse.c.pysam.c:27:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-i686-2.7/samtools/sam_view.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/sam_view.c.pysam.c:9: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/sam_view.c.pysam.c:13:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bam_cat.c.pysam.o In file included from samtools/bam_cat.c.pysam.c:65:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bgzf.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bgzf.c.pysam.o samtools/bgzf.c.pysam.c:46:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bgzf.c.pysam.c:142:14: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bgzf.c.pysam.c: In function 'bgzf_close': samtools/bgzf.c.pysam.c:632:8: warning: variable 'count' set but not used [-Wunused-but-set-variable] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bam_stat.c.pysam.o In file included from samtools/bam_stat.c.pysam.c:5:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bam_rmdup.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/bam_rmdup.c.pysam.c:8: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdup.c.pysam.c:13:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdup.c.pysam.c:14:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdup.c.pysam.c:22:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-i686-2.7/samtools/cut_target.c.pysam.o In file included from samtools/cut_target.c.pysam.c:6:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/cut_target.c.pysam.c: In function 'main_cut_target': samtools/cut_target.c.pysam.c:139:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/kaln.c.pysam.c -o build/temp.linux-i686-2.7/samtools/kaln.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/razf.c.pysam.c -o build/temp.linux-i686-2.7/samtools/razf.c.pysam.o samtools/razf.c.pysam.c:76:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/razf.c.pysam.c: In function 'razf_close': samtools/razf.c.pysam.c:806:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:807:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:812:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c: In function 'razf_end_flush': samtools/razf.c.pysam.c:260:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c: In function '_razf_write': samtools/razf.c.pysam.c:203:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c: In function 'save_zindex': samtools/razf.c.pysam.c:98:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:101:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:108:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:109:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c: In function 'razf_flush': samtools/razf.c.pysam.c:223:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:236:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bedidx.c.pysam.o samtools/bedidx.c.pysam.c:22:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/knetfile.c.pysam.c -o build/temp.linux-i686-2.7/samtools/knetfile.c.pysam.o samtools/knetfile.c.pysam.c: In function 'khttp_connect_file': samtools/knetfile.c.pysam.c:417:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/knetfile.c.pysam.c: In function 'kftp_send_cmd': samtools/knetfile.c.pysam.c:238:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_tview.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bam_tview.c.pysam.o samtools/bam_tview.c.pysam.c:420:2: warning: #warning "No curses library is available; tview is disabled." [-Wcpp] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bam_color.c.pysam.o In file included from samtools/bam_color.c.pysam.c:4:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bam_mate.c.pysam.o In file included from samtools/bam_mate.c.pysam.c:5:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bam2depth.c.pysam.o In file included from samtools/bam2depth.c.pysam.c:13:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bam_sort.c.pysam.o In file included from samtools/bam_sort.c.pysam.c:10:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-i686-2.7/samtools/sample.c.pysam.o samtools/sample.c.pysam.c:7:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bam_import.c.pysam.o In file included from samtools/bam_import.c.pysam.c:14:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_import.c.pysam.c:20:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_import.c.pysam.c: In function 'append_text': samtools/bam_import.c.pysam.c:181:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat] samtools/bam_import.c.pysam.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat] samtools/bam_import.c.pysam.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat] samtools/bam_import.c.pysam.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat] samtools/bam_import.c.pysam.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-i686-2.7/samtools/faidx.c.pysam.o samtools/faidx.c.pysam.c:15:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bam.c.pysam.o In file included from samtools/bam.c.pysam.c:7:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam.c.pysam.c:8:0: samtools/bam_endian.h:6:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.c.pysam.c:47:15: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_maqcns.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bam_maqcns.c.pysam.o In file included from samtools/bam_maqcns.c.pysam.c:5:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam_maqcns.h:4:0, from samtools/bam_maqcns.c.pysam.c:6: samtools/glf.h:43:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam_maqcns.c.pysam.c:6:0: samtools/bam_maqcns.h:44:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_maqcns.h:52:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_maqcns.c.pysam.c:107:15: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_maqcns.c.pysam.c:322:21: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/errmod.c.pysam.c -o build/temp.linux-i686-2.7/samtools/errmod.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bam_plcmd.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/bam_plcmd.c.pysam.c:9: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam_maqcns.h:4:0, from samtools/bam_plcmd.c.pysam.c:11: samtools/glf.h:43:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam_plcmd.c.pysam.c:11:0: samtools/bam_maqcns.h:44:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_maqcns.h:52:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_plcmd.c.pysam.c:17:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam2bcf.h:6:0, from samtools/bam_plcmd.c.pysam.c:529: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/misc/md5.c.pysam.c -o build/temp.linux-i686-2.7/samtools/misc/md5.c.pysam.o samtools/misc/md5.c.pysam.c:33:6: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/prob1.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bcftools/prob1.c.pysam.o In file included from samtools/bcftools/prob1.h:4:0, from samtools/bcftools/prob1.c.pysam.c:9: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/fet.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bcftools/fet.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/kmin.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bcftools/kmin.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/index.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bcftools/index.c.pysam.o In file included from samtools/bcftools/index.c.pysam.c:6:0: samtools/bam_endian.h:6:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bcftools/index.c.pysam.c:8:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/vcf.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bcftools/vcf.c.pysam.o In file included from samtools/bcftools/vcf.c.pysam.c:7:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/call1.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bcftools/call1.c.pysam.o In file included from samtools/bcftools/call1.c.pysam.c:8:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/bcfutils.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bcftools/bcfutils.c.pysam.o In file included from samtools/bcftools/bcfutils.c.pysam.c:5:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bcftools/bcfutils.c.pysam.c:8:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bcftools/bcfutils.c.pysam.c:23:7: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/kfunc.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bcftools/kfunc.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/em.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bcftools/em.c.pysam.o In file included from samtools/bcftools/em.c.pysam.c:6:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bcftools/em.c.pysam.c: In function 'bcf_em1': samtools/bcftools/em.c.pysam.c:176:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/bcf2qcall.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bcftools/bcf2qcall.c.pysam.o In file included from samtools/bcftools/bcf2qcall.c.pysam.c:7:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/bcf.c.pysam.c -o build/temp.linux-i686-2.7/samtools/bcftools/bcf.c.pysam.o In file included from samtools/bcftools/bcf.c.pysam.c:7:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -O2 build/temp.linux-i686-2.7/pysam/csamtools.o build/temp.linux-i686-2.7/pysam/pysam_util.o build/temp.linux-i686-2.7/samtools/sam.c.pysam.o build/temp.linux-i686-2.7/samtools/kprobaln.c.pysam.o build/temp.linux-i686-2.7/samtools/kstring.c.pysam.o build/temp.linux-i686-2.7/samtools/phase.c.pysam.o build/temp.linux-i686-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-i686-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-i686-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-i686-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-i686-2.7/samtools/bam_pileup.c.pysam.o build/temp.linux-i686-2.7/samtools/bam_index.c.pysam.o build/temp.linux-i686-2.7/samtools/sam_header.c.pysam.o build/temp.linux-i686-2.7/samtools/glf.c.pysam.o build/temp.linux-i686-2.7/samtools/bam_md.c.pysam.o build/temp.linux-i686-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-i686-2.7/samtools/sam_view.c.pysam.o build/temp.linux-i686-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-i686-2.7/samtools/bgzf.c.pysam.o build/temp.linux-i686-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-i686-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-i686-2.7/samtools/cut_target.c.pysam.o build/temp.linux-i686-2.7/samtools/kaln.c.pysam.o build/temp.linux-i686-2.7/samtools/razf.c.pysam.o build/temp.linux-i686-2.7/samtools/bedidx.c.pysam.o build/temp.linux-i686-2.7/samtools/knetfile.c.pysam.o build/temp.linux-i686-2.7/samtools/bam_tview.c.pysam.o build/temp.linux-i686-2.7/samtools/bam_color.c.pysam.o build/temp.linux-i686-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-i686-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-i686-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-i686-2.7/samtools/sample.c.pysam.o build/temp.linux-i686-2.7/samtools/bam_import.c.pysam.o build/temp.linux-i686-2.7/samtools/faidx.c.pysam.o build/temp.linux-i686-2.7/samtools/bam.c.pysam.o build/temp.linux-i686-2.7/samtools/bam_maqcns.c.pysam.o build/temp.linux-i686-2.7/samtools/errmod.c.pysam.o build/temp.linux-i686-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-i686-2.7/samtools/misc/md5.c.pysam.o build/temp.linux-i686-2.7/samtools/bcftools/prob1.c.pysam.o build/temp.linux-i686-2.7/samtools/bcftools/fet.c.pysam.o build/temp.linux-i686-2.7/samtools/bcftools/kmin.c.pysam.o build/temp.linux-i686-2.7/samtools/bcftools/index.c.pysam.o build/temp.linux-i686-2.7/samtools/bcftools/vcf.c.pysam.o build/temp.linux-i686-2.7/samtools/bcftools/call1.c.pysam.o build/temp.linux-i686-2.7/samtools/bcftools/bcfutils.c.pysam.o build/temp.linux-i686-2.7/samtools/bcftools/kfunc.c.pysam.o build/temp.linux-i686-2.7/samtools/bcftools/em.c.pysam.o build/temp.linux-i686-2.7/samtools/bcftools/bcf2qcall.c.pysam.o build/temp.linux-i686-2.7/samtools/bcftools/bcf.c.pysam.o -lz -o build/lib.linux-i686-2.7/csamtools.so cythoning pysam/ctabix.pyx to pysam/ctabix.c building 'ctabix' extension creating build/temp.linux-i686-2.7/tabix gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.7 -c pysam/ctabix.c -o build/temp.linux-i686-2.7/pysam/ctabix.o pysam/ctabix.c: In function '__pyx_pf_6ctabix_9Tabixfile_7contigs___get__': pysam/ctabix.c:2760:21: warning: assignment from incompatible pointer type [enabled by default] pysam/ctabix.c: In function '__pyx_pf_6ctabix_13TabixIterator_2__next__': pysam/ctabix.c:3084:15: warning: assignment discards 'const' qualifier from pointer target type [enabled by default] pysam/ctabix.c: In function '__pyx_pf_6ctabix_19TabixHeaderIterator_2__next__': pysam/ctabix.c:3366:13: warning: assignment discards 'const' qualifier from pointer target type [enabled by default] pysam/ctabix.c: In function '__pyx_pf_6ctabix_19TabixIteratorParsed_2__next__': pysam/ctabix.c:4178:15: warning: assignment discards 'const' qualifier from pointer target type [enabled by default] pysam/ctabix.c: In function '__pyx_pf_6ctabix_tabix_compress': pysam/ctabix.c:4553:8: warning: '__pyx_v_c' may be used uninitialized in this function [-Wuninitialized] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.7 -c pysam/tabix_util.c -o build/temp.linux-i686-2.7/pysam/tabix_util.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.7 -c tabix/kstring.c.pysam.c -o build/temp.linux-i686-2.7/tabix/kstring.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.7 -c tabix/bgzip.c.pysam.c -o build/temp.linux-i686-2.7/tabix/bgzip.c.pysam.o tabix/bgzip.c.pysam.c:38:12: warning: function declaration isn't a prototype [-Wstrict-prototypes] tabix/bgzip.c.pysam.c: In function 'main': tabix/bgzip.c.pysam.c:200:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] tabix/bgzip.c.pysam.c: In function 'write_open': tabix/bgzip.c.pysam.c:59:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.7 -c tabix/index.c.pysam.c -o build/temp.linux-i686-2.7/tabix/index.c.pysam.o In file included from tabix/index.c.pysam.c:9:0: tabix/bam_endian.h:6:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] tabix/index.c.pysam.c:36:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] tabix/index.c.pysam.c:37:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.7 -c tabix/bgzf.c.pysam.c -o build/temp.linux-i686-2.7/tabix/bgzf.c.pysam.o tabix/bgzf.c.pysam.c:46:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] tabix/bgzf.c.pysam.c:142:14: warning: function declaration isn't a prototype [-Wstrict-prototypes] tabix/bgzf.c.pysam.c: In function 'bgzf_close': tabix/bgzf.c.pysam.c:632:8: warning: variable 'count' set but not used [-Wunused-but-set-variable] tabix/bgzf.c.pysam.c: In function 'bgzf_check_EOF': tabix/bgzf.c.pysam.c:683:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.7 -c tabix/bedidx.c.pysam.c -o build/temp.linux-i686-2.7/tabix/bedidx.c.pysam.o tabix/bedidx.c.pysam.c:22:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.7 -c tabix/knetfile.c.pysam.c -o build/temp.linux-i686-2.7/tabix/knetfile.c.pysam.o tabix/knetfile.c.pysam.c: In function 'khttp_connect_file': tabix/knetfile.c.pysam.c:420:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] tabix/knetfile.c.pysam.c: In function 'kftp_send_cmd': tabix/knetfile.c.pysam.c:241:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -O2 build/temp.linux-i686-2.7/pysam/ctabix.o build/temp.linux-i686-2.7/pysam/tabix_util.o build/temp.linux-i686-2.7/tabix/kstring.c.pysam.o build/temp.linux-i686-2.7/tabix/bgzip.c.pysam.o build/temp.linux-i686-2.7/tabix/index.c.pysam.o build/temp.linux-i686-2.7/tabix/bgzf.c.pysam.o build/temp.linux-i686-2.7/tabix/bedidx.c.pysam.o build/temp.linux-i686-2.7/tabix/knetfile.c.pysam.o -lz -o build/lib.linux-i686-2.7/ctabix.so cythoning pysam/TabProxies.pyx to pysam/TabProxies.c building 'TabProxies' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -I/usr/include/python2.7 -c pysam/TabProxies.c -o build/temp.linux-i686-2.7/pysam/TabProxies.o gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -O2 build/temp.linux-i686-2.7/pysam/TabProxies.o -lz -o build/lib.linux-i686-2.7/TabProxies.so cythoning pysam/cvcf.pyx to pysam/cvcf.c building 'cvcf' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -I/usr/include/python2.7 -c pysam/cvcf.c -o build/temp.linux-i686-2.7/pysam/cvcf.o pysam/cvcf.c: In function '__pyx_pf_4cvcf_3VCF_13convertGTback': pysam/cvcf.c:10949:13: warning: variable '__pyx_v_self' set but not used [-Wunused-but-set-variable] pysam/cvcf.c: In function '__pyx_pf_4cvcf_3VCF_38compare_calls': pysam/cvcf.c:19319:13: warning: variable '__pyx_v_self' set but not used [-Wunused-but-set-variable] pysam/cvcf.c: In function '__pyx_pf_4cvcf_3VCF_16parse_data': pysam/cvcf.c:16269:33: warning: '__pyx_v_qual' may be used uninitialized in this function [-Wuninitialized] gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -O2 build/temp.linux-i686-2.7/pysam/cvcf.o -lz -o build/lib.linux-i686-2.7/cvcf.so dh_auto_test -O--buildsystem=python_distutils /usr/bin/fakeroot debian/rules binary dh binary --with python2 --buildsystem=python_distutils dh_testroot -O--buildsystem=python_distutils dh_prep -O--buildsystem=python_distutils dh_installdirs -O--buildsystem=python_distutils dh_auto_install -O--buildsystem=python_distutils running install running build running build_py running build_ext skipping 'pysam/csamtools.c' Cython extension (up-to-date) building 'csamtools' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c pysam/csamtools.c -o build/temp.linux-i686-2.6/pysam/csamtools.o In file included from pysam/csamtools.c:232:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from pysam/csamtools.c:234:0: samtools/glf.h:43:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from pysam/csamtools.c:235:0: samtools/bam_maqcns.h:44:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_maqcns.h:52:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] pysam/csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_9fetch': pysam/csamtools.c:8415:124: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type [enabled by default] samtools/bam.h:621:6: note: expected 'bam_fetch_f' but argument is of type 'int (*)(struct bam1_t *, void *)' pysam/csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_10mate': pysam/csamtools.c:8806:318: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type [enabled by default] samtools/bam.h:621:6: note: expected 'bam_fetch_f' but argument is of type 'int (*)(struct bam1_t *, void *)' pysam/csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_11count': pysam/csamtools.c:9293:95: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type [enabled by default] samtools/bam.h:621:6: note: expected 'bam_fetch_f' but argument is of type 'int (*)(struct bam1_t *, void *)' pysam/csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_12pileup': pysam/csamtools.c:9730:97: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type [enabled by default] samtools/bam.h:621:6: note: expected 'bam_fetch_f' but argument is of type 'int (*)(struct bam1_t *, void *)' pysam/csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_17__exit__': pysam/csamtools.c:10206:13: warning: variable '__pyx_v_traceback' set but not used [-Wunused-but-set-variable] pysam/csamtools.c:10205:13: warning: variable '__pyx_v_exc_value' set but not used [-Wunused-but-set-variable] pysam/csamtools.c:10204:13: warning: variable '__pyx_v_exc_type' set but not used [-Wunused-but-set-variable] pysam/csamtools.c: In function '__pyx_f_9csamtools___advance_snpcalls': pysam/csamtools.c:15024:7: warning: implicit declaration of function 'bam_prob_realn' [-Wimplicit-function-declaration] pysam/csamtools.c:15052:7: warning: implicit declaration of function 'bam_cap_mapQ' [-Wimplicit-function-declaration] pysam/csamtools.c: In function '__pyx_f_9csamtools_13SNPCallerBase___dump': pysam/csamtools.c:26979:3: warning: format not a string literal and no format arguments [-Wformat-security] pysam/csamtools.c: In function '__pyx_pf_9csamtools_16IteratorSNPCalls_2__next__': pysam/csamtools.c:27355:5: warning: this decimal constant is unsigned only in ISO C90 [enabled by default] pysam/csamtools.c: In function '__pyx_pf_9csamtools_9SNPCaller_1call': pysam/csamtools.c:27878:5: warning: this decimal constant is unsigned only in ISO C90 [enabled by default] pysam/csamtools.c: In function '__pyx_pf_9csamtools_15IndelCallerBase_2_call': pysam/csamtools.c:29327:15: warning: assignment discards 'const' qualifier from pointer target type [enabled by default] pysam/csamtools.c: In function '__Pyx_InitGlobals': pysam/csamtools.c:36689:3: warning: this decimal constant is unsigned only in ISO C90 [enabled by default] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c pysam/pysam_util.c -o build/temp.linux-i686-2.6/pysam/pysam_util.o In file included from pysam/pysam_util.c:3:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from pysam/pysam_util.c:6:0: samtools/bam_endian.h:6:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from pysam/pysam_util.h:52:0, from pysam/pysam_util.c:8: samtools/glf.h:43:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from pysam/pysam_util.h:55:0, from pysam/pysam_util.c:8: samtools/bam_maqcns.h:44:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_maqcns.h:52:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] pysam/pysam_util.c:49:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] pysam/pysam_util.c:50:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] pysam/pysam_util.c:81:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] pysam/pysam_util.c: In function 'pysam_pileup_next': pysam/pysam_util.c:178:8: warning: assignment discards 'const' qualifier from pointer target type [enabled by default] pysam/pysam_util.c: At top level: pysam/pysam_util.c:81:19: warning: 'mp_init' defined but not used [-Wunused-function] pysam/pysam_util.c:87:13: warning: 'mp_destroy' defined but not used [-Wunused-function] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/sam.c.pysam.c -o build/temp.linux-i686-2.6/samtools/sam.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/sam.c.pysam.c:6: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/kprobaln.c.pysam.c -o build/temp.linux-i686-2.6/samtools/kprobaln.c.pysam.o samtools/kprobaln.c.pysam.c: In function 'kpa_glocal': samtools/kprobaln.c.pysam.c:80:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/kstring.c.pysam.c -o build/temp.linux-i686-2.6/samtools/kstring.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/phase.c.pysam.c -o build/temp.linux-i686-2.6/samtools/phase.c.pysam.o In file included from samtools/phase.c.pysam.c:9:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/phase.c.pysam.c:47:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/phase.c.pysam.c:48:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam2bcf_indel.c.pysam.o In file included from samtools/bam2bcf_indel.c.pysam.c:6:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam2bcf.h:6:0, from samtools/bam2bcf_indel.c.pysam.c:7: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam2bcf_indel.c.pysam.c:12:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam2bcf.c.pysam.o In file included from samtools/bam2bcf.c.pysam.c:5:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam2bcf.h:6:0, from samtools/bam2bcf.c.pysam.c:7: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_aux.c.pysam.o In file included from samtools/bam_aux.c.pysam.c:4:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_aux.c.pysam.c:7:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_aux.c.pysam.c:8:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_lpileup.c.pysam.o In file included from samtools/bam_lpileup.c.pysam.c:6:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_lpileup.c.pysam.c:25:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_pileup.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_pileup.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/bam_pileup.c.pysam.c:7: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_pileup.c.pysam.c:29:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_pileup.c.pysam.c: In function 'resolve_cigar2': samtools/bam_pileup.c.pysam.c:77:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_index.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_index.c.pysam.o In file included from samtools/bam_index.c.pysam.c:5:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam_index.c.pysam.c:8:0: samtools/bam_endian.h:6:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_index.c.pysam.c:66:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_index.c.pysam.c: In function 'bam_index_load_core': samtools/bam_index.c.pysam.c:328:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:348:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:351:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:355:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:359:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:369:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c.pysam.c:373:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/sam_header.c.pysam.c -o build/temp.linux-i686-2.6/samtools/sam_header.c.pysam.o samtools/sam_header.c.pysam.c:11:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/glf.c.pysam.c -o build/temp.linux-i686-2.6/samtools/glf.c.pysam.o In file included from samtools/glf.c.pysam.c:5:0: samtools/glf.h:43:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/glf.c.pysam.c:24:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/glf.c.pysam.c:30:16: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_md.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_md.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/bam_md.c.pysam.c:9: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_rmdupse.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/bam_rmdupse.c.pysam.c:4: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdupse.c.pysam.c:17:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdupse.c.pysam.c:17:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdupse.c.pysam.c:20:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdupse.c.pysam.c:27:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/sam_view.c.pysam.c -o build/temp.linux-i686-2.6/samtools/sam_view.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/sam_view.c.pysam.c:9: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/sam_view.c.pysam.c:13:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_cat.c.pysam.o In file included from samtools/bam_cat.c.pysam.c:65:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bgzf.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bgzf.c.pysam.o samtools/bgzf.c.pysam.c:46:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bgzf.c.pysam.c:142:14: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bgzf.c.pysam.c: In function 'bgzf_close': samtools/bgzf.c.pysam.c:632:8: warning: variable 'count' set but not used [-Wunused-but-set-variable] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_stat.c.pysam.o In file included from samtools/bam_stat.c.pysam.c:5:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_rmdup.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/bam_rmdup.c.pysam.c:8: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdup.c.pysam.c:13:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdup.c.pysam.c:14:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_rmdup.c.pysam.c:22:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/cut_target.c.pysam.c -o build/temp.linux-i686-2.6/samtools/cut_target.c.pysam.o In file included from samtools/cut_target.c.pysam.c:6:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/cut_target.c.pysam.c: In function 'main_cut_target': samtools/cut_target.c.pysam.c:139:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/kaln.c.pysam.c -o build/temp.linux-i686-2.6/samtools/kaln.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/razf.c.pysam.c -o build/temp.linux-i686-2.6/samtools/razf.c.pysam.o samtools/razf.c.pysam.c:76:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/razf.c.pysam.c: In function 'razf_close': samtools/razf.c.pysam.c:806:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:807:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:812:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c: In function 'razf_end_flush': samtools/razf.c.pysam.c:260:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c: In function '_razf_write': samtools/razf.c.pysam.c:203:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c: In function 'save_zindex': samtools/razf.c.pysam.c:98:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:101:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:108:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:109:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c: In function 'razf_flush': samtools/razf.c.pysam.c:223:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c.pysam.c:236:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bedidx.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bedidx.c.pysam.o samtools/bedidx.c.pysam.c:22:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/knetfile.c.pysam.c -o build/temp.linux-i686-2.6/samtools/knetfile.c.pysam.o samtools/knetfile.c.pysam.c: In function 'khttp_connect_file': samtools/knetfile.c.pysam.c:417:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] samtools/knetfile.c.pysam.c: In function 'kftp_send_cmd': samtools/knetfile.c.pysam.c:238:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_tview.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_tview.c.pysam.o samtools/bam_tview.c.pysam.c:420:2: warning: #warning "No curses library is available; tview is disabled." [-Wcpp] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_color.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_color.c.pysam.o In file included from samtools/bam_color.c.pysam.c:4:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_mate.c.pysam.o In file included from samtools/bam_mate.c.pysam.c:5:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam2depth.c.pysam.o In file included from samtools/bam2depth.c.pysam.c:13:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_sort.c.pysam.o In file included from samtools/bam_sort.c.pysam.c:10:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/sample.c.pysam.c -o build/temp.linux-i686-2.6/samtools/sample.c.pysam.o samtools/sample.c.pysam.c:7:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_import.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_import.c.pysam.o In file included from samtools/bam_import.c.pysam.c:14:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_import.c.pysam.c:20:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_import.c.pysam.c: In function 'append_text': samtools/bam_import.c.pysam.c:181:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat] samtools/bam_import.c.pysam.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat] samtools/bam_import.c.pysam.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat] samtools/bam_import.c.pysam.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat] samtools/bam_import.c.pysam.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/faidx.c.pysam.c -o build/temp.linux-i686-2.6/samtools/faidx.c.pysam.o samtools/faidx.c.pysam.c:15:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam.c.pysam.o In file included from samtools/bam.c.pysam.c:7:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam.c.pysam.c:8:0: samtools/bam_endian.h:6:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.c.pysam.c:47:15: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_maqcns.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_maqcns.c.pysam.o In file included from samtools/bam_maqcns.c.pysam.c:5:0: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam_maqcns.h:4:0, from samtools/bam_maqcns.c.pysam.c:6: samtools/glf.h:43:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam_maqcns.c.pysam.c:6:0: samtools/bam_maqcns.h:44:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_maqcns.h:52:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_maqcns.c.pysam.c:107:15: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_maqcns.c.pysam.c:322:21: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/errmod.c.pysam.c -o build/temp.linux-i686-2.6/samtools/errmod.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bam_plcmd.c.pysam.o In file included from samtools/sam.h:4:0, from samtools/bam_plcmd.c.pysam.c:9: samtools/bam.h:362:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam.h:377:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam_maqcns.h:4:0, from samtools/bam_plcmd.c.pysam.c:11: samtools/glf.h:43:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam_plcmd.c.pysam.c:11:0: samtools/bam_maqcns.h:44:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_maqcns.h:52:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bam_plcmd.c.pysam.c:17:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bam2bcf.h:6:0, from samtools/bam_plcmd.c.pysam.c:529: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/misc/md5.c.pysam.c -o build/temp.linux-i686-2.6/samtools/misc/md5.c.pysam.o samtools/misc/md5.c.pysam.c:33:6: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/prob1.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/prob1.c.pysam.o In file included from samtools/bcftools/prob1.h:4:0, from samtools/bcftools/prob1.c.pysam.c:9: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/fet.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/fet.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/kmin.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/kmin.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/index.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/index.c.pysam.o In file included from samtools/bcftools/index.c.pysam.c:6:0: samtools/bam_endian.h:6:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] In file included from samtools/bcftools/index.c.pysam.c:8:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/vcf.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/vcf.c.pysam.o In file included from samtools/bcftools/vcf.c.pysam.c:7:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/call1.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/call1.c.pysam.o In file included from samtools/bcftools/call1.c.pysam.c:8:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/bcfutils.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/bcfutils.c.pysam.o In file included from samtools/bcftools/bcfutils.c.pysam.c:5:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bcftools/bcfutils.c.pysam.c:8:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bcftools/bcfutils.c.pysam.c:23:7: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/kfunc.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/kfunc.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/em.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/em.c.pysam.o In file included from samtools/bcftools/em.c.pysam.c:6:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] samtools/bcftools/em.c.pysam.c: In function 'bcf_em1': samtools/bcftools/em.c.pysam.c:176:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/bcf2qcall.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/bcf2qcall.c.pysam.o In file included from samtools/bcftools/bcf2qcall.c.pysam.c:7:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c samtools/bcftools/bcf.c.pysam.c -o build/temp.linux-i686-2.6/samtools/bcftools/bcf.c.pysam.o In file included from samtools/bcftools/bcf.c.pysam.c:7:0: samtools/bcftools/bcf.h:160:2: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -O2 build/temp.linux-i686-2.6/pysam/csamtools.o build/temp.linux-i686-2.6/pysam/pysam_util.o build/temp.linux-i686-2.6/samtools/sam.c.pysam.o build/temp.linux-i686-2.6/samtools/kprobaln.c.pysam.o build/temp.linux-i686-2.6/samtools/kstring.c.pysam.o build/temp.linux-i686-2.6/samtools/phase.c.pysam.o build/temp.linux-i686-2.6/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-i686-2.6/samtools/bam2bcf.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_aux.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_lpileup.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_pileup.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_index.c.pysam.o build/temp.linux-i686-2.6/samtools/sam_header.c.pysam.o build/temp.linux-i686-2.6/samtools/glf.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_md.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_rmdupse.c.pysam.o build/temp.linux-i686-2.6/samtools/sam_view.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_cat.c.pysam.o build/temp.linux-i686-2.6/samtools/bgzf.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_stat.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_rmdup.c.pysam.o build/temp.linux-i686-2.6/samtools/cut_target.c.pysam.o build/temp.linux-i686-2.6/samtools/kaln.c.pysam.o build/temp.linux-i686-2.6/samtools/razf.c.pysam.o build/temp.linux-i686-2.6/samtools/bedidx.c.pysam.o build/temp.linux-i686-2.6/samtools/knetfile.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_tview.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_color.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_mate.c.pysam.o build/temp.linux-i686-2.6/samtools/bam2depth.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_sort.c.pysam.o build/temp.linux-i686-2.6/samtools/sample.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_import.c.pysam.o build/temp.linux-i686-2.6/samtools/faidx.c.pysam.o build/temp.linux-i686-2.6/samtools/bam.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_maqcns.c.pysam.o build/temp.linux-i686-2.6/samtools/errmod.c.pysam.o build/temp.linux-i686-2.6/samtools/bam_plcmd.c.pysam.o build/temp.linux-i686-2.6/samtools/misc/md5.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/prob1.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/fet.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/kmin.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/index.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/vcf.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/call1.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/bcfutils.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/kfunc.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/em.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/bcf2qcall.c.pysam.o build/temp.linux-i686-2.6/samtools/bcftools/bcf.c.pysam.o -lz -o build/lib.linux-i686-2.6/csamtools.so skipping 'pysam/ctabix.c' Cython extension (up-to-date) building 'ctabix' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.6 -c pysam/ctabix.c -o build/temp.linux-i686-2.6/pysam/ctabix.o pysam/ctabix.c: In function '__pyx_pf_6ctabix_9Tabixfile_7contigs___get__': pysam/ctabix.c:2760:21: warning: assignment from incompatible pointer type [enabled by default] pysam/ctabix.c: In function '__pyx_pf_6ctabix_13TabixIterator_2__next__': pysam/ctabix.c:3084:15: warning: assignment discards 'const' qualifier from pointer target type [enabled by default] pysam/ctabix.c: In function '__pyx_pf_6ctabix_19TabixHeaderIterator_2__next__': pysam/ctabix.c:3366:13: warning: assignment discards 'const' qualifier from pointer target type [enabled by default] pysam/ctabix.c: In function '__pyx_pf_6ctabix_19TabixIteratorParsed_2__next__': pysam/ctabix.c:4178:15: warning: assignment discards 'const' qualifier from pointer target type [enabled by default] pysam/ctabix.c: In function '__pyx_pf_6ctabix_tabix_compress': pysam/ctabix.c:4553:8: warning: '__pyx_v_c' may be used uninitialized in this function [-Wuninitialized] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.6 -c pysam/tabix_util.c -o build/temp.linux-i686-2.6/pysam/tabix_util.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.6 -c tabix/kstring.c.pysam.c -o build/temp.linux-i686-2.6/tabix/kstring.c.pysam.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.6 -c tabix/bgzip.c.pysam.c -o build/temp.linux-i686-2.6/tabix/bgzip.c.pysam.o tabix/bgzip.c.pysam.c:38:12: warning: function declaration isn't a prototype [-Wstrict-prototypes] tabix/bgzip.c.pysam.c: In function 'main': tabix/bgzip.c.pysam.c:200:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] tabix/bgzip.c.pysam.c: In function 'write_open': tabix/bgzip.c.pysam.c:59:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.6 -c tabix/index.c.pysam.c -o build/temp.linux-i686-2.6/tabix/index.c.pysam.o In file included from tabix/index.c.pysam.c:9:0: tabix/bam_endian.h:6:19: warning: function declaration isn't a prototype [-Wstrict-prototypes] tabix/index.c.pysam.c:36:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] tabix/index.c.pysam.c:37:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.6 -c tabix/bgzf.c.pysam.c -o build/temp.linux-i686-2.6/tabix/bgzf.c.pysam.o tabix/bgzf.c.pysam.c:46:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] tabix/bgzf.c.pysam.c:142:14: warning: function declaration isn't a prototype [-Wstrict-prototypes] tabix/bgzf.c.pysam.c: In function 'bgzf_close': tabix/bgzf.c.pysam.c:632:8: warning: variable 'count' set but not used [-Wunused-but-set-variable] tabix/bgzf.c.pysam.c: In function 'bgzf_check_EOF': tabix/bgzf.c.pysam.c:683:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.6 -c tabix/bedidx.c.pysam.c -o build/temp.linux-i686-2.6/tabix/bedidx.c.pysam.o tabix/bedidx.c.pysam.c:22:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -Ipysam -I/usr/include/python2.6 -c tabix/knetfile.c.pysam.c -o build/temp.linux-i686-2.6/tabix/knetfile.c.pysam.o tabix/knetfile.c.pysam.c: In function 'khttp_connect_file': tabix/knetfile.c.pysam.c:420:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] tabix/knetfile.c.pysam.c: In function 'kftp_send_cmd': tabix/knetfile.c.pysam.c:241:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -O2 build/temp.linux-i686-2.6/pysam/ctabix.o build/temp.linux-i686-2.6/pysam/tabix_util.o build/temp.linux-i686-2.6/tabix/kstring.c.pysam.o build/temp.linux-i686-2.6/tabix/bgzip.c.pysam.o build/temp.linux-i686-2.6/tabix/index.c.pysam.o build/temp.linux-i686-2.6/tabix/bgzf.c.pysam.o build/temp.linux-i686-2.6/tabix/bedidx.c.pysam.o build/temp.linux-i686-2.6/tabix/knetfile.c.pysam.o -lz -o build/lib.linux-i686-2.6/ctabix.so skipping 'pysam/TabProxies.c' Cython extension (up-to-date) building 'TabProxies' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -I/usr/include/python2.6 -c pysam/TabProxies.c -o build/temp.linux-i686-2.6/pysam/TabProxies.o gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -O2 build/temp.linux-i686-2.6/pysam/TabProxies.o -lz -o build/lib.linux-i686-2.6/TabProxies.so skipping 'pysam/cvcf.c' Cython extension (up-to-date) building 'cvcf' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -Itabix -I/usr/include/python2.6 -c pysam/cvcf.c -o build/temp.linux-i686-2.6/pysam/cvcf.o pysam/cvcf.c: In function '__pyx_pf_4cvcf_3VCF_13convertGTback': pysam/cvcf.c:10949:13: warning: variable '__pyx_v_self' set but not used [-Wunused-but-set-variable] pysam/cvcf.c: In function '__pyx_pf_4cvcf_3VCF_38compare_calls': pysam/cvcf.c:19319:13: warning: variable '__pyx_v_self' set but not used [-Wunused-but-set-variable] pysam/cvcf.c: In function '__pyx_pf_4cvcf_3VCF_16parse_data': pysam/cvcf.c:16269:33: warning: '__pyx_v_qual' may be used uninitialized in this function [-Wuninitialized] gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -O2 build/temp.linux-i686-2.6/pysam/cvcf.o -lz -o build/lib.linux-i686-2.6/cvcf.so running install_lib creating /build/buildd/pysam-0.5/debian/python-pysam/usr creating /build/buildd/pysam-0.5/debian/python-pysam/usr/lib creating /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.6 creating /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.6/dist-packages copying build/lib.linux-i686-2.6/ctabix.so -> /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.6/dist-packages copying build/lib.linux-i686-2.6/TabProxies.so -> /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.6/dist-packages copying build/lib.linux-i686-2.6/csamtools.so -> /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.6/dist-packages creating /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.6/dist-packages/pysam copying build/lib.linux-i686-2.6/pysam/namedtuple.py -> /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.6/dist-packages/pysam copying build/lib.linux-i686-2.6/pysam/Pileup.py -> /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.6/dist-packages/pysam copying build/lib.linux-i686-2.6/pysam/version.py -> /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.6/dist-packages/pysam copying build/lib.linux-i686-2.6/pysam/__init__.py -> /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.6/dist-packages/pysam copying build/lib.linux-i686-2.6/cvcf.so -> /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.6/dist-packages running install_egg_info running egg_info writing requirements to pysam.egg-info/requires.txt writing pysam.egg-info/PKG-INFO writing top-level names to pysam.egg-info/top_level.txt writing dependency_links to pysam.egg-info/dependency_links.txt reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.6/dist-packages/pysam-0.5.egg-info running install_scripts running install running build running build_py running build_ext skipping 'pysam/csamtools.c' Cython extension (up-to-date) skipping 'pysam/ctabix.c' Cython extension (up-to-date) skipping 'pysam/TabProxies.c' Cython extension (up-to-date) skipping 'pysam/cvcf.c' Cython extension (up-to-date) running install_lib creating /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.7 creating /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.7/dist-packages copying build/lib.linux-i686-2.7/ctabix.so -> /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.7/dist-packages copying build/lib.linux-i686-2.7/TabProxies.so -> /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.7/dist-packages copying build/lib.linux-i686-2.7/csamtools.so -> /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.7/dist-packages creating /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying build/lib.linux-i686-2.7/pysam/namedtuple.py -> /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying build/lib.linux-i686-2.7/pysam/Pileup.py -> /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying build/lib.linux-i686-2.7/pysam/version.py -> /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying build/lib.linux-i686-2.7/pysam/__init__.py -> /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying build/lib.linux-i686-2.7/cvcf.so -> /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.7/dist-packages running install_egg_info running egg_info writing requirements to pysam.egg-info/requires.txt writing pysam.egg-info/PKG-INFO writing top-level names to pysam.egg-info/top_level.txt writing dependency_links to pysam.egg-info/dependency_links.txt reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /build/buildd/pysam-0.5/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam-0.5.egg-info running install_scripts dh_install -O--buildsystem=python_distutils dh_installdocs -O--buildsystem=python_distutils dh_installchangelogs -O--buildsystem=python_distutils dh_installexamples -O--buildsystem=python_distutils dh_installman -O--buildsystem=python_distutils dh_installcatalogs -O--buildsystem=python_distutils dh_installcron -O--buildsystem=python_distutils dh_installdebconf -O--buildsystem=python_distutils dh_installemacsen -O--buildsystem=python_distutils dh_installifupdown -O--buildsystem=python_distutils dh_installinfo -O--buildsystem=python_distutils dh_installinit -O--buildsystem=python_distutils dh_installmenu -O--buildsystem=python_distutils dh_installmime -O--buildsystem=python_distutils dh_installmodules -O--buildsystem=python_distutils dh_installlogcheck -O--buildsystem=python_distutils dh_installlogrotate -O--buildsystem=python_distutils dh_installpam -O--buildsystem=python_distutils dh_installppp -O--buildsystem=python_distutils dh_installudev -O--buildsystem=python_distutils dh_installwm -O--buildsystem=python_distutils dh_installxfonts -O--buildsystem=python_distutils dh_installgsettings -O--buildsystem=python_distutils dh_bugfiles -O--buildsystem=python_distutils dh_ucf -O--buildsystem=python_distutils dh_lintian -O--buildsystem=python_distutils dh_gconf -O--buildsystem=python_distutils dh_icons -O--buildsystem=python_distutils dh_perl -O--buildsystem=python_distutils dh_python2 -O--buildsystem=python_distutils dh_usrlocal -O--buildsystem=python_distutils dh_link -O--buildsystem=python_distutils dh_compress -O--buildsystem=python_distutils dh_fixperms -O--buildsystem=python_distutils dh_strip -O--buildsystem=python_distutils 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 -O--buildsystem=python_distutils dh_shlibdeps -O--buildsystem=python_distutils dh_installdeb -O--buildsystem=python_distutils dh_gencontrol -O--buildsystem=python_distutils dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Versions} dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Provides} dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Depends} dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${shlibs:Depends} dh_md5sums -O--buildsystem=python_distutils dh_builddeb -O--buildsystem=python_distutils 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 `python-pysam' in `../python-pysam_0.5-1_i386.deb'. dpkg-genchanges -b -mUbuntu/i386 Build Daemon >../pysam_0.5-1_i386.changes dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build pysam-0.5 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20111109-1304 chroot-autobuild/build/buildd/python-pysam_0.5-1_i386.deb: new debian package, version 2.0. size 1174006 bytes: control archive= 1250 bytes. 342 bytes, 10 lines control 1496 bytes, 19 lines md5sums 162 bytes, 9 lines * postinst #!/bin/sh 261 bytes, 14 lines * prerm #!/bin/sh Package: python-pysam Source: pysam Version: 0.5-1 Architecture: i386 Maintainer: Johannes Koester Installed-Size: 3244 Depends: cython (>= 0.12) Section: python Priority: optional Description: Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. chroot-autobuild/build/buildd/python-pysam_0.5-1_i386.deb: drwxr-xr-x root/root 0 2011-11-09 13:04 ./ drwxr-xr-x root/root 0 2011-11-09 13:04 ./usr/ drwxr-xr-x root/root 0 2011-11-09 13:04 ./usr/share/ drwxr-xr-x root/root 0 2011-11-09 13:04 ./usr/share/doc/ drwxr-xr-x root/root 0 2011-11-09 13:04 ./usr/share/doc/python-pysam/ -rw-r--r-- root/root 169 2011-11-07 14:50 ./usr/share/doc/python-pysam/changelog.Debian.gz drwxr-xr-x root/root 0 2011-11-09 13:04 ./usr/share/pyshared/ drwxr-xr-x root/root 0 2011-11-09 13:04 ./usr/share/pyshared/pysam-0.5.egg-info/ -rw-r--r-- root/root 3172 2011-11-09 13:04 ./usr/share/pyshared/pysam-0.5.egg-info/SOURCES.txt -rw-r--r-- root/root 1 2011-04-26 07:51 ./usr/share/pyshared/pysam-0.5.egg-info/not-zip-safe -rw-r--r-- root/root 92 2011-11-09 13:04 ./usr/share/pyshared/pysam-0.5.egg-info/top_level.txt -rw-r--r-- root/root 287 2011-11-09 13:04 ./usr/share/pyshared/pysam-0.5.egg-info/PKG-INFO -rw-r--r-- root/root 14 2011-11-09 13:04 ./usr/share/pyshared/pysam-0.5.egg-info/requires.txt -rw-r--r-- root/root 1 2011-11-09 13:04 ./usr/share/pyshared/pysam-0.5.egg-info/dependency_links.txt drwxr-xr-x root/root 0 2011-11-09 13:04 ./usr/share/pyshared/pysam/ -rw-r--r-- root/root 5056 2010-12-15 11:54 ./usr/share/pyshared/pysam/namedtuple.py -rw-r--r-- root/root 8305 2011-05-06 12:07 ./usr/share/pyshared/pysam/Pileup.py -rw-r--r-- root/root 114 2011-06-07 15:41 ./usr/share/pyshared/pysam/version.py -rw-r--r-- root/root 3921 2011-05-03 11:58 ./usr/share/pyshared/pysam/__init__.py drwxr-xr-x root/root 0 2011-11-09 13:04 ./usr/lib/ drwxr-xr-x root/root 0 2011-11-09 13:04 ./usr/lib/pyshared/ drwxr-xr-x root/root 0 2011-11-09 13:04 ./usr/lib/pyshared/python2.7/ drwxr-xr-x root/root 0 2011-11-09 13:04 ./usr/lib/pyshared/python2.6/ drwxr-xr-x root/root 0 2011-11-09 13:04 ./usr/lib/python2.7/ drwxr-xr-x root/root 0 2011-11-09 13:04 ./usr/lib/python2.7/dist-packages/ -rw-r--r-- root/root 153964 2011-11-09 13:04 ./usr/lib/python2.7/dist-packages/ctabix.so -rw-r--r-- root/root 84748 2011-11-09 13:04 ./usr/lib/python2.7/dist-packages/TabProxies.so -rw-r--r-- root/root 908600 2011-11-09 13:04 ./usr/lib/python2.7/dist-packages/csamtools.so drwxr-xr-x root/root 0 2011-11-09 13:04 ./usr/lib/python2.7/dist-packages/pysam-0.5.egg-info/ drwxr-xr-x root/root 0 2011-11-09 13:04 ./usr/lib/python2.7/dist-packages/pysam/ -rw-r--r-- root/root 410356 2011-11-09 13:04 ./usr/lib/python2.7/dist-packages/cvcf.so drwxr-xr-x root/root 0 2011-11-09 13:04 ./usr/lib/python2.6/ drwxr-xr-x root/root 0 2011-11-09 13:04 ./usr/lib/python2.6/dist-packages/ -rw-r--r-- root/root 153964 2011-11-09 13:04 ./usr/lib/python2.6/dist-packages/ctabix.so -rw-r--r-- root/root 84748 2011-11-09 13:04 ./usr/lib/python2.6/dist-packages/TabProxies.so -rw-r--r-- root/root 908600 2011-11-09 13:04 ./usr/lib/python2.6/dist-packages/csamtools.so drwxr-xr-x root/root 0 2011-11-09 13:04 ./usr/lib/python2.6/dist-packages/pysam-0.5.egg-info/ drwxr-xr-x root/root 0 2011-11-09 13:04 ./usr/lib/python2.6/dist-packages/pysam/ -rw-r--r-- root/root 410356 2011-11-09 13:04 ./usr/lib/python2.6/dist-packages/cvcf.so lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/pyshared/python2.7/ctabix.so -> ../../python2.7/dist-packages/ctabix.so lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/pyshared/python2.7/TabProxies.so -> ../../python2.7/dist-packages/TabProxies.so lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/pyshared/python2.7/csamtools.so -> ../../python2.7/dist-packages/csamtools.so lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/pyshared/python2.7/cvcf.so -> ../../python2.7/dist-packages/cvcf.so lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/pyshared/python2.6/ctabix.so -> ../../python2.6/dist-packages/ctabix.so lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/pyshared/python2.6/TabProxies.so -> ../../python2.6/dist-packages/TabProxies.so lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/pyshared/python2.6/csamtools.so -> ../../python2.6/dist-packages/csamtools.so lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/pyshared/python2.6/cvcf.so -> ../../python2.6/dist-packages/cvcf.so lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/python2.7/dist-packages/pysam-0.5.egg-info/SOURCES.txt -> ../../../../share/pyshared/pysam-0.5.egg-info/SOURCES.txt lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/python2.7/dist-packages/pysam-0.5.egg-info/not-zip-safe -> ../../../../share/pyshared/pysam-0.5.egg-info/not-zip-safe lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/python2.7/dist-packages/pysam-0.5.egg-info/top_level.txt -> ../../../../share/pyshared/pysam-0.5.egg-info/top_level.txt lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/python2.7/dist-packages/pysam-0.5.egg-info/PKG-INFO -> ../../../../share/pyshared/pysam-0.5.egg-info/PKG-INFO lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/python2.7/dist-packages/pysam-0.5.egg-info/requires.txt -> ../../../../share/pyshared/pysam-0.5.egg-info/requires.txt lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/python2.7/dist-packages/pysam-0.5.egg-info/dependency_links.txt -> ../../../../share/pyshared/pysam-0.5.egg-info/dependency_links.txt lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/python2.7/dist-packages/pysam/namedtuple.py -> ../../../../share/pyshared/pysam/namedtuple.py lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/python2.7/dist-packages/pysam/Pileup.py -> ../../../../share/pyshared/pysam/Pileup.py lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/python2.7/dist-packages/pysam/version.py -> ../../../../share/pyshared/pysam/version.py lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/python2.7/dist-packages/pysam/__init__.py -> ../../../../share/pyshared/pysam/__init__.py lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/python2.6/dist-packages/pysam-0.5.egg-info/SOURCES.txt -> ../../../../share/pyshared/pysam-0.5.egg-info/SOURCES.txt lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/python2.6/dist-packages/pysam-0.5.egg-info/not-zip-safe -> ../../../../share/pyshared/pysam-0.5.egg-info/not-zip-safe lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/python2.6/dist-packages/pysam-0.5.egg-info/top_level.txt -> ../../../../share/pyshared/pysam-0.5.egg-info/top_level.txt lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/python2.6/dist-packages/pysam-0.5.egg-info/PKG-INFO -> ../../../../share/pyshared/pysam-0.5.egg-info/PKG-INFO lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/python2.6/dist-packages/pysam-0.5.egg-info/requires.txt -> ../../../../share/pyshared/pysam-0.5.egg-info/requires.txt lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/python2.6/dist-packages/pysam-0.5.egg-info/dependency_links.txt -> ../../../../share/pyshared/pysam-0.5.egg-info/dependency_links.txt lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/python2.6/dist-packages/pysam/namedtuple.py -> ../../../../share/pyshared/pysam/namedtuple.py lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/python2.6/dist-packages/pysam/Pileup.py -> ../../../../share/pyshared/pysam/Pileup.py lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/python2.6/dist-packages/pysam/version.py -> ../../../../share/pyshared/pysam/version.py lrwxrwxrwx root/root 0 2011-11-09 13:04 ./usr/lib/python2.6/dist-packages/pysam/__init__.py -> ../../../../share/pyshared/pysam/__init__.py pysam_0.5-1_i386.changes: Format: 1.8 Date: Mon, 07 Nov 2011 15:47:56 +0100 Source: pysam Binary: python-pysam Architecture: i386 Version: 0.5-1 Distribution: oneiric Urgency: low Maintainer: Ubuntu/i386 Build Daemon Changed-By: Johannes Koester Description: python-pysam - Pysam is a python module for reading and manipulating Samfiles. I Changes: pysam (0.5-1) oneiric; urgency=low . * source package automatically created by stdeb 0.6.0+git Checksums-Sha1: 2a47adca9781c33c30f83eb7571757688077b7b9 1174006 python-pysam_0.5-1_i386.deb Checksums-Sha256: b17261d735c22a07962920f09535ca2aae13d4d920dd6d84326d2d7a3121316e 1174006 python-pysam_0.5-1_i386.deb Files: 0e9ed1e5fa7bcd193feb0b8e0d306aef 1174006 python optional python-pysam_0.5-1_i386.deb ****************************************************************************** Built successfully Purging chroot-autobuild/build/buildd/pysam-0.5 ------------------------------------------------------------------------------ /usr/bin/sudo dpkg --purge groff-base python2.6-minimal mime-support gettext file zlib1g-dev po-debconf libdb4.8 python2.6 libcroco3 python-pkg-resources python-support libxml2 libpython2.6 python-all-dev python-all python-dev man-db intltool-debian python2.7-dev python2.7 cython libexpat1-dev python-setuptools libpython2.7 html2text gettext-base python2.6-dev debhelper libunistring0 python libmagic1 libpipeline1 libexpat1 libsqlite3-0 libssl-dev bsdmainutils (Reading database ... 17414 files and directories currently installed.) Removing python-all-dev ... Removing python-all ... Removing python-dev ... Removing python2.7-dev ... Removing cython ... Removing libexpat1-dev ... Removing python-setuptools ... Removing libpython2.7 ... Purging configuration files for libpython2.7 ... Removing python2.6-dev ... Removing debhelper ... Removing libssl-dev ... Removing file ... Removing zlib1g-dev ... Removing po-debconf ... Removing python-pkg-resources ... Removing python-support ... Purging configuration files for python-support ... Removing libpython2.6 ... Purging configuration files for libpython2.6 ... Removing man-db ... Purging configuration files for man-db ... Removing catpages as well as /var/cache/man hierarchy. Removing intltool-debian ... Removing html2text ... Purging configuration files for html2text ... Removing python ... Purging configuration files for python ... Removing libmagic1 ... Purging configuration files for libmagic1 ... Removing libpipeline1 ... Purging configuration files for libpipeline1 ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing groff-base ... Purging configuration files for groff-base ... Removing gettext ... Removing python2.6 ... Purging configuration files for python2.6 ... Removing libcroco3 ... Purging configuration files for libcroco3 ... Removing libxml2 ... Purging configuration files for libxml2 ... Removing python2.7 ... Purging configuration files for python2.7 ... Removing gettext-base ... Removing libunistring0 ... Purging configuration files for libunistring0 ... Removing libexpat1 ... Purging configuration files for libexpat1 ... Removing libsqlite3-0 ... Purging configuration files for libsqlite3-0 ... Removing python2.6-minimal ... Unlinking and removing bytecode for runtime python2.6 Purging configuration files for python2.6-minimal ... Removing mime-support ... Purging configuration files for mime-support ... Removing libdb4.8 ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place ****************************************************************************** Finished at 20111109-1304 Build needed 00:04:16, 31192k 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', 'f9ebd2fab1b4859cce3989cabf22edfbc04b01a4'] Scanning for processes to kill in build /home/buildd/build-f9ebd2fab1b4859cce3989cabf22edfbc04b01a4/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'f9ebd2fab1b4859cce3989cabf22edfbc04b01a4'] Unmounting chroot for build f9ebd2fab1b4859cce3989cabf22edfbc04b01a4... none /home/buildd/build-f9ebd2fab1b4859cce3989cabf22edfbc04b01a4/chroot-autobuild/proc proc rw,relatime 0 0 none /home/buildd/build-f9ebd2fab1b4859cce3989cabf22edfbc04b01a4/chroot-autobuild/dev/pts devpts rw,relatime 0 0 none /home/buildd/build-f9ebd2fab1b4859cce3989cabf22edfbc04b01a4/chroot-autobuild/sys sysfs rw,relatime 0 0 none /home/buildd/build-f9ebd2fab1b4859cce3989cabf22edfbc04b01a4/chroot-autobuild/dev/shm tmpfs rw,relatime 0 0 RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'f9ebd2fab1b4859cce3989cabf22edfbc04b01a4'] Removing build f9ebd2fab1b4859cce3989cabf22edfbc04b01a4