RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux fisher01 3.13.0-8-generic #28-Ubuntu SMP Tue Feb 11 17:58:07 UTC 2014 ppc64le Buildd toolchain package versions: launchpad-buildd_121~0.IS.08.04.0 python-lpbuildd_121~0.IS.08.04.0 dpkg-dev_1.17.5ubuntu4. Syncing the system clock with the buildd NTP service... 19 Feb 19:06:40 ntpdate[29120]: adjust time server 10.211.37.1 offset 0.000026 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-5605334', '/home/buildd/filecache-default/1418c9e5f0eb143d9f77e4665c5b7c89c42011cc'] Unpacking chroot for build PACKAGEBUILD-5605334 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-5605334'] Mounting chroot for build PACKAGEBUILD-5605334 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-5605334', 'deb http://ftpmaster.internal/ubuntu trusty main universe'] Overriding sources.list in build-PACKAGEBUILD-5605334 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-5605334', 'ppc64el'] Updating debian chroot for build PACKAGEBUILD-5605334 Ign http://archive-team.internal trusty InRelease Ign http://ftpmaster.internal trusty InRelease Ign http://archive-team.internal trusty Release.gpg Ign http://ftpmaster.internal trusty InRelease Hit http://archive-team.internal trusty Release Get:1 http://ftpmaster.internal trusty Release.gpg [933 B] Ign http://archive-team.internal trusty/main ppc64el Packages/DiffIndex Get:2 http://ftpmaster.internal trusty Release.gpg [933 B] Get:3 http://ftpmaster.internal trusty Release [58.5 kB] Get:4 http://ftpmaster.internal trusty Release [58.5 kB] Get:5 http://ftpmaster.internal trusty/main ppc64el Packages [1222 kB] Ign http://archive-team.internal trusty/main Translation-en Hit http://archive-team.internal trusty/main ppc64el Packages Get:6 http://ftpmaster.internal trusty/universe ppc64el Packages [4622 kB] Get:7 http://ftpmaster.internal trusty/main Translation-en [760 kB] Get:8 http://ftpmaster.internal trusty/universe Translation-en [4059 kB] Get:9 http://ftpmaster.internal trusty/main ppc64el Packages [1226 kB] Get:10 http://ftpmaster.internal trusty/universe ppc64el Packages [5005 kB] Get:11 http://ftpmaster.internal trusty/main Translation-en [760 kB] Get:12 http://ftpmaster.internal trusty/universe Translation-en [4056 kB] Fetched 21.8 MB in 14s (1465 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: cpp-4.8 dash e2fslibs e2fsprogs g++-4.8 gcc-4.8 gcc-4.8-base gcc-4.9-base libasn1-8-heimdal libatomic1 libcomerr2 libgcc-4.8-dev libgcc1 libgomp1 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libitm1 libkrb5-26-heimdal libroken18-heimdal libss2 libstdc++-4.8-dev libstdc++6 libwind0-heimdal linux-libc-dev upstart 28 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 20.1 MB of archives. After this operation, 137 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ trusty/main dash ppc64el 0.5.7-4ubuntu1 [94.5 kB] Get:2 http://ftpmaster.internal/ubuntu/ trusty/main e2fslibs ppc64el 1.42.9-3ubuntu1 [185 kB] Get:3 http://ftpmaster.internal/ubuntu/ trusty/main e2fsprogs ppc64el 1.42.9-3ubuntu1 [662 kB] Get:4 http://ftpmaster.internal/ubuntu/ trusty/main libitm1 ppc64el 4.8.2-16ubuntu1 [28.8 kB] Get:5 http://ftpmaster.internal/ubuntu/ trusty/main libgomp1 ppc64el 4.8.2-16ubuntu1 [21.9 kB] Get:6 http://ftpmaster.internal/ubuntu/ trusty/main g++-4.8 ppc64el 4.8.2-16ubuntu1 [6242 kB] Get:7 http://ftpmaster.internal/ubuntu/ trusty/main gcc-4.8 ppc64el 4.8.2-16ubuntu1 [4809 kB] Get:8 http://ftpmaster.internal/ubuntu/ trusty/main cpp-4.8 ppc64el 4.8.2-16ubuntu1 [4425 kB] Get:9 http://ftpmaster.internal/ubuntu/ trusty/main libatomic1 ppc64el 4.8.2-16ubuntu1 [7868 B] Get:10 http://ftpmaster.internal/ubuntu/ trusty/main gcc-4.9-base ppc64el 4.9-20140217-0ubuntu1 [14.3 kB] Get:11 http://ftpmaster.internal/ubuntu/ trusty/main libgcc1 ppc64el 1:4.9-20140217-0ubuntu1 [29.1 kB] Get:12 http://ftpmaster.internal/ubuntu/ trusty/main libstdc++-4.8-dev ppc64el 4.8.2-16ubuntu1 [1087 kB] Get:13 http://ftpmaster.internal/ubuntu/ trusty/main libgcc-4.8-dev ppc64el 4.8.2-16ubuntu1 [245 kB] Get:14 http://ftpmaster.internal/ubuntu/ trusty/main gcc-4.8-base ppc64el 4.8.2-16ubuntu1 [14.8 kB] Get:15 http://ftpmaster.internal/ubuntu/ trusty/main libstdc++6 ppc64el 4.8.2-16ubuntu1 [270 kB] Get:16 http://ftpmaster.internal/ubuntu/ trusty/main libcomerr2 ppc64el 1.42.9-3ubuntu1 [62.4 kB] Get:17 http://ftpmaster.internal/ubuntu/ trusty/main libss2 ppc64el 1.42.9-3ubuntu1 [66.5 kB] Get:18 http://ftpmaster.internal/ubuntu/ trusty/main libroken18-heimdal ppc64el 1.6~git20131207+dfsg-1ubuntu1 [39.6 kB] Get:19 http://ftpmaster.internal/ubuntu/ trusty/main libasn1-8-heimdal ppc64el 1.6~git20131207+dfsg-1ubuntu1 [132 kB] Get:20 http://ftpmaster.internal/ubuntu/ trusty/main libhcrypto4-heimdal ppc64el 1.6~git20131207+dfsg-1ubuntu1 [90.1 kB] Get:21 http://ftpmaster.internal/ubuntu/ trusty/main libheimbase1-heimdal ppc64el 1.6~git20131207+dfsg-1ubuntu1 [28.4 kB] Get:22 http://ftpmaster.internal/ubuntu/ trusty/main libwind0-heimdal ppc64el 1.6~git20131207+dfsg-1ubuntu1 [47.8 kB] Get:23 http://ftpmaster.internal/ubuntu/ trusty/main libhx509-5-heimdal ppc64el 1.6~git20131207+dfsg-1ubuntu1 [97.8 kB] Get:24 http://ftpmaster.internal/ubuntu/ trusty/main libkrb5-26-heimdal ppc64el 1.6~git20131207+dfsg-1ubuntu1 [188 kB] Get:25 http://ftpmaster.internal/ubuntu/ trusty/main libheimntlm0-heimdal ppc64el 1.6~git20131207+dfsg-1ubuntu1 [15.7 kB] Get:26 http://ftpmaster.internal/ubuntu/ trusty/main libgssapi3-heimdal ppc64el 1.6~git20131207+dfsg-1ubuntu1 [83.6 kB] Get:27 http://ftpmaster.internal/ubuntu/ trusty/main upstart ppc64el 1.11-0ubuntu4 [338 kB] Get:28 http://ftpmaster.internal/ubuntu/ trusty/main linux-libc-dev ppc64el 3.13.0-10.30 [754 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 20.1 MB in 21s (941 kB/s) (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../dash_0.5.7-4ubuntu1_ppc64el.deb ... Unpacking dash (0.5.7-4ubuntu1) over (0.5.7-3ubuntu1) ... Setting up dash (0.5.7-4ubuntu1) ... (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../e2fslibs_1.42.9-3ubuntu1_ppc64el.deb ... Unpacking e2fslibs:ppc64el (1.42.9-3ubuntu1) over (1.42.9-2ubuntu1) ... Setting up e2fslibs:ppc64el (1.42.9-3ubuntu1) ... Processing triggers for libc-bin (2.18-0ubuntu7) ... (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.42.9-3ubuntu1_ppc64el.deb ... Unpacking e2fsprogs (1.42.9-3ubuntu1) over (1.42.9-2ubuntu1) ... Setting up e2fsprogs (1.42.9-3ubuntu1) ... (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../libitm1_4.8.2-16ubuntu1_ppc64el.deb ... Unpacking libitm1:ppc64el (4.8.2-16ubuntu1) over (4.8.2-15ubuntu3) ... Preparing to unpack .../libgomp1_4.8.2-16ubuntu1_ppc64el.deb ... Unpacking libgomp1:ppc64el (4.8.2-16ubuntu1) over (4.8.2-15ubuntu3) ... Preparing to unpack .../g++-4.8_4.8.2-16ubuntu1_ppc64el.deb ... Unpacking g++-4.8 (4.8.2-16ubuntu1) over (4.8.2-15ubuntu3) ... Preparing to unpack .../gcc-4.8_4.8.2-16ubuntu1_ppc64el.deb ... Unpacking gcc-4.8 (4.8.2-16ubuntu1) over (4.8.2-15ubuntu3) ... Preparing to unpack .../cpp-4.8_4.8.2-16ubuntu1_ppc64el.deb ... Unpacking cpp-4.8 (4.8.2-16ubuntu1) over (4.8.2-15ubuntu3) ... Preparing to unpack .../libatomic1_4.8.2-16ubuntu1_ppc64el.deb ... Unpacking libatomic1:ppc64el (4.8.2-16ubuntu1) over (4.8.2-15ubuntu3) ... Preparing to unpack .../gcc-4.9-base_4.9-20140217-0ubuntu1_ppc64el.deb ... Unpacking gcc-4.9-base:ppc64el (4.9-20140217-0ubuntu1) over (4.9-20140213-0ubuntu2) ... Setting up gcc-4.9-base:ppc64el (4.9-20140217-0ubuntu1) ... (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../libgcc1_1%3a4.9-20140217-0ubuntu1_ppc64el.deb ... Unpacking libgcc1:ppc64el (1:4.9-20140217-0ubuntu1) over (1:4.9-20140213-0ubuntu2) ... Setting up libgcc1:ppc64el (1:4.9-20140217-0ubuntu1) ... Processing triggers for libc-bin (2.18-0ubuntu7) ... (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../libstdc++-4.8-dev_4.8.2-16ubuntu1_ppc64el.deb ... Unpacking libstdc++-4.8-dev:ppc64el (4.8.2-16ubuntu1) over (4.8.2-15ubuntu3) ... Preparing to unpack .../libgcc-4.8-dev_4.8.2-16ubuntu1_ppc64el.deb ... Unpacking libgcc-4.8-dev:ppc64el (4.8.2-16ubuntu1) over (4.8.2-15ubuntu3) ... Preparing to unpack .../gcc-4.8-base_4.8.2-16ubuntu1_ppc64el.deb ... Unpacking gcc-4.8-base:ppc64el (4.8.2-16ubuntu1) over (4.8.2-15ubuntu3) ... Setting up gcc-4.8-base:ppc64el (4.8.2-16ubuntu1) ... (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../libstdc++6_4.8.2-16ubuntu1_ppc64el.deb ... Unpacking libstdc++6:ppc64el (4.8.2-16ubuntu1) over (4.8.2-15ubuntu3) ... Setting up libstdc++6:ppc64el (4.8.2-16ubuntu1) ... Processing triggers for libc-bin (2.18-0ubuntu7) ... (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../libcomerr2_1.42.9-3ubuntu1_ppc64el.deb ... Unpacking libcomerr2:ppc64el (1.42.9-3ubuntu1) over (1.42.9-2ubuntu1) ... Setting up libcomerr2:ppc64el (1.42.9-3ubuntu1) ... Processing triggers for libc-bin (2.18-0ubuntu7) ... (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../libss2_1.42.9-3ubuntu1_ppc64el.deb ... Unpacking libss2:ppc64el (1.42.9-3ubuntu1) over (1.42.9-2ubuntu1) ... Setting up libss2:ppc64el (1.42.9-3ubuntu1) ... Processing triggers for libc-bin (2.18-0ubuntu7) ... (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../libroken18-heimdal_1.6~git20131207+dfsg-1ubuntu1_ppc64el.deb ... Unpacking libroken18-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) over (1.6~git20120403+dfsg1-3ubuntu0.2) ... Preparing to unpack .../libasn1-8-heimdal_1.6~git20131207+dfsg-1ubuntu1_ppc64el.deb ... Unpacking libasn1-8-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) over (1.6~git20120403+dfsg1-3ubuntu0.2) ... Preparing to unpack .../libhcrypto4-heimdal_1.6~git20131207+dfsg-1ubuntu1_ppc64el.deb ... Unpacking libhcrypto4-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) over (1.6~git20120403+dfsg1-3ubuntu0.2) ... Preparing to unpack .../libheimbase1-heimdal_1.6~git20131207+dfsg-1ubuntu1_ppc64el.deb ... Unpacking libheimbase1-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) over (1.6~git20120403+dfsg1-3ubuntu0.2) ... Preparing to unpack .../libwind0-heimdal_1.6~git20131207+dfsg-1ubuntu1_ppc64el.deb ... Unpacking libwind0-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) over (1.6~git20120403+dfsg1-3ubuntu0.2) ... Preparing to unpack .../libhx509-5-heimdal_1.6~git20131207+dfsg-1ubuntu1_ppc64el.deb ... Unpacking libhx509-5-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) over (1.6~git20120403+dfsg1-3ubuntu0.2) ... Preparing to unpack .../libkrb5-26-heimdal_1.6~git20131207+dfsg-1ubuntu1_ppc64el.deb ... Unpacking libkrb5-26-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) over (1.6~git20120403+dfsg1-3ubuntu0.2) ... Preparing to unpack .../libheimntlm0-heimdal_1.6~git20131207+dfsg-1ubuntu1_ppc64el.deb ... Unpacking libheimntlm0-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) over (1.6~git20120403+dfsg1-3ubuntu0.2) ... Preparing to unpack .../libgssapi3-heimdal_1.6~git20131207+dfsg-1ubuntu1_ppc64el.deb ... Unpacking libgssapi3-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) over (1.6~git20120403+dfsg1-3ubuntu0.2) ... Preparing to unpack .../upstart_1.11-0ubuntu4_ppc64el.deb ... Unpacking upstart (1.11-0ubuntu4) over (1.11-0ubuntu3) ... Preparing to unpack .../linux-libc-dev_3.13.0-10.30_ppc64el.deb ... Unpacking linux-libc-dev:ppc64el (3.13.0-10.30) over (3.13.0-8.28) ... Setting up libitm1:ppc64el (4.8.2-16ubuntu1) ... Setting up libgomp1:ppc64el (4.8.2-16ubuntu1) ... Setting up cpp-4.8 (4.8.2-16ubuntu1) ... Setting up gcc-4.8 (4.8.2-16ubuntu1) ... Setting up libatomic1:ppc64el (4.8.2-16ubuntu1) ... Setting up libgcc-4.8-dev:ppc64el (4.8.2-16ubuntu1) ... Setting up libstdc++-4.8-dev:ppc64el (4.8.2-16ubuntu1) ... Setting up g++-4.8 (4.8.2-16ubuntu1) ... Setting up libroken18-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) ... Setting up libasn1-8-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) ... Setting up libhcrypto4-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) ... Setting up libheimbase1-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) ... Setting up libwind0-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) ... Setting up libhx509-5-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) ... Setting up libkrb5-26-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) ... Setting up libheimntlm0-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) ... Setting up libgssapi3-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) ... Setting up upstart (1.11-0ubuntu4) ... Setting up linux-libc-dev:ppc64el (3.13.0-10.30) ... Processing triggers for libc-bin (2.18-0ubuntu7) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-5605334', 'ppc64el', 'trusty', '--nolog', '--batch', '--archive=ubuntu', '--dist=trusty', '--purpose=PRIMARY', '--architecture=ppc64el', '--comp=universe', 'samtools_0.1.19-1.dsc'] Initiating build PACKAGEBUILD-5605334 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 3.13.0-8-generic #28-Ubuntu SMP Tue Feb 11 17:58:07 UTC 2014 ppc64le Automatic build of samtools_0.1.19-1 on fisher01 by sbuild/ppc64el 1.170.5 Build started at 20140219-1907 ****************************************************************************** samtools_0.1.19-1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev Checking for already installed source dependencies... debhelper: missing bash-completion: missing cdbs: missing quilt: missing libncurses5-dev: missing zlib1g-dev: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: apparmor-easyprof autoconf automake autotools-dev bsdmainutils ca-certificates dh-apparmor dh-python dh-translations diffstat file gettext gettext-base groff-base intltool intltool-debian libasprintf0c2 libcroco3 libencode-locale-perl libexpat1 libfile-listing-perl libglib2.0-0 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libio-html-perl libio-socket-ssl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic1 libmpdec2 libnet-http-perl libnet-ssleay-perl libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.4-minimal libpython3.4-stdlib libsigsegv2 libssl1.0.0 libtinfo-dev libunistring0 liburi-perl libwww-perl libwww-robotrules-perl libxml-parser-perl libxml2 m4 man-db mime-support netbase openssl po-debconf python python-minimal python-scour python2.7 python2.7-minimal python3 python3-minimal python3.4 python3.4-minimal Suggested packages: autoconf2.13 autoconf-archive gnu-standards autoconf-doc libtool wamerican wordlist whois vacation devscripts dh-make gettext-doc groff libdata-dump-perl libcrypt-ssleay-perl ncurses-doc libauthen-ntlm-perl less www-browser libmail-box-perl python-doc python-tk python-rsvg python-cairo python2.7-doc binfmt-support python3-doc python3-tk python3.4-doc procmail graphviz default-mta mail-transport-agent Recommended packages: curl wget lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info libhtml-format-perl libio-socket-inet6-perl libio-socket-ip-perl libhtml-form-perl libhttp-daemon-perl libmailtools-perl xml-core libmail-sendmail-perl The following NEW packages will be installed: apparmor-easyprof autoconf automake autotools-dev bash-completion bsdmainutils ca-certificates cdbs debhelper dh-apparmor dh-python dh-translations diffstat file gettext gettext-base groff-base intltool intltool-debian libasprintf0c2 libcroco3 libencode-locale-perl libexpat1 libfile-listing-perl libglib2.0-0 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libio-html-perl libio-socket-ssl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic1 libmpdec2 libncurses5-dev libnet-http-perl libnet-ssleay-perl libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.4-minimal libpython3.4-stdlib libsigsegv2 libssl1.0.0 libtinfo-dev libunistring0 liburi-perl libwww-perl libwww-robotrules-perl libxml-parser-perl libxml2 m4 man-db mime-support netbase openssl po-debconf python python-minimal python-scour python2.7 python2.7-minimal python3 python3-minimal python3.4 python3.4-minimal quilt zlib1g-dev 0 upgraded, 74 newly installed, 0 to remove and 0 not upgraded. Need to get 18.4 MB of archives. After this operation, 79.3 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ trusty/main libexpat1 ppc64el 2.1.0-4ubuntu1 [79.5 kB] Get:2 http://ftpmaster.internal/ubuntu/ trusty/main libmagic1 ppc64el 1:5.14-2ubuntu1 [194 kB] Get:3 http://ftpmaster.internal/ubuntu/ trusty/main libssl1.0.0 ppc64el 1.0.1f-1ubuntu1 [762 kB] Get:4 http://ftpmaster.internal/ubuntu/ trusty/main bash-completion all 1:2.1-2ubuntu2 [153 kB] Get:5 http://ftpmaster.internal/ubuntu/ trusty/main libasprintf0c2 ppc64el 0.18.3.1-1ubuntu2 [6748 B] Get:6 http://ftpmaster.internal/ubuntu/ trusty/main libglib2.0-0 ppc64el 2.39.90-0ubuntu1 [985 kB] Get:7 http://ftpmaster.internal/ubuntu/ trusty/main libpipeline1 ppc64el 1.2.6-2 [22.6 kB] Get:8 http://ftpmaster.internal/ubuntu/ trusty/main libxml2 ppc64el 2.9.1+dfsg1-3ubuntu3 [601 kB] Get:9 http://ftpmaster.internal/ubuntu/ trusty/main groff-base ppc64el 1.22.2-5 [1249 kB] Get:10 http://ftpmaster.internal/ubuntu/ trusty/main bsdmainutils ppc64el 9.0.5ubuntu1 [173 kB] Get:11 http://ftpmaster.internal/ubuntu/ trusty/main man-db ppc64el 2.6.6-1 [847 kB] Get:12 http://ftpmaster.internal/ubuntu/ trusty/main libcroco3 ppc64el 0.6.8-2ubuntu1 [75.4 kB] Get:13 http://ftpmaster.internal/ubuntu/ trusty/main libmpdec2 ppc64el 2.4.0-6 [83.9 kB] Get:14 http://ftpmaster.internal/ubuntu/ trusty/main libpython3.4-minimal ppc64el 3.4~rc1-1build1 [440 kB] Get:15 http://ftpmaster.internal/ubuntu/ trusty/main mime-support all 3.54ubuntu1 [31.7 kB] Get:16 http://ftpmaster.internal/ubuntu/ trusty/main libpython3.4-stdlib ppc64el 3.4~rc1-1build1 [1972 kB] Get:17 http://ftpmaster.internal/ubuntu/ trusty/main libsigsegv2 ppc64el 2.10-2 [13.8 kB] Get:18 http://ftpmaster.internal/ubuntu/ trusty/main libunistring0 ppc64el 0.9.3-5ubuntu3 [262 kB] Get:19 http://ftpmaster.internal/ubuntu/ trusty/main libpython2.7-minimal ppc64el 2.7.6-5 [307 kB] Get:20 http://ftpmaster.internal/ubuntu/ trusty/main python2.7-minimal ppc64el 2.7.6-5 [932 kB] Get:21 http://ftpmaster.internal/ubuntu/ trusty/main python3.4-minimal ppc64el 3.4~rc1-1build1 [1147 kB] Get:22 http://ftpmaster.internal/ubuntu/ trusty/main python3.4 ppc64el 3.4~rc1-1build1 [159 kB] Get:23 http://ftpmaster.internal/ubuntu/ trusty/main python3-minimal ppc64el 3.4~rc1-1 [23.4 kB] Get:24 http://ftpmaster.internal/ubuntu/ trusty/main libpython3-stdlib ppc64el 3.4~rc1-1 [6976 B] Get:25 http://ftpmaster.internal/ubuntu/ trusty/main python3 ppc64el 3.4~rc1-1 [8654 B] Get:26 http://ftpmaster.internal/ubuntu/ trusty/main dh-python all 1.20140128-1ubuntu2 [51.0 kB] Get:27 http://ftpmaster.internal/ubuntu/ trusty/main file ppc64el 1:5.14-2ubuntu1 [19.2 kB] Get:28 http://ftpmaster.internal/ubuntu/ trusty/main netbase all 5.2 [12.9 kB] Get:29 http://ftpmaster.internal/ubuntu/ trusty/main openssl ppc64el 1.0.1f-1ubuntu1 [479 kB] Get:30 http://ftpmaster.internal/ubuntu/ trusty/main ca-certificates all 20130906ubuntu2 [175 kB] Get:31 http://ftpmaster.internal/ubuntu/ trusty/main gettext-base ppc64el 0.18.3.1-1ubuntu2 [47.2 kB] Get:32 http://ftpmaster.internal/ubuntu/ trusty/main m4 ppc64el 1.4.17-2ubuntu1 [194 kB] Get:33 http://ftpmaster.internal/ubuntu/ trusty/main autoconf all 2.69-4 [320 kB] Get:34 http://ftpmaster.internal/ubuntu/ trusty/main autotools-dev all 20130810.1 [44.3 kB] Get:35 http://ftpmaster.internal/ubuntu/ trusty/main automake all 1:1.14.1-2ubuntu1 [510 kB] Get:36 http://ftpmaster.internal/ubuntu/ trusty/main gettext ppc64el 0.18.3.1-1ubuntu2 [840 kB] Get:37 http://ftpmaster.internal/ubuntu/ trusty/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:38 http://ftpmaster.internal/ubuntu/ trusty/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:39 http://ftpmaster.internal/ubuntu/ trusty/main apparmor-easyprof all 2.8.0-0ubuntu38 [20.1 kB] Get:40 http://ftpmaster.internal/ubuntu/ trusty/main dh-apparmor all 2.8.0-0ubuntu38 [7286 B] Get:41 http://ftpmaster.internal/ubuntu/ trusty/main debhelper all 9.20131227ubuntu1 [604 kB] Get:42 http://ftpmaster.internal/ubuntu/ trusty/main liburi-perl all 1.60-1 [89.6 kB] Get:43 http://ftpmaster.internal/ubuntu/ trusty/main libencode-locale-perl all 1.03-1 [12.4 kB] Get:44 http://ftpmaster.internal/ubuntu/ trusty/main libhttp-date-perl all 6.02-1 [10.4 kB] Get:45 http://ftpmaster.internal/ubuntu/ trusty/main libfile-listing-perl all 6.04-1 [9774 B] Get:46 http://ftpmaster.internal/ubuntu/ trusty/main libhtml-tagset-perl all 3.20-2 [13.5 kB] Get:47 http://ftpmaster.internal/ubuntu/ trusty/main libhtml-parser-perl ppc64el 3.71-1build1 [94.9 kB] Get:48 http://ftpmaster.internal/ubuntu/ trusty/main libhtml-tree-perl all 5.03-1 [215 kB] Get:49 http://ftpmaster.internal/ubuntu/ trusty/main libio-html-perl all 1.00-1 [15.7 kB] Get:50 http://ftpmaster.internal/ubuntu/ trusty/main liblwp-mediatypes-perl all 6.02-1 [21.7 kB] Get:51 http://ftpmaster.internal/ubuntu/ trusty/main libhttp-message-perl all 6.06-1 [78.7 kB] Get:52 http://ftpmaster.internal/ubuntu/ trusty/main libhttp-cookies-perl all 6.00-2 [23.3 kB] Get:53 http://ftpmaster.internal/ubuntu/ trusty/main libhttp-negotiate-perl all 6.00-2 [13.4 kB] Get:54 http://ftpmaster.internal/ubuntu/ trusty/main libnet-ssleay-perl ppc64el 1.58-1 [231 kB] Get:55 http://ftpmaster.internal/ubuntu/ trusty/main libio-socket-ssl-perl all 1.965-1ubuntu1 [73.7 kB] Get:56 http://ftpmaster.internal/ubuntu/ trusty/main libnet-http-perl all 6.06-1 [24.2 kB] Get:57 http://ftpmaster.internal/ubuntu/ trusty/main liblwp-protocol-https-perl all 6.04-2 [7330 B] Get:58 http://ftpmaster.internal/ubuntu/ trusty/main libwww-robotrules-perl all 6.01-1 [14.1 kB] Get:59 http://ftpmaster.internal/ubuntu/ trusty/main libwww-perl all 6.05-2 [146 kB] Get:60 http://ftpmaster.internal/ubuntu/ trusty/main libxml-parser-perl ppc64el 2.41-1build3 [198 kB] Get:61 http://ftpmaster.internal/ubuntu/ trusty/main intltool all 0.50.2-2 [52.0 kB] Get:62 http://ftpmaster.internal/ubuntu/ trusty/main dh-translations all 119 [21.5 kB] Get:63 http://ftpmaster.internal/ubuntu/ trusty/main libpython2.7-stdlib ppc64el 2.7.6-5 [1770 kB] Get:64 http://ftpmaster.internal/ubuntu/ trusty/main python2.7 ppc64el 2.7.6-5 [193 kB] Get:65 http://ftpmaster.internal/ubuntu/ trusty/main python-minimal ppc64el 2.7.5-5ubuntu3 [27.6 kB] Get:66 http://ftpmaster.internal/ubuntu/ trusty/main libpython-stdlib ppc64el 2.7.5-5ubuntu3 [7020 B] Get:67 http://ftpmaster.internal/ubuntu/ trusty/main python ppc64el 2.7.5-5ubuntu3 [133 kB] Get:68 http://ftpmaster.internal/ubuntu/ trusty/main python-scour all 0.26-3 [46.5 kB] Get:69 http://ftpmaster.internal/ubuntu/ trusty/main cdbs all 0.4.122ubuntu2 [42.1 kB] Get:70 http://ftpmaster.internal/ubuntu/ trusty/main diffstat ppc64el 1.58-1 [24.4 kB] Get:71 http://ftpmaster.internal/ubuntu/ trusty/main libtinfo-dev ppc64el 5.9+20131221-1ubuntu1 [86.1 kB] Get:72 http://ftpmaster.internal/ubuntu/ trusty/main libncurses5-dev ppc64el 5.9+20131221-1ubuntu1 [187 kB] Get:73 http://ftpmaster.internal/ubuntu/ trusty/main quilt all 0.61-1 [271 kB] Get:74 http://ftpmaster.internal/ubuntu/ trusty/main zlib1g-dev ppc64el 1:1.2.8.dfsg-1ubuntu1 [166 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 18.4 MB in 23s (800 kB/s) Selecting previously unselected package libexpat1:ppc64el. (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../libexpat1_2.1.0-4ubuntu1_ppc64el.deb ... Unpacking libexpat1:ppc64el (2.1.0-4ubuntu1) ... Selecting previously unselected package libmagic1:ppc64el. Preparing to unpack .../libmagic1_1%3a5.14-2ubuntu1_ppc64el.deb ... Unpacking libmagic1:ppc64el (1:5.14-2ubuntu1) ... Selecting previously unselected package libssl1.0.0:ppc64el. Preparing to unpack .../libssl1.0.0_1.0.1f-1ubuntu1_ppc64el.deb ... Unpacking libssl1.0.0:ppc64el (1.0.1f-1ubuntu1) ... Selecting previously unselected package bash-completion. Preparing to unpack .../bash-completion_1%3a2.1-2ubuntu2_all.deb ... Unpacking bash-completion (1:2.1-2ubuntu2) ... Selecting previously unselected package libasprintf0c2:ppc64el. Preparing to unpack .../libasprintf0c2_0.18.3.1-1ubuntu2_ppc64el.deb ... Unpacking libasprintf0c2:ppc64el (0.18.3.1-1ubuntu2) ... Selecting previously unselected package libglib2.0-0:ppc64el. 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No schema files found: doing nothing. Setting up libpipeline1:ppc64el (1.2.6-2) ... Setting up libxml2:ppc64el (2.9.1+dfsg1-3ubuntu3) ... Setting up groff-base (1.22.2-5) ... Setting up bsdmainutils (9.0.5ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up man-db (2.6.6-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcroco3:ppc64el (0.6.8-2ubuntu1) ... Setting up libmpdec2:ppc64el (2.4.0-6) ... Setting up libpython3.4-minimal:ppc64el (3.4~rc1-1build1) ... Setting up mime-support (3.54ubuntu1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode Setting up libpython3.4-stdlib:ppc64el (3.4~rc1-1build1) ... Setting up libsigsegv2:ppc64el (2.10-2) ... Setting up libunistring0:ppc64el (0.9.3-5ubuntu3) ... Setting up libpython2.7-minimal:ppc64el (2.7.6-5) ... Setting up python2.7-minimal (2.7.6-5) ... Linking and byte-compiling packages for runtime python2.7... Setting up python3.4-minimal (3.4~rc1-1build1) ... Setting up python3.4 (3.4~rc1-1build1) ... Setting up python3-minimal (3.4~rc1-1) ... Setting up libpython3-stdlib:ppc64el (3.4~rc1-1) ... Setting up file (1:5.14-2ubuntu1) ... Setting up netbase (5.2) ... Setting up openssl (1.0.1f-1ubuntu1) ... Setting up ca-certificates (20130906ubuntu2) ... Setting up gettext-base (0.18.3.1-1ubuntu2) ... Setting up m4 (1.4.17-2ubuntu1) ... Setting up autoconf (2.69-4) ... Setting up autotools-dev (20130810.1) ... Setting up automake (1:1.14.1-2ubuntu1) ... update-alternatives: using /usr/bin/automake-1.14 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.18.3.1-1ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2ubuntu1) ... Setting up liburi-perl (1.60-1) ... Setting up libencode-locale-perl (1.03-1) ... Setting up libhttp-date-perl (6.02-1) ... Setting up libfile-listing-perl (6.04-1) ... Setting up libhtml-tagset-perl (3.20-2) ... Setting up libhtml-parser-perl (3.71-1build1) ... Setting up libhtml-tree-perl (5.03-1) ... Setting up libio-html-perl (1.00-1) ... Setting up liblwp-mediatypes-perl (6.02-1) ... Setting up libhttp-message-perl (6.06-1) ... Setting up libhttp-cookies-perl (6.00-2) ... Setting up libhttp-negotiate-perl (6.00-2) ... Setting up libnet-ssleay-perl (1.58-1) ... Setting up libio-socket-ssl-perl (1.965-1ubuntu1) ... Setting up libnet-http-perl (6.06-1) ... Setting up libwww-robotrules-perl (6.01-1) ... Setting up libpython2.7-stdlib:ppc64el (2.7.6-5) ... Setting up python2.7 (2.7.6-5) ... Setting up python-minimal (2.7.5-5ubuntu3) ... Setting up libpython-stdlib:ppc64el (2.7.5-5ubuntu3) ... Setting up python (2.7.5-5ubuntu3) ... Setting up python-scour (0.26-3) ... Setting up diffstat (1.58-1) ... Setting up libtinfo-dev:ppc64el (5.9+20131221-1ubuntu1) ... Setting up libncurses5-dev:ppc64el (5.9+20131221-1ubuntu1) ... Setting up quilt (0.61-1) ... Setting up zlib1g-dev:ppc64el (1:1.2.8.dfsg-1ubuntu1) ... Setting up libwww-perl (6.05-2) ... Setting up libxml-parser-perl (2.41-1build3) ... Setting up intltool (0.50.2-2) ... Setting up python3 (3.4~rc1-1) ... running python rtupdate hooks for python3.4... running python post-rtupdate hooks for python3.4... Setting up dh-python (1.20140128-1ubuntu2) ... Setting up apparmor-easyprof (2.8.0-0ubuntu38) ... Setting up dh-apparmor (2.8.0-0ubuntu38) ... Setting up debhelper (9.20131227ubuntu1) ... Setting up liblwp-protocol-https-perl (6.04-2) ... Setting up dh-translations (119) ... Setting up cdbs (0.4.122ubuntu2) ... Processing triggers for libc-bin (2.18-0ubuntu7) ... Processing triggers for ca-certificates (20130906ubuntu2) ... Updating certificates in /etc/ssl/certs... 164 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d....done. Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.18-0ubuntu7 make_3.81-8.2ubuntu3 dpkg-dev_1.17.5ubuntu4 gcc-4.8_4.8.2-16ubuntu1 g++-4.8_4.8.2-16ubuntu1 binutils_2.24-2ubuntu3.1 libstdc++-4.8-dev_4.8.2-16ubuntu1 libstdc++6_4.8.2-16ubuntu1 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::Quilt gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc dpkg-source: info: extracting samtools in samtools-0.1.19 dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz dpkg-source: info: applying fix_example_makefile.patch dpkg-source: info: applying fix_segfault_with_small_ref.patch dpkg-source: info: applying fix_coverage_cap.patch dpkg-buildpackage: source package samtools dpkg-buildpackage: source version 0.1.19-1 dpkg-buildpackage: source distribution unstable dpkg-source --before-build samtools-0.1.19 dpkg-buildpackage: host architecture ppc64el /usr/bin/fakeroot debian/rules clean test -x debian/rules rm -f debian/stamp-makefile-build debian/stamp-makefile-install /usr/bin/make -C . CFLAGS="-g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro" -k clean make[1]: Entering directory `/build/buildd/samtools-0.1.19' make[2]: Entering directory `/build/buildd/samtools-0.1.19' rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib make[2]: Leaving directory `/build/buildd/samtools-0.1.19' make[2]: Entering directory `/build/buildd/samtools-0.1.19/bcftools' rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so* make[2]: Leaving directory `/build/buildd/samtools-0.1.19/bcftools' make[2]: Entering directory `/build/buildd/samtools-0.1.19/misc' rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a make[2]: Leaving directory `/build/buildd/samtools-0.1.19/misc' make[1]: Leaving directory `/build/buildd/samtools-0.1.19' rm -f debian/stamp-makefile-check dh_clean /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/build/buildd/samtools-0.1.19' make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/build/buildd/samtools-0.1.19' if [ -d "." ]; then \ cd . && QUILT_PATCHES=/build/buildd/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \ fi Removing patch fix_coverage_cap.patch Restoring bam2depth.c Removing patch fix_segfault_with_small_ref.patch Restoring bam_plcmd.c Removing patch fix_example_makefile.patch Restoring examples/Makefile No patches applied rm -rf ./.pc rm -f debian/stamp-patch* rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf debian/rules build-arch test -x debian/rules mkdir -p "." /usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable /usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/build/buildd/samtools-0.1.19' make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/build/buildd/samtools-0.1.19' cd . && QUILT_PATCHES=/build/buildd/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2 Applying patch fix_example_makefile.patch patching file examples/Makefile Applying patch fix_segfault_with_small_ref.patch patching file bam_plcmd.c Applying patch fix_coverage_cap.patch patching file bam2depth.c Now at patch fix_coverage_cap.patch touch debian/stamp-patched /usr/bin/make -f debian/rules update-config make[1]: Entering directory `/build/buildd/samtools-0.1.19' make[1]: Nothing to be done for `update-config'. make[1]: Leaving directory `/build/buildd/samtools-0.1.19' /usr/bin/make -C . CFLAGS="-g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro" all all-recur razip lib make[1]: Entering directory `/build/buildd/samtools-0.1.19' make[2]: Entering directory `/build/buildd/samtools-0.1.19' gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o bgzf.c: In function 'worker_aux': bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] int i, tmp, stop = 0; ^ bgzf.c: In function 'bgzf_close': bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable] int ret, count, block_length; ^ gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o bam_index.c: In function 'bam_index_load_core': bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(magic, 1, 4, fp); ^ bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&idx->n, 4, 1, fp); ^ bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&size, 4, 1, fp); ^ bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&key, 4, 1, fp); ^ bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&p->n, 4, 1, fp); ^ bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p->list, 16, p->n, fp); ^ bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&index2->n, 4, 1, fp); ^ bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(index2->offset, index2->n, 8, fp); ^ gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o bam_pileup.c: In function 'resolve_cigar2': bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable] int k, is_head = 0; ^ gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o razf.c: In function 'razf_flush': razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^ razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^ razf.c: In function '_razf_write': razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^ razf.c: In function 'razf_close': razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &rz->in, sizeof(int64_t)); ^ razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &rz->out, sizeof(int64_t)); ^ razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &v64, sizeof(int64_t)); ^ razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &v64, sizeof(int64_t)); ^ razf.c: In function 'razf_end_flush': razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^ razf.c: In function 'save_zindex': razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] if(is_be) write(fd, &rz->index->size, sizeof(int)); ^ razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd, &v32, sizeof(uint32_t)); ^ razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); ^ razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); ^ gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o In file included from knetfile.c:46:0: knetfile.c: In function 'kftp_send_cmd': knetfile.h:9:37: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] #define netwrite(fd, ptr, len) write(fd, ptr, len) ^ knetfile.c:236:2: note: in expansion of macro 'netwrite' netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); ^ knetfile.c: In function 'khttp_connect_file': knetfile.h:9:37: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] #define netwrite(fd, ptr, len) write(fd, ptr, len) ^ knetfile.c:415:2: note: in expansion of macro 'netwrite' netwrite(fp->fd, buf, l); ^ gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o bam_reheader.c: In function 'bam_reheader': bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable] bam_header_t *old; ^ gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o kprobaln.c: In function 'kpa_glocal': kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable] int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; ^ gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o make[2]: Leaving directory `/build/buildd/samtools-0.1.19' make[2]: Entering directory `/build/buildd/samtools-0.1.19/bcftools' gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o bcf.c: In function 'bcf_fmt_core': bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable] int iPL = -1; ^ gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o bcfutils.c: In function 'bcf_fit_alt': bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable] int ipl=-1, igt=-1; ^ gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o em.c: In function 'bcf_em1': em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable] int i, n, n2; ^ gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o make[2]: Leaving directory `/build/buildd/samtools-0.1.19/bcftools' make[2]: Entering directory `/build/buildd/samtools-0.1.19/misc' make[2]: Nothing to be done for `lib'. make[2]: Leaving directory `/build/buildd/samtools-0.1.19/misc' gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o cut_target.c: In function 'main_cut_target': cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable] int c, tid, pos, n, lasttid = -1, lastpos = -1, l, max_l; ^ gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o gcc -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-Bsymbolic-functions -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread make[2]: Entering directory `/build/buildd/samtools-0.1.19' make[3]: Entering directory `/build/buildd/samtools-0.1.19' make[3]: Nothing to be done for `lib'. make[3]: Leaving directory `/build/buildd/samtools-0.1.19' make[3]: Entering directory `/build/buildd/samtools-0.1.19/bcftools' make[3]: Nothing to be done for `lib'. make[3]: Leaving directory `/build/buildd/samtools-0.1.19/bcftools' make[3]: Entering directory `/build/buildd/samtools-0.1.19/misc' make[3]: Nothing to be done for `lib'. make[3]: Leaving directory `/build/buildd/samtools-0.1.19/misc' gcc -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-Bsymbolic-functions -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread make[2]: Leaving directory `/build/buildd/samtools-0.1.19' make[2]: Entering directory `/build/buildd/samtools-0.1.19/bcftools' gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o gcc -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread make[2]: Leaving directory `/build/buildd/samtools-0.1.19/bcftools' make[2]: Entering directory `/build/buildd/samtools-0.1.19/misc' gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c md5.c: In function 'MD5Final': md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((uint32_t *) ctx->in)[14] = ctx->bits[0]; ^ md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((uint32_t *) ctx->in)[15] = ctx->bits[1]; ^ md5.c:155:26: warning: argument to 'sizeof' in 'memset' call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess] memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ ^ gcc -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o md5.c: In function 'MD5Final': md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((uint32_t *) ctx->in)[14] = ctx->bits[0]; ^ md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((uint32_t *) ctx->in)[15] = ctx->bits[1]; ^ md5.c:155:26: warning: argument to 'sizeof' in 'memset' call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess] memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ ^ gcc -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c gcc -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz gcc -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz gcc -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz gcc -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c gcc -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz gcc -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c gcc -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz gcc -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c gcc -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz make[2]: Leaving directory `/build/buildd/samtools-0.1.19/misc' gcc -c -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o razip.c: In function 'main': razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(f_dst, buffer, c); ^ razip.c: In function 'write_open': razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%c", &c); ^ gcc -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz make[1]: Nothing to be done for `lib'. make[1]: Leaving directory `/build/buildd/samtools-0.1.19' touch debian/stamp-makefile-build /usr/bin/make -C . CFLAGS="-g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro" -C examples all make[1]: Entering directory `/build/buildd/samtools-0.1.19/examples' ../samtools faidx ex1.fa ../samtools import ex1.fa.fai ex1.sam.gz ex1.bam [sam_header_read2] 2 sequences loaded. ../samtools index ex1.bam ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam [samopen] SAM header is present: 2 sequences. ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam [samopen] SAM header is present: 2 sequences. (echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg ../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam ../samtools rmdup ex1f.bam ex1f-rmduppe.bam [bam_rmdup_core] processing reference seq1... [bam_rmdup_core] processing reference seq2... [bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1' [bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b' ../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam [bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1' [bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b' ../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf [mpileup] 1 samples in 1 input files Set max per-file depth to 8000 gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread # You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa' make[1]: Leaving directory `/build/buildd/samtools-0.1.19/examples' touch debian/stamp-makefile-check /usr/bin/fakeroot debian/rules binary-arch test -x debian/rules dh_testroot dh_prep dh_installdirs -A mkdir -p "." /usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable /usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target Adding cdbs dependencies to debian/samtools.substvars dh_installdirs -psamtools Adding cdbs dependencies to debian/libbam-dev.substvars dh_installdirs -plibbam-dev dh_installdocs -psamtools ./NEWS ./AUTHORS dh_installexamples -psamtools dh_installman -psamtools dh_installinfo -psamtools dh_installmenu -psamtools dh_installcron -psamtools dh_installinit -psamtools dh_installdebconf -psamtools dh_installemacsen -psamtools dh_installcatalogs -psamtools dh_installpam -psamtools dh_installlogrotate -psamtools dh_installlogcheck -psamtools dh_installchangelogs -psamtools NEWS dh_installudev -psamtools dh_lintian -psamtools dh_bugfiles -psamtools dh_install -psamtools dh_link -psamtools dh_installmime -psamtools dh_installgsettings -psamtools install -m 644 bcftools/README /build/buildd/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools ln -s samtools.1.gz /build/buildd/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz dh_bash-completion dh_bash-completion: file-list parsing failed, installing as proper snippet dh_installdocs -plibbam-dev ./NEWS ./AUTHORS dh_installexamples -plibbam-dev dh_installman -plibbam-dev dh_installinfo -plibbam-dev dh_installmenu -plibbam-dev dh_installcron -plibbam-dev dh_installinit -plibbam-dev dh_installdebconf -plibbam-dev dh_installemacsen -plibbam-dev dh_installcatalogs -plibbam-dev dh_installpam -plibbam-dev dh_installlogrotate -plibbam-dev dh_installlogcheck -plibbam-dev dh_installchangelogs -plibbam-dev NEWS dh_installudev -plibbam-dev dh_lintian -plibbam-dev dh_bugfiles -plibbam-dev dh_install -plibbam-dev dh_link -plibbam-dev dh_installmime -plibbam-dev dh_installgsettings -plibbam-dev dh_strip -psamtools dh_strip debug symbol extraction: not enabling -a because /CurrentlyBuilding exists dh_strip debug symbol extraction: all non-arch-all packages for this build platform ppc64el: samtools libbam-dev dh_strip debug symbol extraction: packages to act on: samtools dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: building ddeb package dpkg-deb: building package `samtools-dbgsym' in `../samtools-dbgsym_0.1.19-1_ppc64el.ddeb'. dh_compress -psamtools -X .bam dh_fixperms -psamtools dh_makeshlibs -psamtools sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py dh_strip -plibbam-dev dh_strip debug symbol extraction: not enabling -a because /CurrentlyBuilding exists dh_strip debug symbol extraction: all non-arch-all packages for this build platform ppc64el: samtools libbam-dev dh_strip debug symbol extraction: packages to act on: libbam-dev dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 libbam-dev has no unstripped objects, ignoring find: `/build/buildd/samtools-0.1.19/debian/libbam-dev-dbgsym': No such file or directory /usr/bin/pkg_create_dbgsym: nothing in /build/buildd/samtools-0.1.19/debian/libbam-dev-dbgsym and no dbgdepends, ignoring dh_compress -plibbam-dev -X .bam dh_fixperms -plibbam-dev dh_makeshlibs -plibbam-dev dh_installdeb -psamtools dh_perl -psamtools dh_shlibdeps -psamtools dh_installdeb -plibbam-dev dh_perl -plibbam-dev dh_shlibdeps -plibbam-dev dh_gencontrol -psamtools dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends} # only call dh_scour for packages in main if grep -q '^Component:[[:space:]]*main' /CurrentlyBuilding 2>/dev/null; then dh_scour -psamtools ; fi dh_md5sums -psamtools dh_builddeb -psamtools -- -Z=xz INFO: pkgstriptranslations version 119 pkgstriptranslations: processing samtools (in debian/samtools); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/samtools/DEBIAN/control, package samtools, directory debian/samtools .. removing usr/share/doc/samtools/changelog.gz pkgstripfiles: Truncating usr/share/doc/samtools/changelog.Debian.gz to topmost ten records pkgstripfiles: PNG optimization for package samtools took 0 s dpkg-deb: warning: 'debian/samtools/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_ppc64el.deb'. dh_gencontrol -plibbam-dev dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends} dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe # only call dh_scour for packages in main if grep -q '^Component:[[:space:]]*main' /CurrentlyBuilding 2>/dev/null; then dh_scour -plibbam-dev ; fi dh_md5sums -plibbam-dev dh_builddeb -plibbam-dev -- -Z=xz INFO: pkgstriptranslations version 119 pkgstriptranslations: processing libbam-dev (in debian/libbam-dev); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libbam-dev/DEBIAN/control, package libbam-dev, directory debian/libbam-dev .. removing usr/share/doc/libbam-dev/changelog.gz pkgstripfiles: Truncating usr/share/doc/libbam-dev/changelog.Debian.gz to topmost ten records pkgstripfiles: PNG optimization for package libbam-dev took 0 s dpkg-deb: warning: 'debian/libbam-dev/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_ppc64el.deb'. dpkg-genchanges -B -mUbuntu Build Daemon >../samtools_0.1.19-1_ppc64el.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build samtools-0.1.19 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20140219-1908 Publishing debug debs. chroot-autobuild/build/buildd/samtools_0.1.19-1_ppc64el.deb: new debian package, version 2.0. size 570900 bytes: control archive=1975 bytes. 32 bytes, 1 lines conffiles 874 bytes, 17 lines control 2696 bytes, 41 lines md5sums Package: samtools Version: 0.1.19-1 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1499 Depends: libc6 (>= 2.17), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3) Suggests: python Section: science Priority: optional Homepage: http://samtools.sourceforge.net Description: processing sequence alignments in SAM and BAM formats Samtools is a set of utilities that manipulate nucleotide sequence alignments in the binary BAM format. It imports from and exports to the ascii SAM (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows to retrieve reads in any regions swiftly. It is designed to work on a stream, and is able to open a BAM (not SAM) file on a remote FTP or HTTP server. chroot-autobuild/build/buildd/libbam-dev_0.1.19-1_ppc64el.deb: new debian package, version 2.0. size 125256 bytes: control archive=964 bytes. 793 bytes, 18 lines control 643 bytes, 10 lines md5sums Package: libbam-dev Source: samtools Version: 0.1.19-1 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 487 Section: libdevel Priority: optional Homepage: http://samtools.sourceforge.net Description: manipulates nucleotide sequence alignments in BAM or SAM format The BAM library provides I/O and various operations on manipulating nucleotide sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence Alignment/Map) format. It now supports importing from or exporting to SAM, sorting, merging, generating pileup, and quickly retrieval of reads overlapped with a specified region. . This library is part of SAMtools. chroot-autobuild/build/buildd/samtools_0.1.19-1_ppc64el.deb: drwxr-xr-x root/root 0 2014-02-19 19:08 ./ drwxr-xr-x root/root 0 2014-02-19 19:08 ./usr/ drwxr-xr-x root/root 0 2014-02-19 19:08 ./usr/bin/ -rwxr-xr-x root/root 511312 2014-02-19 19:08 ./usr/bin/samtools -rwxr-xr-x root/root 195896 2014-02-19 19:08 ./usr/bin/bcftools -rwxr-xr-x root/root 30768 2014-02-19 19:08 ./usr/bin/razip drwxr-xr-x root/root 0 2014-02-19 19:08 ./usr/lib/ drwxr-xr-x root/root 0 2014-02-19 19:08 ./usr/lib/samtools/ -rwxr-xr-x root/root 204864 2014-02-19 19:08 ./usr/lib/samtools/bamcheck -rwxr-xr-x root/root 10232 2014-02-19 19:08 ./usr/lib/samtools/maq2sam-short -rwxr-xr-x root/root 10232 2014-02-19 19:08 ./usr/lib/samtools/maq2sam-long -rwxr-xr-x root/root 26856 2014-02-19 19:08 ./usr/lib/samtools/wgsim -rwxr-xr-x root/root 10224 2014-02-19 19:08 ./usr/lib/samtools/md5sum-lite -rwxr-xr-x root/root 26616 2014-02-19 19:08 ./usr/lib/samtools/ace2sam -rwxr-xr-x root/root 14320 2014-02-19 19:08 ./usr/lib/samtools/md5fa drwxr-xr-x root/root 0 2014-02-19 19:08 ./usr/share/ drwxr-xr-x root/root 0 2014-02-19 19:08 ./usr/share/samtools/ -rwxr-xr-x root/root 2022 2013-03-18 10:43 ./usr/share/samtools/psl2sam.pl -rwxr-xr-x root/root 5989 2013-03-18 10:43 ./usr/share/samtools/novo2sam.pl -rwxr-xr-x root/root 2696 2013-03-18 10:43 ./usr/share/samtools/soap2sam.pl -rwxr-xr-x root/root 29649 2013-03-18 10:43 ./usr/share/samtools/plot-bamcheck -rwxr-xr-x root/root 2685 2013-03-18 10:43 ./usr/share/samtools/r2plot.lua -rwxr-xr-x root/root 4996 2013-03-18 10:43 ./usr/share/samtools/interpolate_sam.pl -rwxr-xr-x root/root 21028 2013-03-18 10:43 ./usr/share/samtools/vcfutils.lua -rwxr-xr-x root/root 14299 2013-03-18 10:43 ./usr/share/samtools/samtools.pl -rwxr-xr-x root/root 15707 2013-03-18 10:43 ./usr/share/samtools/vcfutils.pl -rwxr-xr-x root/root 5778 2014-02-19 19:08 ./usr/share/samtools/varfilter.py -rwxr-xr-x root/root 18572 2013-03-18 10:43 ./usr/share/samtools/export2sam.pl -rwxr-xr-x root/root 2397 2013-03-18 10:43 ./usr/share/samtools/zoom2sam.pl -rwxr-xr-x root/root 2415 2013-03-18 10:43 ./usr/share/samtools/blast2sam.pl -rwxr-xr-x root/root 7881 2013-03-18 10:43 ./usr/share/samtools/sam2vcf.pl -rwxr-xr-x root/root 2112 2013-03-18 10:43 ./usr/share/samtools/bowtie2sam.pl -rwxr-xr-x root/root 2729 2013-03-18 10:43 ./usr/share/samtools/wgsim_eval.pl drwxr-xr-x root/root 0 2014-02-19 19:08 ./usr/share/man/ drwxr-xr-x root/root 0 2014-02-19 19:08 ./usr/share/man/man1/ -rw-r--r-- root/root 10654 2014-02-19 19:08 ./usr/share/man/man1/samtools.1.gz -rw-r--r-- root/root 430 2014-02-19 19:08 ./usr/share/man/man1/razip.1.gz drwxr-xr-x root/root 0 2014-02-19 19:08 ./usr/share/doc/ drwxr-xr-x root/root 0 2014-02-19 19:08 ./usr/share/doc/samtools/ -rw-r--r-- root/root 592 2012-01-08 21:59 ./usr/share/doc/samtools/reference -rw-r--r-- root/root 916 2013-03-18 10:43 ./usr/share/doc/samtools/AUTHORS -rw-r--r-- root/root 5012 2013-03-30 03:03 ./usr/share/doc/samtools/copyright drwxr-xr-x root/root 0 2014-02-19 19:08 ./usr/share/doc/samtools/examples/ -rw-r--r-- root/root 126580 2014-02-19 19:08 ./usr/share/doc/samtools/examples/ex1.bam -rw-r--r-- root/root 3225 2013-03-18 10:43 ./usr/share/doc/samtools/examples/ex1.fa -rw-r--r-- root/root 886 2013-03-18 10:43 ./usr/share/doc/samtools/examples/00README.txt -rw-r--r-- root/root 786 2013-03-18 10:43 ./usr/share/doc/samtools/examples/toy.sam -rw-r--r-- root/root 98 2013-03-18 10:43 ./usr/share/doc/samtools/examples/toy.fa -rw-r--r-- root/root 114565 2013-03-18 10:43 ./usr/share/doc/samtools/examples/ex1.sam.gz -rw-r--r-- root/root 1966 2014-02-19 19:08 ./usr/share/doc/samtools/README.bcftools -rw-r--r-- root/root 1693 2014-02-19 19:08 ./usr/share/doc/samtools/changelog.Debian.gz -rw-r--r-- root/root 1031 2012-01-08 21:59 ./usr/share/doc/samtools/README.Debian -rw-r--r-- root/root 10421 2013-03-18 10:43 ./usr/share/doc/samtools/NEWS.gz drwxr-xr-x root/root 0 2014-02-19 19:08 ./etc/ drwxr-xr-x root/root 0 2014-02-19 19:08 ./etc/bash_completion.d/ -rw-r--r-- root/root 576 2012-07-26 17:52 ./etc/bash_completion.d/samtools lrwxrwxrwx root/root 0 2014-02-19 19:08 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz chroot-autobuild/build/buildd/libbam-dev_0.1.19-1_ppc64el.deb: drwxr-xr-x root/root 0 2014-02-19 19:08 ./ drwxr-xr-x root/root 0 2014-02-19 19:08 ./usr/ drwxr-xr-x root/root 0 2014-02-19 19:08 ./usr/lib/ -rw-r--r-- root/root 376066 2014-02-19 19:08 ./usr/lib/libbam.a drwxr-xr-x root/root 0 2014-02-19 19:08 ./usr/include/ drwxr-xr-x root/root 0 2014-02-19 19:08 ./usr/include/samtools/ -rw-r--r-- root/root 3188 2013-03-18 10:43 ./usr/include/samtools/faidx.h -rw-r--r-- root/root 6326 2013-03-18 10:43 ./usr/include/samtools/bgzf.h -rw-r--r-- root/root 2688 2013-03-18 10:43 ./usr/include/samtools/sam.h -rw-r--r-- root/root 17815 2013-03-18 10:43 ./usr/include/samtools/khash.h -rw-r--r-- root/root 25788 2013-03-18 10:43 ./usr/include/samtools/bam.h drwxr-xr-x root/root 0 2014-02-19 19:08 ./usr/share/ drwxr-xr-x root/root 0 2014-02-19 19:08 ./usr/share/doc/ drwxr-xr-x root/root 0 2014-02-19 19:08 ./usr/share/doc/libbam-dev/ -rw-r--r-- root/root 916 2013-03-18 10:43 ./usr/share/doc/libbam-dev/AUTHORS -rw-r--r-- root/root 5012 2013-03-30 03:03 ./usr/share/doc/libbam-dev/copyright -rw-r--r-- root/root 1691 2014-02-19 19:08 ./usr/share/doc/libbam-dev/changelog.Debian.gz -rw-r--r-- root/root 10421 2013-03-18 10:43 ./usr/share/doc/libbam-dev/NEWS.gz samtools_0.1.19-1_ppc64el.changes: Format: 1.8 Date: Sat, 30 Mar 2013 17:31:47 +0900 Source: samtools Binary: samtools libbam-dev Architecture: ppc64el Version: 0.1.19-1 Distribution: trusty Urgency: low Maintainer: Ubuntu Build Daemon Changed-By: Charles Plessy Description: libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format samtools - processing sequence alignments in SAM and BAM formats Changes: samtools (0.1.19-1) unstable; urgency=low . cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua. 2f2d5c5 debian/copyright: collapsed copyright notices from main holders. e194f9e Removed fix_float_tag.patch, corrected upstream. 9c0e543 Refreshed patches. 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch. 8d8550e example/Makefile: pass -lpthread when compiling calDepth. fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS. 6f75b48 debian/control: normalised with cme. e13bb5e debian/control: normalised VCS URLs. a1b1b00 debian/control: deleted DM-Upload-Allowed field. ddcd54e Use NEWS as upstream changelog. 81ad760 Conforms to Policy version 3.9.4. Checksums-Sha1: 531554f5263b8f2d25869496dca0b052be40eb80 570900 samtools_0.1.19-1_ppc64el.deb cf2672de6b00ab9f487be140e45517771ba6f938 125256 libbam-dev_0.1.19-1_ppc64el.deb Checksums-Sha256: d098c45b02445434358571ea90775c59f3512ed4a093d887263b2975c25a910d 570900 samtools_0.1.19-1_ppc64el.deb 2f428bcee6f4c9640883681975ea6742cbe79088fd659b0316323cf9d562cf37 125256 libbam-dev_0.1.19-1_ppc64el.deb Files: 38fe8649896ef6d6063e19e6c6815a18 570900 science optional samtools_0.1.19-1_ppc64el.deb b3fc4221ea74235560774171ff95412a 125256 libdevel optional libbam-dev_0.1.19-1_ppc64el.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20140219-1908 Build needed 00:00:52, 17356k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-5605334'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-5605334/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-5605334'] Unmounting chroot for build PACKAGEBUILD-5605334... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-5605334'] Removing build PACKAGEBUILD-5605334