RUN: /bin/echo ['echo', 'Forking build subprocess...'] Forking build subprocess... RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', '1410695-2906951', '/home/buildd/filecache-default/2ca9a4de8d72258f0a15957452446341c2d9357e'] Synching the system clock with the buildd NTP service... 23 Dec 16:39:32 ntpdate[2658]: adjust time server 10.211.37.1 offset -0.000017 sec Unpacking chroot for build 1410695-2906951 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', '1410695-2906951'] Mounting chroot for build 1410695-2906951 RUN: /usr/share/launchpad-buildd/slavebin/apply-ogre-model ['apply-ogre-model', '1410695-2906951', 'universe'] Attempting OGRE for universe in build-1410695-2906951 No OGRE sources.list found. RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', '1410695-2906951', 'deb http://ftpmaster.internal/ubuntu lucid main universe'] Overriding sources.list in build-1410695-2906951 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', '1410695-2906951'] Updating debian chroot for build 1410695-2906951 Get:1 http://ftpmaster.internal lucid Release.gpg [189B] Get:2 http://ftpmaster.internal lucid Release [65.9kB] Get:3 http://ftpmaster.internal lucid/main Packages [1367kB] Get:4 http://ftpmaster.internal lucid/universe Packages [5265kB] Fetched 6698kB in 8s (757kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: libplymouth2 libpng12-0 The following packages will be upgraded: apt apt-transport-https binutils bsdutils cpp-4.4 g++-4.4 gcc-4.4 gcc-4.4-base gcc-4.4-multilib ifupdown lib64gcc1 lib64gomp1 libblkid1 libgcc1 libgnutls26 libgomp1 libstdc++6 libstdc++6-4.4-dev libudev0 libuuid1 linux-libc-dev lsb-base mount mountall procps sed tzdata util-linux 28 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 0B/16.8MB of archives. After this operation, 651kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! mount sed lsb-base tzdata util-linux bsdutils libpng12-0 libplymouth2 mountall lib64gcc1 libgomp1 lib64gomp1 cpp-4.4 gcc-4.4-base libgcc1 gcc-4.4-multilib gcc-4.4 g++-4.4 libstdc++6-4.4-dev libstdc++6 binutils apt libuuid1 libblkid1 ifupdown libgnutls26 libudev0 procps apt-transport-https linux-libc-dev debconf: delaying package configuration, since apt-utils is not installed Authentication warning overridden. (Reading database ... 12891 files and directories currently installed.) Preparing to replace mount 2.16-1ubuntu5 (using .../mount_2.16-1ubuntu6_sparc.deb) ... Unpacking replacement mount ... Setting up mount (2.16-1ubuntu6) ... (Reading database ... 12891 files and directories currently installed.) Preparing to replace sed 4.2.1-4 (using .../archives/sed_4.2.1-6_sparc.deb) ... Unpacking replacement sed ... Setting up sed (4.2.1-6) ... (Reading database ... 12891 files and directories currently installed.) Preparing to replace lsb-base 4.0-0ubuntu6 (using .../lsb-base_4.0-0ubuntu7_all.deb) ... Unpacking replacement lsb-base ... Setting up lsb-base (4.0-0ubuntu7) ... (Reading database ... 12891 files and directories currently installed.) Preparing to replace tzdata 2009s-0ubuntu1 (using .../tzdata_2009s-1_all.deb) ... Unpacking replacement tzdata ... Setting up tzdata (2009s-1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Dec 23 16:39:59 UTC 2009. Universal Time is now: Wed Dec 23 16:39:59 UTC 2009. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 12891 files and directories currently installed.) Preparing to replace util-linux 2.16-1ubuntu5 (using .../util-linux_2.16-1ubuntu6_sparc.deb) ... install-info: warning: maintainer scripts should not call install-info anymore, install-info: warning: this is handled now by a dpkg trigger provided by the install-info: warning: install-info package; package util-linux should be updated. Unpacking replacement util-linux ... Setting up util-linux (2.16-1ubuntu6) ... install-info: warning: maintainer scripts should not call install-info anymore, install-info: warning: this is handled now by a dpkg trigger provided by the install-info: warning: install-info package; package util-linux should be updated. (Reading database ... 12891 files and directories currently installed.) Preparing to replace bsdutils 1:2.16-1ubuntu5 (using .../bsdutils_1%3a2.16-1ubuntu6_sparc.deb) ... Unpacking replacement bsdutils ... Setting up bsdutils (1:2.16-1ubuntu6) ... Selecting previously deselected package libpng12-0. (Reading database ... 12891 files and directories currently installed.) Unpacking libpng12-0 (from .../libpng12-0_1.2.41-1_sparc.deb) ... Selecting previously deselected package libplymouth2. Unpacking libplymouth2 (from .../libplymouth2_0.8.0~-6_sparc.deb) ... Setting up libpng12-0 (1.2.41-1) ... Setting up libplymouth2 (0.8.0~-6) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12914 files and directories currently installed.) Preparing to replace mountall 1.1 (using .../mountall_2.2_sparc.deb) ... Unpacking replacement mountall ... Preparing to replace lib64gcc1 1:4.4.2-5ubuntu1 (using .../lib64gcc1_1%3a4.4.2-6ubuntu1_sparc.deb) ... Unpacking replacement lib64gcc1 ... Preparing to replace libgomp1 4.4.2-5ubuntu1 (using .../libgomp1_4.4.2-6ubuntu1_sparc.deb) ... Unpacking replacement libgomp1 ... Preparing to replace lib64gomp1 4.4.2-5ubuntu1 (using .../lib64gomp1_4.4.2-6ubuntu1_sparc.deb) ... Unpacking replacement lib64gomp1 ... Preparing to replace cpp-4.4 4.4.2-5ubuntu1 (using .../cpp-4.4_4.4.2-6ubuntu1_sparc.deb) ... Unpacking replacement cpp-4.4 ... Preparing to replace gcc-4.4-base 4.4.2-5ubuntu1 (using .../gcc-4.4-base_4.4.2-6ubuntu1_sparc.deb) ... Unpacking replacement gcc-4.4-base ... Setting up gcc-4.4-base (4.4.2-6ubuntu1) ... (Reading database ... 12925 files and directories currently installed.) Preparing to replace libgcc1 1:4.4.2-5ubuntu1 (using .../libgcc1_1%3a4.4.2-6ubuntu1_sparc.deb) ... Unpacking replacement libgcc1 ... Setting up libgcc1 (1:4.4.2-6ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12925 files and directories currently installed.) Preparing to replace gcc-4.4-multilib 4.4.2-5ubuntu1 (using .../gcc-4.4-multilib_4.4.2-6ubuntu1_sparc.deb) ... Unpacking replacement gcc-4.4-multilib ... Preparing to replace gcc-4.4 4.4.2-5ubuntu1 (using .../gcc-4.4_4.4.2-6ubuntu1_sparc.deb) ... Unpacking replacement gcc-4.4 ... Preparing to replace g++-4.4 4.4.2-5ubuntu1 (using .../g++-4.4_4.4.2-6ubuntu1_sparc.deb) ... Unpacking replacement g++-4.4 ... Preparing to replace libstdc++6-4.4-dev 4.4.2-5ubuntu1 (using .../libstdc++6-4.4-dev_4.4.2-6ubuntu1_sparc.deb) ... Unpacking replacement libstdc++6-4.4-dev ... Preparing to replace libstdc++6 4.4.2-5ubuntu1 (using .../libstdc++6_4.4.2-6ubuntu1_sparc.deb) ... Unpacking replacement libstdc++6 ... Setting up libstdc++6 (4.4.2-6ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12925 files and directories currently installed.) Preparing to replace binutils 2.20-4ubuntu3 (using .../binutils_2.20-4ubuntu4_sparc.deb) ... Unpacking replacement binutils ... Preparing to replace apt 0.7.24ubuntu1 (using .../apt_0.7.25ubuntu2_sparc.deb) ... Unpacking replacement apt ... Setting up apt (0.7.25ubuntu2) ... Installing new version of config file /etc/logrotate.d/apt ... Installing new version of config file /etc/cron.daily/apt ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12929 files and directories currently installed.) Preparing to replace libuuid1 2.16-1ubuntu5 (using .../libuuid1_2.16-1ubuntu6_sparc.deb) ... Unpacking replacement libuuid1 ... Setting up libuuid1 (2.16-1ubuntu6) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12929 files and directories currently installed.) Preparing to replace libblkid1 2.16-1ubuntu5 (using .../libblkid1_2.16-1ubuntu6_sparc.deb) ... Unpacking replacement libblkid1 ... Setting up libblkid1 (2.16-1ubuntu6) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12929 files and directories currently installed.) Preparing to replace ifupdown 0.6.8ubuntu23 (using .../ifupdown_0.6.8ubuntu25_sparc.deb) ... Unpacking replacement ifupdown ... Preparing to replace libgnutls26 2.8.4-2 (using .../libgnutls26_2.8.5-2_sparc.deb) ... Unpacking replacement libgnutls26 ... Preparing to replace libudev0 149-3 (using .../libudev0_149-5_sparc.deb) ... Unpacking replacement libudev0 ... Preparing to replace procps 1:3.2.8-1ubuntu3 (using .../procps_1%3a3.2.8-1ubuntu4_sparc.deb) ... Unpacking replacement procps ... Preparing to replace apt-transport-https 0.7.24ubuntu1 (using .../apt-transport-https_0.7.25ubuntu2_sparc.deb) ... Unpacking replacement apt-transport-https ... Preparing to replace linux-libc-dev 2.6.32-8.12 (using .../linux-libc-dev_2.6.32-9.13_sparc.deb) ... Unpacking replacement linux-libc-dev ... Setting up lib64gcc1 (1:4.4.2-6ubuntu1) ... Setting up libgomp1 (4.4.2-6ubuntu1) ... Setting up lib64gomp1 (4.4.2-6ubuntu1) ... Setting up cpp-4.4 (4.4.2-6ubuntu1) ... Setting up binutils (2.20-4ubuntu4) ... Setting up gcc-4.4 (4.4.2-6ubuntu1) ... Setting up gcc-4.4-multilib (4.4.2-6ubuntu1) ... Setting up ifupdown (0.6.8ubuntu25) ... ifupdown.postinst: Warning: No 'iface lo' definition found in /etc/network/interfaces ifupdown.postinst: Warning: No 'auto lo' statement found in /etc/network/interfaces Setting up libgnutls26 (2.8.5-2) ... Setting up libudev0 (149-5) ... Setting up procps (1:3.2.8-1ubuntu4) ... Installing new version of config file /etc/sysctl.d/README ... Installing new version of config file /etc/sysctl.conf ... Setting up apt-transport-https (0.7.25ubuntu2) ... Setting up linux-libc-dev (2.6.32-9.13) ... Setting up mountall (2.2) ... Installing new version of config file /etc/init/mountall.conf ... Installing new version of config file /etc/init/mountall-reboot.conf ... Installing new version of config file /etc/init/mountall-shell.conf ... Setting up libstdc++6-4.4-dev (4.4.2-6ubuntu1) ... Setting up g++-4.4 (4.4.2-6ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', '1410695-2906951', '--nolog', '--batch', '--archive=ubuntu', '--purpose=PRIMARY', '--dist=lucid', '--comp=universe', 'samtools_0.1.7a~dfsg-1.dsc'] Initiating build 1410695-2906951 with 0 processor cores. Automatic build of samtools_0.1.7a~dfsg-1 on sejong by sbuild/sparc 1.170.5 Build started at 20091223-1640 ****************************************************************************** samtools_0.1.7a~dfsg-1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev Checking for already installed source dependencies... debhelper: missing cdbs: 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 cdbs libncurses5-dev zlib1g-dev Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: autoconf automake autotools-dev bsdmainutils fdupes file gettext gettext-base groff-base html2text intltool intltool-debian libcroco3 libexpat1 libglib2.0-0 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libmagic1 libpcre3 liburi-perl libwww-perl libxml-parser-perl libxml2 m4 man-db po-debconf Suggested packages: autoconf2.13 autoconf-archive gnu-standards autoconf-doc libtool wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc groff libdata-dump-perl libcrypt-ssleay-perl libio-socket-ssl-perl less www-browser libmail-box-perl Recommended packages: curl wget lynx cvs libglib2.0-data shared-mime-info libmailtools-perl libhtml-format-perl libcompress-bzip2-perl xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autotools-dev bsdmainutils cdbs debhelper fdupes file gettext gettext-base groff-base html2text intltool intltool-debian libcroco3 libexpat1 libglib2.0-0 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libmagic1 libncurses5-dev libpcre3 liburi-perl libwww-perl libxml-parser-perl libxml2 m4 man-db po-debconf zlib1g-dev 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 0B/13.3MB of archives. After this operation, 43.1MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libmagic1 file libpcre3 libglib2.0-0 libxml2 bsdmainutils gettext-base groff-base libexpat1 liburi-perl libhtml-tagset-perl libhtml-parser-perl libhtml-tree-perl libwww-perl libxml-parser-perl man-db m4 autoconf autotools-dev automake html2text libcroco3 gettext intltool-debian po-debconf debhelper fdupes intltool cdbs libncurses5-dev zlib1g-dev debconf: delaying package configuration, since apt-utils is not installed Authentication warning overridden. Selecting previously deselected package libmagic1. (Reading database ... 12930 files and directories currently installed.) Unpacking libmagic1 (from .../libmagic1_5.03-4ubuntu1_sparc.deb) ... Selecting previously deselected package file. Unpacking file (from .../file_5.03-4ubuntu1_sparc.deb) ... Selecting previously deselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_7.8-3_sparc.deb) ... Selecting previously deselected package libglib2.0-0. Unpacking libglib2.0-0 (from .../libglib2.0-0_2.23.0-1ubuntu3_sparc.deb) ... Selecting previously deselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.6.dfsg-1ubuntu1_sparc.deb) ... Selecting previously deselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.0.1ubuntu1_sparc.deb) ... Selecting previously deselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.17-8ubuntu2_sparc.deb) ... Selecting previously deselected package groff-base. Unpacking groff-base (from .../groff-base_1.20.1-6_sparc.deb) ... Selecting previously deselected package libexpat1. Unpacking libexpat1 (from .../libexpat1_2.0.1-4ubuntu1_sparc.deb) ... Selecting previously deselected package liburi-perl. Unpacking liburi-perl (from .../liburi-perl_1.50-1ubuntu1_all.deb) ... Selecting previously deselected package libhtml-tagset-perl. Unpacking libhtml-tagset-perl (from .../libhtml-tagset-perl_3.20-2_all.deb) ... Selecting previously deselected package libhtml-parser-perl. Unpacking libhtml-parser-perl (from .../libhtml-parser-perl_3.64-1_sparc.deb) ... Selecting previously deselected package libhtml-tree-perl. Unpacking libhtml-tree-perl (from .../libhtml-tree-perl_3.23-1_all.deb) ... Selecting previously deselected package libwww-perl. Unpacking libwww-perl (from .../libwww-perl_5.831-1_all.deb) ... Selecting previously deselected package libxml-parser-perl. Unpacking libxml-parser-perl (from .../libxml-parser-perl_2.36-1.1build2_sparc.deb) ... Selecting previously deselected package man-db. Unpacking man-db (from .../man-db_2.5.6-4_sparc.deb) ... Selecting previously deselected package m4. Unpacking m4 (from .../archives/m4_1.4.13-3_sparc.deb) ... Selecting previously deselected package autoconf. Unpacking autoconf (from .../autoconf_2.65-3ubuntu1_all.deb) ... Selecting previously deselected package autotools-dev. Unpacking autotools-dev (from .../autotools-dev_20090611.1_all.deb) ... Selecting previously deselected package automake. Unpacking automake (from .../automake_1%3a1.11-1_all.deb) ... Selecting previously deselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-14_sparc.deb) ... Selecting previously deselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.2-1_sparc.deb) ... Selecting previously deselected package gettext. Unpacking gettext (from .../gettext_0.17-8ubuntu2_sparc.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_all.deb) ... Selecting previously deselected package debhelper. Unpacking debhelper (from .../debhelper_7.4.10ubuntu1_all.deb) ... Selecting previously deselected package fdupes. Unpacking fdupes (from .../fdupes_1.50-PR2-2_sparc.deb) ... Selecting previously deselected package intltool. Unpacking intltool (from .../intltool_0.41.0-0ubuntu1_all.deb) ... Selecting previously deselected package cdbs. Unpacking cdbs (from .../cdbs_0.4.62+nmu1ubuntu2_all.deb) ... Selecting previously deselected package libncurses5-dev. Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20090803-2ubuntu2_sparc.deb) ... Selecting previously deselected package zlib1g-dev. Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.3.dfsg-15ubuntu1_sparc.deb) ... Setting up libmagic1 (5.03-4ubuntu1) ... Setting up file (5.03-4ubuntu1) ... Setting up libpcre3 (7.8-3) ... Setting up libglib2.0-0 (2.23.0-1ubuntu3) ... Setting up libxml2 (2.7.6.dfsg-1ubuntu1) ... Setting up bsdmainutils (8.0.1ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. Setting up gettext-base (0.17-8ubuntu2) ... Setting up groff-base (1.20.1-6) ... Setting up libexpat1 (2.0.1-4ubuntu1) ... Setting up liburi-perl (1.50-1ubuntu1) ... Setting up libhtml-tagset-perl (3.20-2) ... Setting up libhtml-parser-perl (3.64-1) ... Setting up libhtml-tree-perl (3.23-1) ... Setting up libwww-perl (5.831-1) ... Setting up libxml-parser-perl (2.36-1.1build2) ... Setting up man-db (2.5.6-4) ... Building database of manual pages ... Setting up m4 (1.4.13-3) ... Setting up autoconf (2.65-3ubuntu1) ... Setting up autotools-dev (20090611.1) ... Setting up automake (1:1.11-1) ... update-alternatives: using /usr/bin/automake-1.11 to provide /usr/bin/automake (automake) in auto mode. Setting up html2text (1.3.2a-14) ... Setting up libcroco3 (0.6.2-1) ... Setting up gettext (0.17-8ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16) ... Setting up debhelper (7.4.10ubuntu1) ... Setting up fdupes (1.50-PR2-2) ... Setting up intltool (0.41.0-0ubuntu1) ... Setting up cdbs (0.4.62+nmu1ubuntu2) ... Setting up libncurses5-dev (5.7+20090803-2ubuntu2) ... Setting up zlib1g-dev (1:1.2.3.3.dfsg-15ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.10.2-2ubuntu3 make_3.81-7 dpkg-dev_1.15.4.1ubuntu1 g++-4.4_4.4.2-6ubuntu1 gcc-4.4_4.4.2-6ubuntu1 binutils_2.20-4ubuntu4 libstdc++6_4.4.2-6ubuntu1 libstdc++6-4.4-dev_4.4.2-6ubuntu1 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt gpgv: Signature made Wed Nov 18 05:34:48 2009 UTC using DSA key ID BAFEC7F2 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./samtools_0.1.7a~dfsg-1.dsc dpkg-source: info: extracting samtools in samtools-0.1.7a~dfsg dpkg-source: info: unpacking samtools_0.1.7a~dfsg.orig.tar.bz2 dpkg-source: info: unpacking samtools_0.1.7a~dfsg-1.debian.tar.gz dpkg-buildpackage: set CFLAGS to default value: -g -O2 dpkg-buildpackage: set CPPFLAGS to default value: dpkg-buildpackage: set LDFLAGS to default value: -Wl,-Bsymbolic-functions dpkg-buildpackage: set FFLAGS to default value: -g -O2 dpkg-buildpackage: set CXXFLAGS to default value: -g -O2 dpkg-buildpackage: source package samtools dpkg-buildpackage: source version 0.1.7a~dfsg-1 dpkg-buildpackage: host architecture sparc /usr/bin/fakeroot debian/rules clean test -x debian/rules dh_testroot /usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="-Wl,-Bsymbolic-functions" -k clean make[1]: Entering directory `/build/buildd/samtools-0.1.7a~dfsg' make[2]: Entering directory `/build/buildd/samtools-0.1.7a~dfsg' rm -fr gmon.out *.o a.out *.dSYM razip samtools *~ *.a make[2]: Leaving directory `/build/buildd/samtools-0.1.7a~dfsg' make[2]: Entering directory `/build/buildd/samtools-0.1.7a~dfsg/misc' rm -fr gmon.out *.o a.out *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a make[2]: Leaving directory `/build/buildd/samtools-0.1.7a~dfsg/misc' make[1]: Leaving directory `/build/buildd/samtools-0.1.7a~dfsg' rm -f debian/stamp-makefile-build rm -f debian/stamp-makefile-check dh_clean 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 debian/rules build test -x debian/rules mkdir -p "." /usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="-Wl,-Bsymbolic-functions" all all-recur razip lib make[1]: Entering directory `/build/buildd/samtools-0.1.7a~dfsg' gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bgzf.c -o bgzf.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 kstring.c -o kstring.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_aux.c -o bam_aux.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam.c -o bam.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_import.c -o bam_import.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 sam.c -o sam.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_index.c -o bam_index.o bam_index.c: In function 'bam_index_load_core': bam_index.c:276: warning: ignoring return value of 'fread', declared with attribute warn_unused_result bam_index.c:283: warning: ignoring return value of 'fread', declared with attribute warn_unused_result bam_index.c:296: warning: ignoring return value of 'fread', declared with attribute warn_unused_result bam_index.c:299: warning: ignoring return value of 'fread', declared with attribute warn_unused_result bam_index.c:303: warning: ignoring return value of 'fread', declared with attribute warn_unused_result bam_index.c:307: warning: ignoring return value of 'fread', declared with attribute warn_unused_result bam_index.c:317: warning: ignoring return value of 'fread', declared with attribute warn_unused_result bam_index.c:321: warning: ignoring return value of 'fread', declared with attribute warn_unused_result gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_pileup.c -o bam_pileup.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_lpileup.c -o bam_lpileup.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_md.c -o bam_md.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 glf.c -o glf.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 razf.c -o razf.o razf.c: In function 'save_zindex': razf.c:96: warning: ignoring return value of 'write', declared with attribute warn_unused_result razf.c:99: warning: ignoring return value of 'write', declared with attribute warn_unused_result razf.c:106: warning: ignoring return value of 'write', declared with attribute warn_unused_result razf.c:107: warning: ignoring return value of 'write', declared with attribute warn_unused_result razf.c: In function '_razf_write': razf.c:201: warning: ignoring return value of 'write', declared with attribute warn_unused_result razf.c: In function 'razf_flush': razf.c:221: warning: ignoring return value of 'write', declared with attribute warn_unused_result razf.c:234: warning: ignoring return value of 'write', declared with attribute warn_unused_result razf.c: In function 'razf_end_flush': razf.c:258: warning: ignoring return value of 'write', declared with attribute warn_unused_result razf.c: In function 'razf_close': razf.c:804: warning: ignoring return value of 'write', declared with attribute warn_unused_result razf.c:805: warning: ignoring return value of 'write', declared with attribute warn_unused_result razf.c:808: warning: ignoring return value of 'write', declared with attribute warn_unused_result razf.c:810: warning: ignoring return value of 'write', declared with attribute warn_unused_result gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 faidx.c -o faidx.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 knetfile.c -o knetfile.o knetfile.c: In function 'kftp_send_cmd': knetfile.c:239: warning: ignoring return value of 'write', declared with attribute warn_unused_result knetfile.c: In function 'khttp_connect_file': knetfile.c:418: warning: ignoring return value of 'write', declared with attribute warn_unused_result gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_sort.c -o bam_sort.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 sam_header.c -o sam_header.o ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_tview.c -o bam_tview.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_maqcns.c -o bam_maqcns.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_plcmd.c -o bam_plcmd.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 sam_view.c -o sam_view.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_rmdup.c -o bam_rmdup.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_rmdupse.c -o bam_rmdupse.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_mate.c -o bam_mate.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_stat.c -o bam_stat.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_color.c -o bam_color.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bamtk.c -o bamtk.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 kaln.c -o kaln.o gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -lm -lcurses -lz -L. -lbam make[2]: Entering directory `/build/buildd/samtools-0.1.7a~dfsg' gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -lm -lcurses -lz -L. -lbam make[2]: Leaving directory `/build/buildd/samtools-0.1.7a~dfsg' make[2]: Entering directory `/build/buildd/samtools-0.1.7a~dfsg/misc' gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 md5.c -o md5.o gcc -g -O2 -g -Wall -O2 -fPIC -c -I.. -o md5fa.o md5fa.c gcc -g -O2 -g -Wall -O2 -fPIC -o md5fa md5.o md5fa.o -lz gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 wgsim.c -o wgsim.o gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm make[2]: Leaving directory `/build/buildd/samtools-0.1.7a~dfsg/misc' gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 razip.c -o razip.o razip.c: In function 'write_open': razip.c:32: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result razip.c: In function 'main': razip.c:131: warning: ignoring return value of 'write', declared with attribute warn_unused_result gcc -g -O2 -g -Wall -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz make[1]: Nothing to be done for `lib'. make[1]: Leaving directory `/build/buildd/samtools-0.1.7a~dfsg' touch debian/stamp-makefile-build /usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="-Wl,-Bsymbolic-functions" -C examples all make[1]: Entering directory `/build/buildd/samtools-0.1.7a~dfsg/examples' ../samtools faidx ex1.fa ../samtools import ex1.fa.fai ex1.sam.gz ex1.bam [sam_header_read2] 2 sequences loaded. make[1]: *** [ex1.bam] Bus error make[1]: *** Deleting file `ex1.bam' make[1]: Leaving directory `/build/buildd/samtools-0.1.7a~dfsg/examples' make: *** [debian/stamp-makefile-check] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ****************************************************************************** Build finished at 20091223-1641 FAILED [dpkg-buildpackage died] Purging chroot-autobuild/build/buildd/samtools-0.1.7a~dfsg ------------------------------------------------------------------------------ /usr/bin/sudo dpkg --purge intltool-debian groff-base libglib2.0-0 m4 gettext file zlib1g-dev libhtml-parser-perl intltool cdbs libwww-perl liburi-perl html2text gettext-base debhelper libhtml-tree-perl autotools-dev po-debconf libncurses5-dev libxml-parser-perl libcroco3 libmagic1 libhtml-tagset-perl libxml2 libexpat1 bsdmainutils fdupes automake libpcre3 man-db autoconf (Reading database ... 15800 files and directories currently installed.) Removing zlib1g-dev ... Removing cdbs ... Removing debhelper ... Removing po-debconf ... Removing libncurses5-dev ... Removing fdupes ... Removing man-db ... Purging configuration files for man-db ... Removing intltool-debian ... Removing groff-base ... Purging configuration files for groff-base ... Removing intltool ... Removing html2text ... Purging configuration files for html2text ... Removing libxml-parser-perl ... Removing libexpat1 ... Purging configuration files for libexpat1 ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing automake ... Removing autoconf ... Purging configuration files for autoconf ... Removing m4 ... Removing gettext ... Removing file ... Purging configuration files for file ... Removing libwww-perl ... Removing gettext-base ... Removing libhtml-tree-perl ... Removing autotools-dev ... Removing libcroco3 ... Purging configuration files for libcroco3 ... Removing libmagic1 ... Purging configuration files for libmagic1 ... Removing libxml2 ... Purging configuration files for libxml2 ... Removing libglib2.0-0 ... Purging configuration files for libglib2.0-0 ... Removing libhtml-parser-perl ... Removing liburi-perl ... Removing libhtml-tagset-perl ... Removing libpcre3 ... Purging configuration files for libpcre3 ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place ****************************************************************************** Finished at 20091223-1641 Build needed 00:00:44, 3436k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', '1410695-2906951'] Scanning for processes to kill in build /home/buildd/build-1410695-2906951/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', '1410695-2906951'] Unmounting chroot for build 1410695-2906951... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', '1410695-2906951'] Removing build 1410695-2906951