RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: 2.6.32-40-powerpc64-smp #87-Ubuntu SMP Tue Mar 6 13:11:42 UTC 2012 ppc64 Buildd toolchain package versions: launchpad-buildd_113~0.IS.08.04 python-lpbuildd_113~0.IS.08.04 bzr_2.4.0-0ubuntu2~9.IS.10.04.3. Syncing the system clock with the buildd NTP service... 6 May 15:28:51 ntpdate[28744]: adjust time server 10.211.37.1 offset -0.000040 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'ed9f1489de3e980f4f0a5b961c735485be8b8e4d', '/home/buildd/filecache-default/4ae1fba19e79520104eb5dac391cb38388a005f0'] Unpacking chroot for build ed9f1489de3e980f4f0a5b961c735485be8b8e4d RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'ed9f1489de3e980f4f0a5b961c735485be8b8e4d'] Mounting chroot for build ed9f1489de3e980f4f0a5b961c735485be8b8e4d RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'ed9f1489de3e980f4f0a5b961c735485be8b8e4d', 'deb http://ftpmaster.internal/ubuntu quantal main universe'] Overriding sources.list in build-ed9f1489de3e980f4f0a5b961c735485be8b8e4d RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'ed9f1489de3e980f4f0a5b961c735485be8b8e4d', 'powerpc'] Updating debian chroot for build ed9f1489de3e980f4f0a5b961c735485be8b8e4d Ign http://ftpmaster.internal quantal InRelease Get:1 http://ftpmaster.internal quantal Release.gpg [198 B] Get:2 http://ftpmaster.internal quantal Release [49.6 kB] Get:3 http://ftpmaster.internal quantal/main powerpc Packages [1291 kB] Get:4 http://ftpmaster.internal quantal/universe powerpc Packages [4864 kB] Get:5 http://ftpmaster.internal quantal/main TranslationIndex [74 B] Get:6 http://ftpmaster.internal quantal/universe TranslationIndex [75 B] Get:7 http://ftpmaster.internal quantal/main Translation-en [740 kB] Get:8 http://ftpmaster.internal quantal/universe Translation-en [3455 kB] Fetched 10.4 MB in 6s (1607 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'ed9f1489de3e980f4f0a5b961c735485be8b8e4d', 'powerpc', 'quantal', '--nolog', '--batch', '--archive=ubuntu', '--dist=quantal', '--purpose=PRIMARY', '--architecture=powerpc', '--comp=universe', 'maq_0.7.1-5.dsc'] Initiating build ed9f1489de3e980f4f0a5b961c735485be8b8e4d with 4 jobs across 4 processor cores. Automatic build of maq_0.7.1-5 on sulfur by sbuild/powerpc 1.170.5 Build started at 20120506-1529 ****************************************************************************** maq_0.7.1-5.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 9), autotools-dev, zlib1g-dev, dh-autoreconf Checking for already installed source dependencies... debhelper: missing autotools-dev: missing zlib1g-dev: missing dh-autoreconf: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper autotools-dev zlib1g-dev dh-autoreconf Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: autoconf automake bsdmainutils dh-apparmor file gettext gettext-base groff-base html2text intltool-debian libcroco3 libgettextpo0 libmagic1 libpipeline1 libtool libunistring0 libxml2 m4 man-db po-debconf Suggested packages: autoconf2.13 autoconf-archive gnu-standards autoconf-doc wamerican wordlist whois vacation dh-make gettext-doc groff libtool-doc automaken gfortran fortran95-compiler gcj less www-browser libmail-box-perl Recommended packages: autopoint curl wget lynx-cur libltdl-dev xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autotools-dev bsdmainutils debhelper dh-apparmor dh-autoreconf file gettext gettext-base groff-base html2text intltool-debian libcroco3 libgettextpo0 libmagic1 libpipeline1 libtool libunistring0 libxml2 m4 man-db po-debconf zlib1g-dev 0 upgraded, 24 newly installed, 0 to remove and 0 not upgraded. Need to get 7492 kB of archives. After this operation, 23.8 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libmagic1 libpipeline1 libxml2 libcroco3 libunistring0 libgettextpo0 file bsdmainutils gettext-base groff-base man-db m4 autoconf autotools-dev automake html2text gettext intltool-debian po-debconf dh-apparmor debhelper libtool dh-autoreconf zlib1g-dev Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ quantal/main libmagic1 powerpc 5.11-1 [224 kB] Get:2 http://ftpmaster.internal/ubuntu/ quantal/main libpipeline1 powerpc 1.2.1-1 [26.0 kB] Get:3 http://ftpmaster.internal/ubuntu/ quantal/main libxml2 powerpc 2.7.8.dfsg-5.1ubuntu4 [619 kB] Get:4 http://ftpmaster.internal/ubuntu/ quantal/main libcroco3 powerpc 0.6.5-1 [91.4 kB] Get:5 http://ftpmaster.internal/ubuntu/ quantal/main libunistring0 powerpc 0.9.3-5 [409 kB] Get:6 http://ftpmaster.internal/ubuntu/ quantal/main libgettextpo0 powerpc 0.18.1.1-5ubuntu3 [113 kB] Get:7 http://ftpmaster.internal/ubuntu/ quantal/main file powerpc 5.11-1 [19.7 kB] Get:8 http://ftpmaster.internal/ubuntu/ quantal/main bsdmainutils powerpc 8.2.3ubuntu1 [197 kB] Get:9 http://ftpmaster.internal/ubuntu/ quantal/main gettext-base powerpc 0.18.1.1-5ubuntu3 [57.1 kB] Get:10 http://ftpmaster.internal/ubuntu/ quantal/main groff-base powerpc 1.21-7 [1043 kB] Get:11 http://ftpmaster.internal/ubuntu/ quantal/main man-db powerpc 2.6.1-2 [747 kB] Get:12 http://ftpmaster.internal/ubuntu/ quantal/main m4 powerpc 1.4.16-2ubuntu1 [192 kB] Get:13 http://ftpmaster.internal/ubuntu/ quantal/main autoconf all 2.68-1ubuntu2 [560 kB] Get:14 http://ftpmaster.internal/ubuntu/ quantal/main autotools-dev all 20120210.1ubuntu1 [42.4 kB] Get:15 http://ftpmaster.internal/ubuntu/ quantal/main automake all 1:1.11.5-1 [575 kB] Get:16 http://ftpmaster.internal/ubuntu/ quantal/main html2text powerpc 1.3.2a-15 [106 kB] Get:17 http://ftpmaster.internal/ubuntu/ quantal/main gettext powerpc 0.18.1.1-5ubuntu3 [1131 kB] Get:18 http://ftpmaster.internal/ubuntu/ quantal/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:19 http://ftpmaster.internal/ubuntu/ quantal/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:20 http://ftpmaster.internal/ubuntu/ quantal/main dh-apparmor all 2.7.102-0ubuntu3 [9622 B] Get:21 http://ftpmaster.internal/ubuntu/ quantal/main debhelper all 9.20120419ubuntu2 [609 kB] Get:22 http://ftpmaster.internal/ubuntu/ quantal/main libtool powerpc 2.4.2-1ubuntu1 [302 kB] Get:23 http://ftpmaster.internal/ubuntu/ quantal/main dh-autoreconf all 6 [15.3 kB] Get:24 http://ftpmaster.internal/ubuntu/ quantal/main zlib1g-dev powerpc 1:1.2.3.4.dfsg-3ubuntu4 [161 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7492 kB in 0s (12.0 MB/s) Selecting previously unselected package libmagic1. (Reading database ... 12197 files and directories currently installed.) Unpacking libmagic1 (from .../libmagic1_5.11-1_powerpc.deb) ... Selecting previously unselected package libpipeline1. Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_powerpc.deb) ... Selecting previously unselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1ubuntu4_powerpc.deb) ... Selecting previously unselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.5-1_powerpc.deb) ... Selecting previously unselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-5_powerpc.deb) ... Selecting previously unselected package libgettextpo0. Unpacking libgettextpo0 (from .../libgettextpo0_0.18.1.1-5ubuntu3_powerpc.deb) ... Selecting previously unselected package file. Unpacking file (from .../file_5.11-1_powerpc.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3ubuntu1_powerpc.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-5ubuntu3_powerpc.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-7_powerpc.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.1-2_powerpc.deb) ... Selecting previously unselected package m4. Unpacking m4 (from .../m4_1.4.16-2ubuntu1_powerpc.deb) ... Selecting previously unselected package autoconf. Unpacking autoconf (from .../autoconf_2.68-1ubuntu2_all.deb) ... Selecting previously unselected package autotools-dev. Unpacking autotools-dev (from .../autotools-dev_20120210.1ubuntu1_all.deb) ... Selecting previously unselected package automake. Unpacking automake (from .../automake_1%3a1.11.5-1_all.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_powerpc.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-5ubuntu3_powerpc.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2ubuntu1_all.deb) ... Selecting previously unselected package dh-apparmor. Unpacking dh-apparmor (from .../dh-apparmor_2.7.102-0ubuntu3_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_9.20120419ubuntu2_all.deb) ... Selecting previously unselected package libtool. Unpacking libtool (from .../libtool_2.4.2-1ubuntu1_powerpc.deb) ... Selecting previously unselected package dh-autoreconf. Unpacking dh-autoreconf (from .../dh-autoreconf_6_all.deb) ... Selecting previously unselected package zlib1g-dev. Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3ubuntu4_powerpc.deb) ... Setting up libmagic1 (5.11-1) ... Setting up libpipeline1 (1.2.1-1) ... Setting up libxml2 (2.7.8.dfsg-5.1ubuntu4) ... Setting up libcroco3 (0.6.5-1) ... Setting up libunistring0 (0.9.3-5) ... Setting up libgettextpo0 (0.18.1.1-5ubuntu3) ... Setting up file (5.11-1) ... Setting up bsdmainutils (8.2.3ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode. Setting up gettext-base (0.18.1.1-5ubuntu3) ... Setting up groff-base (1.21-7) ... Setting up man-db (2.6.1-2) ... Building database of manual pages ... Setting up m4 (1.4.16-2ubuntu1) ... Setting up autoconf (2.68-1ubuntu2) ... Setting up autotools-dev (20120210.1ubuntu1) ... Setting up automake (1:1.11.5-1) ... update-alternatives: using /usr/bin/automake-1.11 to provide /usr/bin/automake (automake) in auto mode. Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2ubuntu1) ... Setting up dh-apparmor (2.7.102-0ubuntu3) ... Setting up debhelper (9.20120419ubuntu2) ... Setting up libtool (2.4.2-1ubuntu1) ... Setting up dh-autoreconf (6) ... Setting up zlib1g-dev (1:1.2.3.4.dfsg-3ubuntu4) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.15-0ubuntu11 make_3.81-8.1ubuntu1 dpkg-dev_1.16.1.2ubuntu8 gcc-4.7_4.7.0-7ubuntu3 g++-4.7_4.7.0-7ubuntu3 binutils_2.22-6ubuntu1 libstdc++6-4.7-dev_4.7.0-7ubuntu3 libstdc++6_4.7.0-7ubuntu3 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt gpgv: Signature made Wed Apr 25 13:42:43 2012 UTC using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./maq_0.7.1-5.dsc dpkg-source: info: extracting maq in maq-0.7.1 dpkg-source: info: unpacking maq_0.7.1.orig.tar.gz dpkg-source: info: unpacking maq_0.7.1-5.debian.tar.gz dpkg-source: info: applying 10_prevent_-64_option.patch dpkg-source: info: applying gcc-4.7.patch dpkg-buildpackage: source package maq dpkg-buildpackage: source version 0.7.1-5 dpkg-source --before-build maq-0.7.1 dpkg-buildpackage: host architecture powerpc /usr/bin/fakeroot debian/rules clean dh clean --with autoreconf dh_testdir dh_auto_clean dh_autoreconf_clean dh_clean debian/rules build dh build --with autoreconf dh_testdir dh_autoreconf dh_auto_configure configure: WARNING: unrecognized options: --disable-maintainer-mode, --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking build system type... powerpc-unknown-linux-gnu checking host system type... powerpc-unknown-linux-gnu checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes configure: creating ./config.status config.status: creating Makefile config.status: creating config.h configure: WARNING: unrecognized options: --disable-maintainer-mode, --disable-dependency-tracking dh_auto_build make[1]: Entering directory `/build/buildd/maq-0.7.1' make all-am make[2]: Entering directory `/build/buildd/maq-0.7.1' gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c main.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c const.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c seq.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c bfa.c bfa.c: In function 'nst_bfa_len': bfa.c:46:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bfa.c:48:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bfa.c: In function 'nst_load_bfa1': bfa.c:31:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bfa.c:32:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bfa.c:33:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bfa.c:35:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bfa.c:37:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c -o read.o read.cc gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c fasta2bfa.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c fastq2bfq.c g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c -o merge.o merge.cc g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c -o match_aux.o match_aux.cc g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c -o match.o match.cc match.cc: In function 'int alt_cal_mm(bit64_t)': match.cc:58:21: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] match.cc:61:22: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] match.cc: In function 'int alt_cal_err(bit64_t, bit64_t)': match.cc:67:21: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] match.cc:70:22: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] match.cc: In function 'void match_search(const match_aux_t*, match_data_t*, const nst_bfa1_t*, int, ref_canlist_t*)': match.cc:292:10: warning: variable 'n_reads' set but not used [-Wunused-but-set-variable] match.cc: In function 'int ma_match(int, char**)': match.cc:525:32: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c -o sort_mapping.o sort_mapping.cc sort_mapping.cc: In function 'int ma_make_pair(const match_aux_t*, const match_info_t*, const match_info_t*, pair_info_t*)': sort_mapping.cc:59:62: warning: suggest parentheses around arithmetic in operand of '^' [-Wparentheses] g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c -o assemble.o assemble.cc assemble.cc: In function 'base_call_aux_t* assemble_cns_collect(assemble_pos_t*, const assemble_aux_t*)': assemble.cc:106:64: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c -o pileup.o pileup.cc g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c -o mapcheck.o mapcheck.cc mapcheck.cc: In function 'int ma_mapcheck(int, char**)': mapcheck.cc:60:17: warning: variable 'fpout' set but not used [-Wunused-but-set-variable] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c get_pos.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c assopt.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c aux_utils.c g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c -o rbcc.o rbcc.cc g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c -o subsnp.o subsnp.cc g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c -o pair_stat.o pair_stat.cc g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c -o indel_soa.o indel_soa.cc indel_soa.cc: In function 'void fill_counter(bit32_t*, int, nst_bfa1_t*, gzFile)': indel_soa.cc:42:44: warning: suggest parentheses around '-' inside '<<' [-Wparentheses] indel_soa.cc:56:44: warning: suggest parentheses around '-' inside '<<' [-Wparentheses] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c maqmap.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c maqmap_conv.c g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c -o altchr.o altchr.cc gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c submap.c g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c -o rmdup.o rmdup.cc gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c simulate.c In file included from /usr/include/string.h:642:0, from maqmap.h:23, from simulate.c:11: In function 'memset', inlined from 'simustat_core' at simulate.c:386:8: /usr/include/powerpc-linux-gnu/bits/string3.h:85:3: warning: call to __builtin___memset_chk will always overflow destination buffer [enabled by default] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c genran.c g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c -o indel_pe.o indel_pe.cc gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c stdaln.c stdaln.c: In function 'aln_local_core': stdaln.c:534:25: warning: variable 'b' set but not used [-Wunused-but-set-variable] g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c -o indel_call.o indel_call.cc indel_call.cc: In function 'int maq_indelpe(int, char**)': indel_call.cc:68:3: warning: 'last.indel_info_t::indelpos.assemble_indelpos_t::n_ungap' may be used uninitialized in this function [-Wmaybe-uninitialized] indel_call.cc:86:21: note: 'last.indel_info_t::indelpos.assemble_indelpos_t::n_ungap' was declared here indel_call.cc:23:56: warning: 'last.indel_info_t::indelpos.assemble_indelpos_t::n_types' may be used uninitialized in this function [-Wmaybe-uninitialized] indel_call.cc:86:21: note: 'last.indel_info_t::indelpos.assemble_indelpos_t::n_types' was declared here indel_call.cc:73:5: warning: 'last.indel_info_t::coor' may be used uninitialized in this function [-Wmaybe-uninitialized] g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c -o eland2maq.o eland2maq.cc eland2maq.cc: In function 'hash_map_char* read_list(FILE*)': eland2maq.cc:33:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] eland2maq.cc: In function 'void novo2maq_core(FILE*, FILE*, gzFile)': eland2maq.cc:323:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] eland2maq.cc: In function 'void eland2maq_core(FILE*, FILE*, gzFile)': eland2maq.cc:88:30: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] eland2maq.cc:96:30: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] eland2maq.cc:99:73: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c -o csmap2ntmap.o csmap2ntmap.cc gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c break_pair.c g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c -o glfgen.o glfgen.cc glfgen.cc: In function 'glf1_t* glfgen1_core(assemble_pos_t*, const assemble_aux_t*, bit8_t)': glfgen.cc:43:64: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] g++ -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o maq main.o const.o seq.o bfa.o read.o fasta2bfa.o fastq2bfq.o merge.o match_aux.o match.o sort_mapping.o assemble.o pileup.o mapcheck.o get_pos.o assopt.o aux_utils.o rbcc.o subsnp.o pair_stat.o indel_soa.o maqmap.o maqmap_conv.o altchr.o submap.o rmdup.o simulate.o genran.o indel_pe.o stdaln.o indel_call.o eland2maq.o csmap2ntmap.o break_pair.o glfgen.o -lm -lz make[2]: Leaving directory `/build/buildd/maq-0.7.1' make[1]: Leaving directory `/build/buildd/maq-0.7.1' dh_auto_test /usr/bin/fakeroot debian/rules binary-arch dh binary-arch --with autoreconf dh_testroot -a dh_prep -a dh_installdirs -a dh_auto_install -a make[1]: Entering directory `/build/buildd/maq-0.7.1' make[2]: Entering directory `/build/buildd/maq-0.7.1' /bin/mkdir -p '/build/buildd/maq-0.7.1/debian/maq/usr/bin' /usr/bin/install -c maq '/build/buildd/maq-0.7.1/debian/maq/usr/bin' /bin/mkdir -p '/build/buildd/maq-0.7.1/debian/maq/usr/bin' /usr/bin/install -c scripts/maq.pl scripts/farm-run.pl scripts/maq_plot.pl scripts/maq_eval.pl '/build/buildd/maq-0.7.1/debian/maq/usr/bin' make[2]: Nothing to be done for `install-data-am'. make[2]: Leaving directory `/build/buildd/maq-0.7.1' make[1]: Leaving directory `/build/buildd/maq-0.7.1' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_installcatalogs -a dh_installcron -a dh_installdebconf -a dh_installemacsen -a dh_installifupdown -a dh_installinfo -a dh_installinit -a dh_installmenu -a dh_installmime -a dh_installmodules -a dh_installlogcheck -a dh_installlogrotate -a dh_installpam -a dh_installppp -a dh_installudev -a dh_installwm -a dh_installxfonts -a dh_installgsettings -a dh_bugfiles -a dh_ucf -a dh_lintian -a dh_gconf -a dh_icons -a dh_perl -a dh_usrlocal -a dh_link -a debian/rules override_dh_compress make[1]: Entering directory `/build/buildd/maq-0.7.1' dh_compress --exclude=.pdf make[1]: Leaving directory `/build/buildd/maq-0.7.1' dh_fixperms -a dh_strip -a dh_strip debug symbol extraction: all non-arch-all packages for this build platform powerpc: maq dh_strip debug symbol extraction: packages to act on: maq dh_strip debug symbol extraction: ignored packages: dpkg-deb: building package `maq-dbgsym' in `../maq-dbgsym_0.7.1-5_powerpc.ddeb'. dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: package maq: unused substitution variable ${perl:Depends} dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 116 pkgstriptranslations: processing maq (in debian/maq); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/maq/DEBIAN/control, package maq, directory debian/maq pkgstripfiles: PNG optimization for package maq took 0 s dpkg-deb: warning: 'debian/maq/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `maq' in `../maq_0.7.1-5_powerpc.deb'. dpkg-genchanges -B -mUbuntu/powerpc Build Daemon >../maq_0.7.1-5_powerpc.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 maq-0.7.1 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20120506-1530 Publishing debug debs. chroot-autobuild/build/buildd/maq_0.7.1-5_powerpc.deb: new debian package, version 2.0. size 335460 bytes: control archive= 1359 bytes. 919 bytes, 19 lines control 1116 bytes, 19 lines md5sums Package: maq Version: 0.7.1-5 Architecture: powerpc Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 584 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.2.1), libstdc++6 (>= 4.1.1), zlib1g (>= 1:1.2.3.3.dfsg) Suggests: bwa, samtools Section: science Priority: optional Homepage: http://maq.sourceforge.net/ Description: maps short fixed-length polymorphic DNA sequence reads to reference sequences Maq (short for Mapping and Assembly with Quality) builds mapping assemblies from short reads generated by the next-generation sequencing machines. It was particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has a preliminary functionality to handle ABI SOLiD data. Maq is previously known as mapass2. . Developmemt of Maq stopped in 2008. Its successors are BWA and SAMtools. chroot-autobuild/build/buildd/maq_0.7.1-5_powerpc.deb: drwxr-xr-x root/root 0 2012-05-06 15:30 ./ drwxr-xr-x root/root 0 2012-05-06 15:30 ./usr/ drwxr-xr-x root/root 0 2012-05-06 15:30 ./usr/share/ drwxr-xr-x root/root 0 2012-05-06 15:30 ./usr/share/doc-base/ -rw-r--r-- root/root 295 2011-03-16 07:59 ./usr/share/doc-base/maq drwxr-xr-x root/root 0 2012-05-06 15:30 ./usr/share/maq/ -rwxr-xr-x root/root 6326 2008-07-27 18:14 ./usr/share/maq/maq_sanger.pl -rwxr-xr-x root/root 4568 2008-06-23 14:15 ./usr/share/maq/maq_post.pl -rwxr-xr-x root/root 3590 2008-09-22 08:54 ./usr/share/maq/asub -rwxr-xr-x root/root 3066 2008-03-28 23:36 ./usr/share/maq/solid2fastq.pl -rwxr-xr-x root/root 9729 2008-09-22 08:54 ./usr/share/maq/fq_all2std.pl -rwxr-xr-x root/root 13683 2008-07-27 18:14 ./usr/share/maq/paf_utils.pl drwxr-xr-x root/root 0 2012-05-06 15:30 ./usr/share/lintian/ drwxr-xr-x root/root 0 2012-05-06 15:30 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 132 2008-11-17 06:37 ./usr/share/lintian/overrides/maq drwxr-xr-x root/root 0 2012-05-06 15:30 ./usr/share/man/ drwxr-xr-x root/root 0 2012-05-06 15:30 ./usr/share/man/man1/ -rw-r--r-- root/root 12557 2012-05-06 15:30 ./usr/share/man/man1/maq.1.gz drwxr-xr-x root/root 0 2012-05-06 15:30 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-05-06 15:30 ./usr/share/doc/maq/ -rw-r--r-- root/root 939 2008-03-15 12:06 ./usr/share/doc/maq/README -rw-r--r-- root/root 47 2008-03-15 12:06 ./usr/share/doc/maq/AUTHORS -rw-r--r-- root/root 2147 2012-04-25 12:45 ./usr/share/doc/maq/copyright -rw-r--r-- root/root 148751 2008-09-26 14:47 ./usr/share/doc/maq/maq.pdf -rw-r--r-- root/root 1623 2012-04-25 13:40 ./usr/share/doc/maq/changelog.Debian.gz drwxr-xr-x root/root 0 2012-05-06 15:30 ./usr/bin/ -rwxr-xr-x root/root 4007 2012-05-06 15:30 ./usr/bin/farm-run.pl -rwxr-xr-x root/root 288064 2012-05-06 15:30 ./usr/bin/maq -rwxr-xr-x root/root 10995 2012-05-06 15:30 ./usr/bin/maq_eval.pl -rwxr-xr-x root/root 28813 2012-05-06 15:30 ./usr/bin/maq.pl -rwxr-xr-x root/root 4892 2012-05-06 15:30 ./usr/bin/maq_plot.pl maq_0.7.1-5_powerpc.changes: Format: 1.8 Date: Wed, 25 Apr 2012 14:20:16 +0200 Source: maq Binary: maq Architecture: powerpc Version: 0.7.1-5 Distribution: quantal Urgency: low Maintainer: Ubuntu/powerpc Build Daemon Changed-By: Andreas Tille Description: maq - maps short fixed-length polymorphic DNA sequence reads to referen Closes: 667270 Changes: maq (0.7.1-5) unstable; urgency=low . [ Charles Plessy ] * renamed debian/upstream-metadata.yaml to debian/upstream . [ Andreas Tille ] * debian/upstream: - Removed duplicated entry DOI - Moved PMID to references * debian/source/format: 3.0 (quilt) * debian/reference: removed because references are kept in debian/upstream (also removed from debian/docs) * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Fixed Vcs fields - Build-Depends: dh-autoreconf - Dropped from Build-Depends: quilt, cdbs * debian/patches/20_prevent_-64_option.patch: Dropped in favour of using dh-autoreconf * debian/rules: converted to dh * debian/copyright: cme fix dpkg-copyright * debian/patches/gcc-4.7.patch: Enable building with g++-4.7 Closes: #667270 * debian/README.source: Removed because there is no point any more to explain how to use quilt Checksums-Sha1: b294daf117f547865ce43072338727c2b0a58568 335460 maq_0.7.1-5_powerpc.deb Checksums-Sha256: 42bbec447bef01b00ffbb8309f0de7e64532af6bf0cb18cd38dd5a5a4642cf96 335460 maq_0.7.1-5_powerpc.deb Files: 42517fb5e9c74cec2bc054a9d6b35262 335460 science optional maq_0.7.1-5_powerpc.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20120506-1530 Build needed 00:00:53, 5884k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', 'ed9f1489de3e980f4f0a5b961c735485be8b8e4d'] Scanning for processes to kill in build /srv/home/buildd/build-ed9f1489de3e980f4f0a5b961c735485be8b8e4d/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'ed9f1489de3e980f4f0a5b961c735485be8b8e4d'] Unmounting chroot for build ed9f1489de3e980f4f0a5b961c735485be8b8e4d... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'ed9f1489de3e980f4f0a5b961c735485be8b8e4d'] Removing build ed9f1489de3e980f4f0a5b961c735485be8b8e4d