DC-Build-Header: tophat 2.0.3-1 / Mon Jul 02 18:45:33 +0000 2012 DC-Task: logfile:/tmp/tophat_2.0.3-1_unstable_clang.log version:2.0.3-1 modes:clang chroot:unstable source:tophat esttime:133 architecture:any DC-Sbuild-call: su user -c 'sbuild -n -A -s --force-orig-source --apt-update -d unstable -v --chroot-setup-commands=/tmp/switch-to-clang tophat_2.0.3-1' sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on ip-10-28-121-108.ec2.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ tophat 2.0.3-1 (amd64) 02 Jul 2012 18:45 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: tophat Version: 2.0.3-1 Source Version: 2.0.3-1 Distribution: unstable Architecture: amd64 I: NOTICE: Log filtering will replace 'build/tophat-LB2OWO/tophat-2.0.3' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/tophat-LB2OWO' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-64e126d5-4b9a-4e94-9604-b8d06bc1177a' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost unstable InRelease Hit http://localhost unstable Release.gpg Hit http://localhost unstable Release Hit http://localhost unstable/main Sources/DiffIndex Hit http://localhost unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Translation-en/DiffIndex Reading package lists... Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'tophat' packaging is maintained in the 'Git' version control system at: git://git.debian.org/debian-med/tophat.git Need to get 436 kB of source archives. Get:1 http://localhost/debian/ unstable/main tophat 2.0.3-1 (dsc) [2135 B] Get:2 http://localhost/debian/ unstable/main tophat 2.0.3-1 (tar) [429 kB] Get:3 http://localhost/debian/ unstable/main tophat 2.0.3-1 (diff) [5600 B] Fetched 436 kB in 0s (1840 kB/s) Download complete and in download only mode Check arch ────────── ┌──────────────────────────────────────────────────────────────────────────────┐ │ Chroot Setup Commands │ └──────────────────────────────────────────────────────────────────────────────┘ /tmp/switch-to-clang ──────────────────── + echo 'Entering customization script...' Entering customization script... + apt-get update Ign http://localhost unstable InRelease Hit http://localhost unstable Release.gpg Hit http://localhost unstable Release Hit http://localhost unstable/main Sources/DiffIndex Hit http://localhost unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Translation-en/DiffIndex Reading package lists... + echo 'Install of clang' Install of clang + apt-get update Ign http://localhost unstable InRelease Hit http://localhost unstable Release.gpg Hit http://localhost unstable Release Hit http://localhost unstable/main Sources/DiffIndex Hit http://localhost unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Translation-en/DiffIndex Reading package lists... + apt-get install --yes --no-install-recommends clang -t unstable Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libclang-common-dev libffi5 libllvm3.1 Recommended packages: llvm-3.1-dev python The following NEW packages will be installed: clang libclang-common-dev libffi5 libllvm3.1 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 13.1 MB of archives. After this operation, 35.6 MB of additional disk space will be used. Get:1 http://localhost/debian/ unstable/main libffi5 amd64 3.0.10-3 [24.8 kB] Get:2 http://localhost/debian/ unstable/main libllvm3.1 amd64 3.1-2 [7275 kB] Get:3 http://localhost/debian/ unstable/main libclang-common-dev amd64 3.1-8 [84.3 kB] Get:4 http://localhost/debian/ unstable/main clang amd64 3.1-8 [5755 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 13.1 MB in 0s (30.2 MB/s) Selecting previously unselected package libffi5:amd64. (Reading database ... 11725 files and directories currently installed.) Unpacking libffi5:amd64 (from .../libffi5_3.0.10-3_amd64.deb) ... Selecting previously unselected package libllvm3.1:amd64. Unpacking libllvm3.1:amd64 (from .../libllvm3.1_3.1-2_amd64.deb) ... Selecting previously unselected package libclang-common-dev. Unpacking libclang-common-dev (from .../libclang-common-dev_3.1-8_amd64.deb) ... Selecting previously unselected package clang. Unpacking clang (from .../archives/clang_3.1-8_amd64.deb) ... Setting up libffi5:amd64 (3.0.10-3) ... Setting up libllvm3.1:amd64 (3.1-2) ... Setting up libclang-common-dev (3.1-8) ... Setting up clang (3.1-8) ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSION=4.7 + cd /usr/bin + rm g++-4.7 gcc-4.7 cpp-4.7 + ln -s clang++ g++-4.7 + ln -s clang gcc-4.7 + ln -s clang cpp-4.7 + cd - /«BUILDDIR» + echo 'Block the installation of new gcc version' Block the installation of new gcc version + dpkg --set-selections + echo 'gcc-4.6 hold' + dpkg --set-selections + echo 'cpp-4.6 hold' + dpkg --set-selections + echo 'g++-4.6 hold' + dpkg --set-selections + echo 'gcc-4.7 hold' + dpkg --set-selections + echo 'cpp-4.7 hold' + dpkg --set-selections + echo 'g++-4.7 hold' + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + grep clang + gcc --version I: Finished running '/tmp/switch-to-clang'. Finished processing commands. ──────────────────────────────────────────────────────────────────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-452pHE/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/708 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 11805 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), autotools-dev, libbam-dev (>= 0.1.16), zlib1g-dev, dh-autoreconf, python (>= 2.6.6-3~), seqan-dev (>= 1.3~), libboost-thread-dev, help2man Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), autotools-dev, libbam-dev (>= 0.1.16), zlib1g-dev, dh-autoreconf, python (>= 2.6.6-3~), seqan-dev (>= 1.3~), libboost-thread-dev, help2man dpkg-deb: building package `sbuild-build-depends-tophat-dummy' in `/«BUILDDIR»/resolver-eHLi9r/apt_archive/sbuild-build-depends-tophat-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install tophat build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: autoconf automake autotools-dev bsdmainutils debhelper dh-autoreconf file gettext gettext-base groff-base help2man html2text intltool-debian libasprintf0c2 libbam-dev libboost-date-time1.49-dev libboost-date-time1.49.0 libboost-serialization1.49-dev libboost-serialization1.49.0 libboost-thread-dev libboost-thread1.49-dev libboost-thread1.49.0 libboost1.49-dev libcroco3 libexpat1 libgettextpo0 libglib2.0-0 libicu48 libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libtool libunistring0 libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal seqan-dev zlib1g-dev Suggested packages: autoconf2.13 autoconf-archive gnu-standards autoconf-doc wamerican wordlist whois vacation dh-make gettext-doc groff libboost1.49-doc libboost-chrono1.49-dev libboost-filesystem1.49-dev libboost-graph-parallel1.49-dev libboost-graph1.49-dev libboost-iostreams1.49-dev libboost-locale1.49-dev libboost-math1.49-dev libboost-mpi1.49-dev libboost-program-options1.49-dev libboost-python1.49-dev libboost-random1.49-dev libboost-regex1.49-dev libboost-signals1.49-dev libboost-system1.49-dev libboost-test1.49-dev libboost-timer1.49-dev libboost-wave1.49-dev xsltproc doxygen docbook-xml docbook-xsl default-jdk fop libtool-doc automaken gfortran fortran95-compiler gcj less www-browser libmail-box-perl python-doc python-tk python2.7-doc binfmt-support Recommended packages: autopoint curl wget lynx-cur libglib2.0-data shared-mime-info libgpm2 libltdl-dev xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autotools-dev bsdmainutils debhelper dh-autoreconf file gettext gettext-base groff-base help2man html2text intltool-debian libasprintf0c2 libbam-dev libboost-date-time1.49-dev libboost-date-time1.49.0 libboost-serialization1.49-dev libboost-serialization1.49.0 libboost-thread-dev libboost-thread1.49-dev libboost-thread1.49.0 libboost1.49-dev libcroco3 libexpat1 libgettextpo0 libglib2.0-0 libicu48 libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libtool libunistring0 libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal sbuild-build-depends-tophat-dummy seqan-dev zlib1g-dev 0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded. Need to get 39.8 MB/39.8 MB of archives. After this operation, 190 MB of additional disk space will be used. Get:1 http://localhost/debian/ unstable/main libncursesw5 amd64 5.9-10 [141 kB] Get:2 http://localhost/debian/ unstable/main libpipeline1 amd64 1.2.1-1 [39.2 kB] Get:3 http://localhost/debian/ unstable/main libssl1.0.0 amd64 1.0.1c-3 [1211 kB] Get:4 http://localhost/debian/ unstable/main libasprintf0c2 amd64 0.18.1.1-9 [26.8 kB] Get:5 http://localhost/debian/ unstable/main libmagic1 amd64 5.11-2 [202 kB] Get:6 http://localhost/debian/ unstable/main libpcre3 amd64 1:8.30-5 [242 kB] Get:7 http://localhost/debian/ unstable/main libsqlite3-0 amd64 3.7.13-1 [455 kB] Get:8 http://localhost/debian/ unstable/main libxml2 amd64 2.8.0+dfsg1-4 [903 kB] Get:9 http://localhost/debian/ unstable/main libglib2.0-0 amd64 2.32.3-1 [2081 kB] Get:10 http://localhost/debian/ unstable/main libcroco3 amd64 0.6.5-1 [151 kB] Get:11 http://localhost/debian/ unstable/main libexpat1 amd64 2.1.0-1 [141 kB] Get:12 http://localhost/debian/ unstable/main libunistring0 amd64 0.9.3-5 [434 kB] Get:13 http://localhost/debian/ unstable/main libgettextpo0 amd64 0.18.1.1-9 [145 kB] Get:14 http://localhost/debian/ unstable/main libicu48 amd64 4.8.1.1-8 [8138 kB] Get:15 http://localhost/debian/ unstable/main bsdmainutils amd64 9.0.3 [209 kB] Get:16 http://localhost/debian/ unstable/main groff-base amd64 1.21-9 [1153 kB] Get:17 http://localhost/debian/ unstable/main man-db amd64 2.6.2-1 [1061 kB] Get:18 http://localhost/debian/ unstable/main file amd64 5.11-2 [51.8 kB] Get:19 http://localhost/debian/ unstable/main gettext-base amd64 0.18.1.1-9 [154 kB] Get:20 http://localhost/debian/ unstable/main m4 amd64 1.4.16-3 [260 kB] Get:21 http://localhost/debian/ unstable/main mime-support all 3.52-1 [35.5 kB] Get:22 http://localhost/debian/ unstable/main python2.7-minimal amd64 2.7.3-1 [1770 kB] Get:23 http://localhost/debian/ unstable/main python2.7 amd64 2.7.3-1 [2726 kB] Get:24 http://localhost/debian/ unstable/main python-minimal all 2.7.3-1 [42.1 kB] Get:25 http://localhost/debian/ unstable/main python all 2.7.3-1 [179 kB] Get:26 http://localhost/debian/ unstable/main autoconf all 2.69-1 [589 kB] Get:27 http://localhost/debian/ unstable/main autotools-dev all 20120608.1 [73.0 kB] Get:28 http://localhost/debian/ unstable/main automake all 1:1.11.5-2 [606 kB] Get:29 http://localhost/debian/ unstable/main html2text amd64 1.3.2a-15 [103 kB] Get:30 http://localhost/debian/ unstable/main gettext amd64 0.18.1.1-9 [1975 kB] Get:31 http://localhost/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:32 http://localhost/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB] Get:33 http://localhost/debian/ unstable/main debhelper all 9.20120608 [700 kB] Get:34 http://localhost/debian/ unstable/main libtool amd64 2.4.2-1.1 [619 kB] Get:35 http://localhost/debian/ unstable/main dh-autoreconf all 6 [15.3 kB] Get:36 http://localhost/debian/ unstable/main help2man amd64 1.40.10 [96.2 kB] Get:37 http://localhost/debian/ unstable/main libbam-dev amd64 0.1.18-1 [154 kB] Get:38 http://localhost/debian/ unstable/main libboost1.49-dev amd64 1.49.0-3.1 [9203 kB] Get:39 http://localhost/debian/ unstable/main libboost-date-time1.49.0 amd64 1.49.0-3.1 [46.7 kB] Get:40 http://localhost/debian/ unstable/main libboost-serialization1.49.0 amd64 1.49.0-3.1 [212 kB] Get:41 http://localhost/debian/ unstable/main libboost-serialization1.49-dev amd64 1.49.0-3.1 [316 kB] Get:42 http://localhost/debian/ unstable/main libboost-date-time1.49-dev amd64 1.49.0-3.1 [49.5 kB] Get:43 http://localhost/debian/ unstable/main libboost-thread1.49.0 amd64 1.49.0-3.1 [61.0 kB] Get:44 http://localhost/debian/ unstable/main libboost-thread1.49-dev amd64 1.49.0-3.1 [67.1 kB] Get:45 http://localhost/debian/ unstable/main libboost-thread-dev amd64 1.49.0.1 [2736 B] Get:46 http://localhost/debian/ unstable/main seqan-dev all 1.3.1-1 [2442 kB] Get:47 http://localhost/debian/ unstable/main zlib1g-dev amd64 1:1.2.7.dfsg-13 [215 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 39.8 MB in 2s (13.8 MB/s) Selecting previously unselected package libncursesw5:amd64. (Reading database ... 11805 files and directories currently installed.) Unpacking libncursesw5:amd64 (from .../libncursesw5_5.9-10_amd64.deb) ... Selecting previously unselected package libpipeline1:amd64. Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.1-1_amd64.deb) ... Selecting previously unselected package libssl1.0.0:amd64. Unpacking libssl1.0.0:amd64 (from .../libssl1.0.0_1.0.1c-3_amd64.deb) ... Selecting previously unselected package libasprintf0c2:amd64. Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.1.1-9_amd64.deb) ... Selecting previously unselected package libmagic1:amd64. Unpacking libmagic1:amd64 (from .../libmagic1_5.11-2_amd64.deb) ... Selecting previously unselected package libpcre3:amd64. Unpacking libpcre3:amd64 (from .../libpcre3_1%3a8.30-5_amd64.deb) ... Selecting previously unselected package libsqlite3-0:amd64. Unpacking libsqlite3-0:amd64 (from .../libsqlite3-0_3.7.13-1_amd64.deb) ... Selecting previously unselected package libxml2:amd64. Unpacking libxml2:amd64 (from .../libxml2_2.8.0+dfsg1-4_amd64.deb) ... Selecting previously unselected package libglib2.0-0:amd64. Unpacking libglib2.0-0:amd64 (from .../libglib2.0-0_2.32.3-1_amd64.deb) ... Selecting previously unselected package libcroco3:amd64. Unpacking libcroco3:amd64 (from .../libcroco3_0.6.5-1_amd64.deb) ... Selecting previously unselected package libexpat1:amd64. Unpacking libexpat1:amd64 (from .../libexpat1_2.1.0-1_amd64.deb) ... Selecting previously unselected package libunistring0:amd64. Unpacking libunistring0:amd64 (from .../libunistring0_0.9.3-5_amd64.deb) ... Selecting previously unselected package libgettextpo0:amd64. Unpacking libgettextpo0:amd64 (from .../libgettextpo0_0.18.1.1-9_amd64.deb) ... Selecting previously unselected package libicu48:amd64. Unpacking libicu48:amd64 (from .../libicu48_4.8.1.1-8_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_amd64.deb) ... 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Unpacking python-minimal (from .../python-minimal_2.7.3-1_all.deb) ... Selecting previously unselected package python. Unpacking python (from .../python_2.7.3-1_all.deb) ... Selecting previously unselected package autoconf. Unpacking autoconf (from .../autoconf_2.69-1_all.deb) ... Selecting previously unselected package autotools-dev. Unpacking autotools-dev (from .../autotools-dev_20120608.1_all.deb) ... Selecting previously unselected package automake. Unpacking automake (from .../automake_1%3a1.11.5-2_all.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-9_amd64.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. 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Selecting previously unselected package libboost-serialization1.49.0. Unpacking libboost-serialization1.49.0 (from .../libboost-serialization1.49.0_1.49.0-3.1_amd64.deb) ... Selecting previously unselected package libboost-serialization1.49-dev. Unpacking libboost-serialization1.49-dev (from .../libboost-serialization1.49-dev_1.49.0-3.1_amd64.deb) ... Selecting previously unselected package libboost-date-time1.49-dev. Unpacking libboost-date-time1.49-dev (from .../libboost-date-time1.49-dev_1.49.0-3.1_amd64.deb) ... Selecting previously unselected package libboost-thread1.49.0. Unpacking libboost-thread1.49.0 (from .../libboost-thread1.49.0_1.49.0-3.1_amd64.deb) ... Selecting previously unselected package libboost-thread1.49-dev. Unpacking libboost-thread1.49-dev (from .../libboost-thread1.49-dev_1.49.0-3.1_amd64.deb) ... Selecting previously unselected package libboost-thread-dev. Unpacking libboost-thread-dev (from .../libboost-thread-dev_1.49.0.1_amd64.deb) ... Selecting previously unselected package seqan-dev. Unpacking seqan-dev (from .../seqan-dev_1.3.1-1_all.deb) ... Selecting previously unselected package zlib1g-dev:amd64. Unpacking zlib1g-dev:amd64 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_amd64.deb) ... Selecting previously unselected package sbuild-build-depends-tophat-dummy. Unpacking sbuild-build-depends-tophat-dummy (from .../sbuild-build-depends-tophat-dummy.deb) ... Setting up libncursesw5:amd64 (5.9-10) ... Setting up libpipeline1:amd64 (1.2.1-1) ... Setting up libssl1.0.0:amd64 (1.0.1c-3) ... Setting up libasprintf0c2:amd64 (0.18.1.1-9) ... Setting up libmagic1:amd64 (5.11-2) ... Setting up libpcre3:amd64 (1:8.30-5) ... Setting up libsqlite3-0:amd64 (3.7.13-1) ... Setting up libxml2:amd64 (2.8.0+dfsg1-4) ... Setting up libglib2.0-0:amd64 (2.32.3-1) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.5-1) ... Setting up libexpat1:amd64 (2.1.0-1) ... Setting up libunistring0:amd64 (0.9.3-5) ... Setting up libgettextpo0:amd64 (0.18.1.1-9) ... Setting up libicu48:amd64 (4.8.1.1-8) ... Setting up bsdmainutils (9.0.3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up groff-base (1.21-9) ... Setting up man-db (2.6.2-1) ... Building database of manual pages ... Setting up file (5.11-2) ... Setting up gettext-base (0.18.1.1-9) ... Setting up m4 (1.4.16-3) ... Setting up mime-support (3.52-1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode Setting up python2.7-minimal (2.7.3-1) ... Setting up python2.7 (2.7.3-1) ... Setting up python-minimal (2.7.3-1) ... Setting up python (2.7.3-1) ... Setting up autoconf (2.69-1) ... Setting up autotools-dev (20120608.1) ... Setting up automake (1:1.11.5-2) ... 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 (0.18.1.1-9) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120608) ... Setting up libtool (2.4.2-1.1) ... Setting up dh-autoreconf (6) ... Setting up help2man (1.40.10) ... Setting up libbam-dev (0.1.18-1) ... Setting up libboost1.49-dev (1.49.0-3.1) ... Setting up libboost-date-time1.49.0 (1.49.0-3.1) ... Setting up libboost-serialization1.49.0 (1.49.0-3.1) ... Setting up libboost-serialization1.49-dev (1.49.0-3.1) ... Setting up libboost-date-time1.49-dev (1.49.0-3.1) ... Setting up libboost-thread1.49.0 (1.49.0-3.1) ... Setting up libboost-thread1.49-dev (1.49.0-3.1) ... Setting up libboost-thread-dev (1.49.0.1) ... Setting up seqan-dev (1.3.1-1) ... Setting up zlib1g-dev:amd64 (1:1.2.7.dfsg-13) ... Setting up sbuild-build-depends-tophat-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-xen-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.22-6.1 dpkg-dev_1.16.6 g++-4.6_4.6.3-8 g++-4.7_4.7.1-2 gcc-4.6_4.6.3-8 gcc-4.7_4.7.1-2 libc6-dev_2.13-34 libstdc++6_4.7.1-2 libstdc++6-4.6-dev_4.6.3-8 libstdc++6-4.7-dev_4.7.1-2 linux-libc-dev_3.2.21-3 Package versions: apt_0.9.7.1 autoconf_2.69-1 automake_1:1.11.5-2 autotools-dev_20120608.1 base-files_6.11 base-passwd_3.5.26 bash_4.2-3 binutils_2.22-6.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 clang_3.1-8 coreutils_8.13-3.2 cpp_4:4.7.1-1 cpp-4.6_4.6.3-8 cpp-4.7_4.7.1-2 dash_0.5.7-3 debconf_1.5.44 debconf-i18n_1.5.44 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 dh-autoreconf_6 diffutils_1:3.2-6 dpkg_1.16.6 dpkg-dev_1.16.6 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.7.1-1 g++-4.6_4.6.3-8 g++-4.7_4.7.1-2 gcc_4:4.7.1-1 gcc-4.4-base_4.4.7-1 gcc-4.5-base_4.5.3-12 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7_4.7.1-2 gcc-4.7-base_4.7.1-2 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 help2man_1.40.10 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-28 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libbam-dev_0.1.18-1 libblkid1_2.20.1-5.1 libboost-date-time1.49-dev_1.49.0-3.1 libboost-date-time1.49.0_1.49.0-3.1 libboost-serialization1.49-dev_1.49.0-3.1 libboost-serialization1.49.0_1.49.0-3.1 libboost-thread-dev_1.49.0.1 libboost-thread1.49-dev_1.49.0-3.1 libboost-thread1.49.0_1.49.0-3.1 libboost1.49-dev_1.49.0-3.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc6_2.13-34 libc6-dev_2.13-34 libclang-common-dev_3.1-8 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.6 libexpat1_2.1.0-1 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-8 libgcc1_1:4.7.1-2 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-2 libicu48_4.8.1.1-8 libitm1_4.7.1-2 libllvm3.1_3.1-2 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncursesw5_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libquadmath0_4.7.1-2 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libsqlite3-0_3.7.13-1 libss2_1.42.4-3 libssl1.0.0_1.0.1c-3 libstdc++6_4.7.1-2 libstdc++6-4.6-dev_4.6.3-8 libstdc++6-4.7-dev_4.7.1-2 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-10 libtool_2.4.2-1.1 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-4 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 m4_1.4.16-3 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mime-support_3.52-1 mount_2.20.1-5.1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 python_2.7.3-1 python-minimal_2.7.3-1 python2.7_2.7.3-1 python2.7-minimal_2.7.3-1 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-tophat-dummy_0.invalid.0 sed_4.2.1-10 sensible-utils_0.0.7 seqan-dev_1.3.1-1 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012c-1 ucf_3.0025+nmu3 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Sat Jun 9 18:04:56 2012 UTC using RSA key ID 1B5228B0 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./tophat_2.0.3-1.dsc dpkg-source: info: extracting tophat in tophat-2.0.3 dpkg-source: info: unpacking tophat_2.0.3.orig.tar.gz dpkg-source: info: unpacking tophat_2.0.3-1.debian.tar.gz dpkg-source: info: applying fix_includes_path.patch dpkg-source: info: applying bashism_in_shell_script.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=root PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/bin/X11 SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=0 SCHROOT_GROUP=root SCHROOT_SESSION_ID=unstable-amd64-sbuild-64e126d5-4b9a-4e94-9604-b8d06bc1177a SCHROOT_UID=0 SCHROOT_USER=root SHELL=/bin/sh USER=root dpkg-buildpackage ───────────────── dpkg-buildpackage: warning: using a gain-root-command while being root dpkg-buildpackage: source package tophat dpkg-buildpackage: source version 2.0.3-1 dpkg-buildpackage: source changed by Alexandre Mestiashvili dpkg-source --before-build tophat-2.0.3 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --with autoreconf dh_testdir dh_auto_clean dh_autoreconf_clean dh_clean rm -f debian/tophat.substvars rm -f debian/tophat.*.debhelper rm -rf debian/tophat/ rm -f debian/*.debhelper.log rm -f debian/files find . \( \( -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} \; \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \) rm -f *-stamp dpkg-source -b tophat-2.0.3 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: building tophat using existing ./tophat_2.0.3.orig.tar.gz dpkg-source: info: building tophat in tophat_2.0.3-1.debian.tar.gz dpkg-source: info: building tophat in tophat_2.0.3-1.dsc debian/rules build dh build --with autoreconf dh_testdir dh_autoreconf find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} \; > debian/autoreconf.before autoreconf -f -i sh: 1: svnversion: not found configure.ac:35: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from... ax_boost_thread.m4:32: AX_BOOST_THREAD is expanded from... configure.ac:35: the top level sh: 1: svnversion: not found configure.ac:35: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from... ax_boost_thread.m4:32: AX_BOOST_THREAD is expanded from... configure.ac:35: the top level sh: 1: svnversion: not found configure.ac:35: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from... ax_boost_thread.m4:32: AX_BOOST_THREAD is expanded from... configure.ac:35: the top level sh: 1: svnversion: not found configure.ac:35: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from... ax_boost_thread.m4:32: AX_BOOST_THREAD is expanded from... configure.ac:35: the top level configure.ac:35: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from... ax_boost_thread.m4:32: AX_BOOST_THREAD is expanded from... configure.ac:35: the top level find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} \; > debian/autoreconf.after dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode 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 for gawk... (cached) mawk checking for g++... g++ 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 g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... none checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... none checking whether make sets $(MAKE)... (cached) yes checking for ranlib... ranlib checking for a Python interpreter with version >= 2.4... python checking for python... /usr/bin/python checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.7/dist-packages checking for python extension module directory... ${exec_prefix}/lib/python2.7/dist-packages checking for boostlib >= 1.38.0... yes checking for bamlib... yes checking build system type... x86_64-pc-linux-gnu checking whether the Boost::Thread library is available... yes checking for exit in -lboost_thread-mt... yes checking how to run the C preprocessor... gcc -E checking for 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 for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for ANSI C header files... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for inline... inline checking for pid_t... yes checking for size_t... yes checking for ptrdiff_t... yes checking for an ANSI C-conforming const... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for gzread in -lz... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for memset... yes checking for strdup... yes checking for strrchr... yes checking for strtol... yes checking for strsep... yes checking host system type... x86_64-pc-linux-gnu checking how to create a pax tar archive... gnutar checking dependency style of gcc... (cached) none checking dependency style of g++... (cached) none configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode -- tophat 2.0.3 Configuration Results -- C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 Linker flags: -Wl,-z,relro GCC version: Debian clang version 3.1-8 (branches/release_31) (based on LLVM 3.1) Host System type: x86_64-pc-linux-gnu Install prefix: /usr Install eprefix: ${prefix} See config.h for further configuration information. Email with questions and bug reports. dh_auto_build make -j1 make[1]: Entering directory `/«PKGBUILDDIR»' make all-recursive make[2]: Entering directory `/«PKGBUILDDIR»' Making all in src make[3]: Entering directory `/«PKGBUILDDIR»/src' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o reads.o reads.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -c alphabet.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o bwt_map.o bwt_map.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o common.o common.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o junctions.o junctions.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o insertions.o insertions.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o deletions.o deletions.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o fusions.o fusions.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o align_status.o align_status.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o fragments.o fragments.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o tokenize.o tokenize.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o inserts.o inserts.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o qual.o qual.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o utils.o utils.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o coverage.o coverage.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' rm -f libtophat.a ar cru libtophat.a reads.o alphabet.o bwt_map.o common.o junctions.o insertions.o deletions.o fusions.o align_status.o fragments.o tokenize.o inserts.o qual.o utils.o coverage.o ranlib libtophat.a g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o GBase.o GBase.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o codons.o codons.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o gdna.o gdna.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o GStr.o GStr.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o GFaSeqGet.o GFaSeqGet.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from GFaSeqGet.cpp:1: In file included from ./GFaSeqGet.h:3: ./GList.hh:1057:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ 1 warning generated. g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o gff.o gff.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from gff.cpp:1: In file included from ./gff.h:7: In file included from ./GFaSeqGet.h:3: ./GList.hh:1057:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ 1 warning generated. rm -f libgc.a ar cru libgc.a GBase.o codons.o gdna.o GStr.o GFaSeqGet.o gff.o ranlib libgc.a g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o prep_reads.o prep_reads.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -Wl,-z,relro -Wl,-z,relro -o prep_reads prep_reads.o ../src/libtophat.a -lbam -lz clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o GTFToFasta.o GTFToFasta.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from GTFToFasta.cpp:7: In file included from ./GTFToFasta.h:28: In file included from ./gff.h:7: In file included from ./GFaSeqGet.h:3: ./GList.hh:1057:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ 1 warning generated. g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o FastaTools.o FastaTools.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -Wl,-z,relro -Wl,-z,relro -o gtf_to_fasta GTFToFasta.o FastaTools.o ../src/libtophat.a libgc.a -lbam -lz clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o fix_map_ordering.o fix_map_ordering.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -Wl,-z,relro -Wl,-z,relro -o fix_map_ordering fix_map_ordering.o ../src/libtophat.a -lbam -lz clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o bam2fastx.o bam2fastx.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -Wl,-z,relro -Wl,-z,relro -o bam2fastx bam2fastx.o ../src/libgc.a -lbam -lz clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -I./SeqAn-1.3 -c -o segment_juncs.o segment_juncs.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' segment_juncs.cpp:2576:54: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if(rightHit.right() + read_length + begin_offset < 0 ) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~ segment_juncs.cpp:4834:47: error: variable length array of non-POD element type 'std::set' std::set vseg_juncs[num_threads]; ^ segment_juncs.cpp:4840:32: error: variable length array of non-POD element type 'std::set' std::set vdeletions[num_threads]; ^ segment_juncs.cpp:4841:34: error: variable length array of non-POD element type 'std::set' std::set vinsertions[num_threads]; ^ segment_juncs.cpp:4842:27: error: variable length array of non-POD element type 'FusionSimpleSet' (aka 'map') FusionSimpleSet vfusions[num_threads]; ^ 1 warning and 4 errors generated. make[3]: *** [segment_juncs.o] Error 1 make[3]: Leaving directory `/«PKGBUILDDIR»/src' make[2]: *** [all-recursive] Error 1 make[1]: *** [all] Error 2 dh_auto_build: make -j1 returned exit code 2 make: *** [build] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 make[2]: Leaving directory `/«PKGBUILDDIR»' make[1]: Leaving directory `/«PKGBUILDDIR»' ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120702-1847 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 23988 Build-Time: 56 Distribution: unstable Fail-Stage: build Install-Time: 17 Job: tophat_2.0.3-1 Package: tophat Package-Time: 94 Source-Version: 2.0.3-1 Space: 23988 Status: attempted Version: 2.0.3-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120702-1847 Build needed 00:01:34, 23988k disc space DC-Status: Failed 94.813186s