DC-Build-Header: tophat 2.0.9-1 / 2013-07-15 13:36:30 +0000 DC-Task: source:tophat version:2.0.9-1 architecture:any chroot:unstable esttime: logfile:/tmp/tophat_2.0.9-1_unstable_clang.log modes:binary-only:clang DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/switch-to-clang --append-to-version "clang1" --maintainer "Lucas Nussbaum " --uploader "Lucas Nussbaum " tophat_2.0.9-1' sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on ip-10-232-71-159.ec2.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ tophat 2.0.9-1clang1 (amd64) 15 Jul 2013 13:36 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: tophat Version: 2.0.9-1clang1 Source Version: 2.0.9-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/tophat-NqFRsY/tophat-2.0.9' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/tophat-NqFRsY' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-28d3f931-d51b-48ec-80df-ef4db8dadeea' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Get:1 http://localhost:9999 unstable InRelease [204 kB] Get:2 http://localhost:9999 unstable/main Sources/DiffIndex [7876 B] Get:3 http://localhost:9999 unstable/main amd64 Packages/DiffIndex [7876 B] Get:4 http://localhost:9999 unstable/main Translation-en/DiffIndex [7876 B] Get:5 http://localhost:9999 unstable/main 2013-07-13-2032.15.pdiff [23.1 kB] Get:6 http://localhost:9999 unstable/main amd64 2013-07-13-2032.15.pdiff [16.9 kB] Get:7 http://localhost:9999 unstable/main 2013-07-13-2032.15.pdiff [23.1 kB] Get:8 http://localhost:9999 unstable/main 2013-07-13-2032.15.pdiff [1809 B] Get:9 http://localhost:9999 unstable/main amd64 2013-07-13-2032.15.pdiff [16.9 kB] Get:10 http://localhost:9999 unstable/main 2013-07-14-0231.07.pdiff [12.9 kB] Get:11 http://localhost:9999 unstable/main 2013-07-13-2032.15.pdiff [1809 B] Get:12 http://localhost:9999 unstable/main amd64 2013-07-14-0231.07.pdiff [14.9 kB] Get:13 http://localhost:9999 unstable/main 2013-07-14-0231.07.pdiff [12.9 kB] Get:14 http://localhost:9999 unstable/main 2013-07-14-0231.07.pdiff [1384 B] Get:15 http://localhost:9999 unstable/main amd64 2013-07-14-0231.07.pdiff [14.9 kB] Get:16 http://localhost:9999 unstable/main 2013-07-14-0832.16.pdiff [4670 B] Get:17 http://localhost:9999 unstable/main 2013-07-14-0231.07.pdiff [1384 B] Get:18 http://localhost:9999 unstable/main amd64 2013-07-14-0832.16.pdiff [1624 B] Get:19 http://localhost:9999 unstable/main 2013-07-14-0832.16.pdiff [4670 B] Get:20 http://localhost:9999 unstable/main 2013-07-14-0832.16.pdiff [337 B] Get:21 http://localhost:9999 unstable/main amd64 2013-07-14-0832.16.pdiff [1624 B] Get:22 http://localhost:9999 unstable/main 2013-07-14-1431.18.pdiff [11.4 kB] Get:23 http://localhost:9999 unstable/main 2013-07-14-0832.16.pdiff [337 B] Get:24 http://localhost:9999 unstable/main amd64 2013-07-14-1431.18.pdiff [8223 B] Get:25 http://localhost:9999 unstable/main 2013-07-14-1431.18.pdiff [11.4 kB] Get:26 http://localhost:9999 unstable/main 2013-07-14-1431.18.pdiff [887 B] Get:27 http://localhost:9999 unstable/main amd64 2013-07-14-1431.18.pdiff [8223 B] Get:28 http://localhost:9999 unstable/main 2013-07-14-2031.21.pdiff [9038 B] Get:29 http://localhost:9999 unstable/main 2013-07-14-1431.18.pdiff [887 B] Get:30 http://localhost:9999 unstable/main amd64 2013-07-14-2031.21.pdiff [9955 B] Get:31 http://localhost:9999 unstable/main 2013-07-14-2031.21.pdiff [9038 B] Get:32 http://localhost:9999 unstable/main 2013-07-14-2031.21.pdiff [2736 B] Get:33 http://localhost:9999 unstable/main amd64 2013-07-14-2031.21.pdiff [9955 B] Get:34 http://localhost:9999 unstable/main 2013-07-15-0229.01.pdiff [9715 B] Get:35 http://localhost:9999 unstable/main 2013-07-14-2031.21.pdiff [2736 B] Get:36 http://localhost:9999 unstable/main amd64 2013-07-15-0229.01.pdiff [12.7 kB] Get:37 http://localhost:9999 unstable/main 2013-07-15-0229.01.pdiff [9715 B] Get:38 http://localhost:9999 unstable/main 2013-07-15-0229.01.pdiff [2239 B] Get:39 http://localhost:9999 unstable/main amd64 2013-07-15-0229.01.pdiff [12.7 kB] Get:40 http://localhost:9999 unstable/main 2013-07-15-0830.19.pdiff [3273 B] Get:41 http://localhost:9999 unstable/main 2013-07-15-0229.01.pdiff [2239 B] Get:42 http://localhost:9999 unstable/main amd64 2013-07-15-0830.19.pdiff [3964 B] Get:43 http://localhost:9999 unstable/main 2013-07-15-0830.19.pdiff [3273 B] Get:44 http://localhost:9999 unstable/main 2013-07-15-0830.19.pdiff [1357 B] Get:45 http://localhost:9999 unstable/main amd64 2013-07-15-0830.19.pdiff [3964 B] Get:46 http://localhost:9999 unstable/main 2013-07-15-0830.19.pdiff [1357 B] Fetched 381 kB in 27s (13.9 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: initscripts sysv-rc sysvinit sysvinit-utils 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 405 kB of archives. After this operation, 20.5 kB disk space will be freed. Get:1 http://localhost:9999/debian/ unstable/main sysvinit amd64 2.88dsf-42 [134 kB] Get:2 http://localhost:9999/debian/ unstable/main sysv-rc all 2.88dsf-42 [80.4 kB] Get:3 http://localhost:9999/debian/ unstable/main sysvinit-utils amd64 2.88dsf-42 [103 kB] Get:4 http://localhost:9999/debian/ unstable/main initscripts amd64 2.88dsf-42 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 405 kB in 0s (5821 kB/s) (Reading database ... 13844 files and directories currently installed.) Preparing to replace sysvinit 2.88dsf-41 (using .../sysvinit_2.88dsf-42_amd64.deb) ... Unpacking replacement sysvinit ... Setting up sysvinit (2.88dsf-42) ... Not restarting sysvinit (Reading database ... 13844 files and directories currently installed.) Preparing to replace sysv-rc 2.88dsf-41 (using .../sysv-rc_2.88dsf-42_all.deb) ... Unpacking replacement sysv-rc ... Preparing to replace sysvinit-utils 2.88dsf-41 (using .../sysvinit-utils_2.88dsf-42_amd64.deb) ... Unpacking replacement sysvinit-utils ... Setting up sysvinit-utils (2.88dsf-42) ... Setting up sysv-rc (2.88dsf-42) ... (Reading database ... 13844 files and directories currently installed.) Preparing to replace initscripts 2.88dsf-41 (using .../initscripts_2.88dsf-42_amd64.deb) ... Removing unmodified and obsolete conffile /etc/init.d/mtab.sh ... Unpacking replacement initscripts ... Setting up initscripts (2.88dsf-42) ... Installing new version of config file /etc/init.d/bootmisc.sh ... Installing new version of config file /etc/init.d/checkfs.sh ... Installing new version of config file /etc/init.d/checkroot.sh ... Installing new version of config file /etc/init.d/checkroot-bootclean.sh ... Installing new version of config file /etc/init.d/mountdevsubfs.sh ... Installing new version of config file /etc/init.d/mountkernfs.sh ... Installing new version of config file /etc/init.d/rmnologin ... Installing new version of config file /etc/network/if-up.d/mountnfs ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ 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://anonscm.debian.org/debian-med/tophat.git Need to get 445 kB of source archives. Get:1 http://localhost:9999/debian/ unstable/main tophat 2.0.9-1 (dsc) [2127 B] Get:2 http://localhost:9999/debian/ unstable/main tophat 2.0.9-1 (tar) [436 kB] Get:3 http://localhost:9999/debian/ unstable/main tophat 2.0.9-1 (diff) [6415 B] Fetched 445 kB in 0s (1726 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... + echo 'Install of clang' Install of clang + apt-get update Hit http://localhost:9999 unstable InRelease Hit http://localhost:9999 unstable/main Sources/DiffIndex Hit http://localhost:9999 unstable/main amd64 Packages/DiffIndex Hit http://localhost:9999 unstable/main Translation-en/DiffIndex Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-3.3 Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libclang-common-3.3-dev libclang1-3.3 libffi6 libllvm3.3 libobjc-4.7-dev libobjc4 libstdc++6-4.7-dev Suggested packages: libstdc++6-4.7-doc Recommended packages: llvm-3.3-dev python The following NEW packages will be installed: clang-3.3 libclang-common-3.3-dev libclang1-3.3 libffi6 libllvm3.3 libobjc-4.7-dev libobjc4 libstdc++6-4.7-dev 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. Need to get 27.2 MB of archives. After this operation, 80.8 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libffi6 amd64 3.0.13-4 [21.6 kB] Get:2 http://localhost:9999/debian/ unstable/main libllvm3.3 amd64 1:3.3-3 [8575 kB] Get:3 http://localhost:9999/debian/ unstable/main libobjc4 amd64 4.8.1-6 [160 kB] Get:4 http://localhost:9999/debian/ unstable/main libstdc++6-4.7-dev amd64 4.7.3-5 [1695 kB] Get:5 http://localhost:9999/debian/ unstable/main libobjc-4.7-dev amd64 4.7.3-5 [719 kB] Get:6 http://localhost:9999/debian/ unstable/main libclang-common-3.3-dev amd64 1:3.3-3 [574 kB] Get:7 http://localhost:9999/debian/ unstable/main libclang1-3.3 amd64 1:3.3-3 [4579 kB] Get:8 http://localhost:9999/debian/ unstable/main clang-3.3 amd64 1:3.3-3 [10.9 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 27.2 MB in 1s (25.7 MB/s) Selecting previously unselected package libffi6:amd64. (Reading database ... 13843 files and directories currently installed.) Unpacking libffi6:amd64 (from .../libffi6_3.0.13-4_amd64.deb) ... Selecting previously unselected package libllvm3.3:amd64. Unpacking libllvm3.3:amd64 (from .../libllvm3.3_1%3a3.3-3_amd64.deb) ... Selecting previously unselected package libobjc4:amd64. Unpacking libobjc4:amd64 (from .../libobjc4_4.8.1-6_amd64.deb) ... Selecting previously unselected package libstdc++6-4.7-dev:amd64. Unpacking libstdc++6-4.7-dev:amd64 (from .../libstdc++6-4.7-dev_4.7.3-5_amd64.deb) ... Selecting previously unselected package libobjc-4.7-dev:amd64. Unpacking libobjc-4.7-dev:amd64 (from .../libobjc-4.7-dev_4.7.3-5_amd64.deb) ... Selecting previously unselected package libclang-common-3.3-dev. Unpacking libclang-common-3.3-dev (from .../libclang-common-3.3-dev_1%3a3.3-3_amd64.deb) ... Selecting previously unselected package libclang1-3.3. Unpacking libclang1-3.3 (from .../libclang1-3.3_1%3a3.3-3_amd64.deb) ... Selecting previously unselected package clang-3.3. Unpacking clang-3.3 (from .../clang-3.3_1%3a3.3-3_amd64.deb) ... Setting up libffi6:amd64 (3.0.13-4) ... Setting up libllvm3.3:amd64 (1:3.3-3) ... Setting up libobjc4:amd64 (4.8.1-6) ... Setting up libstdc++6-4.7-dev:amd64 (4.7.3-5) ... Setting up libobjc-4.7-dev:amd64 (4.7.3-5) ... Setting up libclang-common-3.3-dev (1:3.3-3) ... Setting up libclang1-3.3 (1:3.3-3) ... Setting up clang-3.3 (1:3.3-3) ... Processing triggers for libc-bin ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8' + cd /usr/bin + for VERSION in '$VERSIONS' + rm -f g++-4.6 gcc-4.6 cpp-4.6 + ln -s clang++ g++-4.6 + ln -s clang gcc-4.6 + ln -s clang cpp-4.6 + for VERSION in '$VERSIONS' + rm -f 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 + for VERSION in '$VERSIONS' + rm -f g++-4.8 gcc-4.8 cpp-4.8 + ln -s clang++ g++-4.8 + ln -s clang gcc-4.8 + ln -s clang cpp-4.8 + 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' + dpkg --set-selections + echo 'gcc-4.8 hold' + dpkg --set-selections + echo 'cpp-4.8 hold' + dpkg --set-selections + echo 'g++-4.8 hold' + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + grep clang + gcc --version + grep clang + cpp --version + grep clang + g++ --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-rAEUtB/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/706 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 ... 14698 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, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, 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, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, 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-UpOOhY/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 autopoint autotools-dev bsdmainutils debhelper dh-autoreconf file gettext gettext-base groff-base help2man 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 libglib2.0-0 libicu48 libmagic1 libncursesw5 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 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: curl wget lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info libltdl-dev xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf file gettext gettext-base groff-base help2man 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 libglib2.0-0 libicu48 libmagic1 libncursesw5 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 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, 50 newly installed, 0 to remove and 0 not upgraded. Need to get 36.3 MB/36.3 MB of archives. After this operation, 190 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libncursesw5 amd64 5.9+20130608-1 [141 kB] Get:2 http://localhost:9999/debian/ unstable/main libpipeline1 amd64 1.2.4-1 [41.0 kB] Get:3 http://localhost:9999/debian/ unstable/main libssl1.0.0 amd64 1.0.1e-3 [1242 kB] Get:4 http://localhost:9999/debian/ unstable/main groff-base amd64 1.22.2-3 [747 kB] Get:5 http://localhost:9999/debian/ unstable/main bsdmainutils amd64 9.0.5 [211 kB] Get:6 http://localhost:9999/debian/ unstable/main man-db amd64 2.6.5-2 [976 kB] Get:7 http://localhost:9999/debian/ unstable/main libasprintf0c2 amd64 0.18.2.1-1 [28.9 kB] Get:8 http://localhost:9999/debian/ unstable/main libmagic1 amd64 1:5.14-2 [216 kB] Get:9 http://localhost:9999/debian/ unstable/main libsqlite3-0 amd64 3.7.17-1 [478 kB] Get:10 http://localhost:9999/debian/ unstable/main libxml2 amd64 2.9.1+dfsg1-2 [911 kB] Get:11 http://localhost:9999/debian/ unstable/main libglib2.0-0 amd64 2.36.3-3 [2048 kB] Get:12 http://localhost:9999/debian/ unstable/main libcroco3 amd64 0.6.8-2 [133 kB] Get:13 http://localhost:9999/debian/ unstable/main libexpat1 amd64 2.1.0-4 [138 kB] Get:14 http://localhost:9999/debian/ unstable/main libicu48 amd64 4.8.1.1-12 [4734 kB] Get:15 http://localhost:9999/debian/ unstable/main libsigsegv2 amd64 2.10-2 [29.8 kB] Get:16 http://localhost:9999/debian/ unstable/main libunistring0 amd64 0.9.3-5 [434 kB] Get:17 http://localhost:9999/debian/ unstable/main libpython2.7-minimal amd64 2.7.5-6 [520 kB] Get:18 http://localhost:9999/debian/ unstable/main python2.7-minimal amd64 2.7.5-6 [1552 kB] Get:19 http://localhost:9999/debian/ unstable/main file amd64 1:5.14-2 [54.0 kB] Get:20 http://localhost:9999/debian/ unstable/main gettext-base amd64 0.18.2.1-1 [156 kB] Get:21 http://localhost:9999/debian/ unstable/main m4 amd64 1.4.16-5 [260 kB] Get:22 http://localhost:9999/debian/ unstable/main mime-support all 3.54 [36.4 kB] Get:23 http://localhost:9999/debian/ unstable/main libpython2.7-stdlib amd64 2.7.5-6 [2482 kB] Get:24 http://localhost:9999/debian/ unstable/main python2.7 amd64 2.7.5-6 [229 kB] Get:25 http://localhost:9999/debian/ unstable/main python-minimal amd64 2.7.5-2 [42.7 kB] Get:26 http://localhost:9999/debian/ unstable/main libpython-stdlib amd64 2.7.5-2 [19.6 kB] Get:27 http://localhost:9999/debian/ unstable/main python amd64 2.7.5-2 [186 kB] Get:28 http://localhost:9999/debian/ unstable/main autoconf all 2.69-1 [589 kB] Get:29 http://localhost:9999/debian/ unstable/main autotools-dev all 20130515.1 [73.0 kB] Get:30 http://localhost:9999/debian/ unstable/main automake all 1:1.13.3-1 [758 kB] Get:31 http://localhost:9999/debian/ unstable/main autopoint all 0.18.2.1-1 [390 kB] Get:32 http://localhost:9999/debian/ unstable/main gettext amd64 0.18.2.1-1 [2019 kB] Get:33 http://localhost:9999/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:34 http://localhost:9999/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB] Get:35 http://localhost:9999/debian/ unstable/main debhelper all 9.20130630 [710 kB] Get:36 http://localhost:9999/debian/ unstable/main libtool amd64 2.4.2-1.3 [619 kB] Get:37 http://localhost:9999/debian/ unstable/main dh-autoreconf all 9 [15.5 kB] Get:38 http://localhost:9999/debian/ unstable/main help2man amd64 1.43.3 [105 kB] Get:39 http://localhost:9999/debian/ unstable/main libbam-dev amd64 0.1.19-1 [123 kB] Get:40 http://localhost:9999/debian/ unstable/main libboost1.49-dev amd64 1.49.0-4 [9195 kB] Get:41 http://localhost:9999/debian/ unstable/main libboost-date-time1.49.0 amd64 1.49.0-4 [45.9 kB] Get:42 http://localhost:9999/debian/ unstable/main libboost-serialization1.49.0 amd64 1.49.0-4 [207 kB] Get:43 http://localhost:9999/debian/ unstable/main libboost-serialization1.49-dev amd64 1.49.0-4 [316 kB] Get:44 http://localhost:9999/debian/ unstable/main libboost-date-time1.49-dev amd64 1.49.0-4 [49.5 kB] Get:45 http://localhost:9999/debian/ unstable/main libboost-thread1.49.0 amd64 1.49.0-4 [59.9 kB] Get:46 http://localhost:9999/debian/ unstable/main libboost-thread1.49-dev amd64 1.49.0-4 [67.1 kB] Get:47 http://localhost:9999/debian/ unstable/main libboost-thread-dev amd64 1.49.0.1 [2736 B] Get:48 http://localhost:9999/debian/ unstable/main seqan-dev all 1.3.1-1 [2442 kB] Get:49 http://localhost:9999/debian/ unstable/main zlib1g-dev amd64 1:1.2.8.dfsg-1 [217 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 36.3 MB in 1s (19.8 MB/s) Selecting previously unselected package libncursesw5:amd64. (Reading database ... 14698 files and directories currently installed.) Unpacking libncursesw5:amd64 (from .../libncursesw5_5.9+20130608-1_amd64.deb) ... Selecting previously unselected package libpipeline1:amd64. Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.4-1_amd64.deb) ... Selecting previously unselected package libssl1.0.0:amd64. Unpacking libssl1.0.0:amd64 (from .../libssl1.0.0_1.0.1e-3_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.22.2-3_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.5_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.5-2_amd64.deb) ... Selecting previously unselected package libasprintf0c2:amd64. Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.2.1-1_amd64.deb) ... Selecting previously unselected package libmagic1:amd64. Unpacking libmagic1:amd64 (from .../libmagic1_1%3a5.14-2_amd64.deb) ... Selecting previously unselected package libsqlite3-0:amd64. Unpacking libsqlite3-0:amd64 (from .../libsqlite3-0_3.7.17-1_amd64.deb) ... Selecting previously unselected package libxml2:amd64. Unpacking libxml2:amd64 (from .../libxml2_2.9.1+dfsg1-2_amd64.deb) ... Selecting previously unselected package libglib2.0-0:amd64. Unpacking libglib2.0-0:amd64 (from .../libglib2.0-0_2.36.3-3_amd64.deb) ... Selecting previously unselected package libcroco3:amd64. Unpacking libcroco3:amd64 (from .../libcroco3_0.6.8-2_amd64.deb) ... Selecting previously unselected package libexpat1:amd64. Unpacking libexpat1:amd64 (from .../libexpat1_2.1.0-4_amd64.deb) ... Selecting previously unselected package libicu48:amd64. Unpacking libicu48:amd64 (from .../libicu48_4.8.1.1-12_amd64.deb) ... Selecting previously unselected package libsigsegv2:amd64. Unpacking libsigsegv2:amd64 (from .../libsigsegv2_2.10-2_amd64.deb) ... Selecting previously unselected package libunistring0:amd64. Unpacking libunistring0:amd64 (from .../libunistring0_0.9.3-5_amd64.deb) ... Selecting previously unselected package libpython2.7-minimal. Unpacking libpython2.7-minimal (from .../libpython2.7-minimal_2.7.5-6_amd64.deb) ... Selecting previously unselected package python2.7-minimal. Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.5-6_amd64.deb) ... Selecting previously unselected package file. Unpacking file (from .../file_1%3a5.14-2_amd64.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.2.1-1_amd64.deb) ... Selecting previously unselected package m4. Unpacking m4 (from .../archives/m4_1.4.16-5_amd64.deb) ... Selecting previously unselected package mime-support. Unpacking mime-support (from .../mime-support_3.54_all.deb) ... Selecting previously unselected package libpython2.7-stdlib. Unpacking libpython2.7-stdlib (from .../libpython2.7-stdlib_2.7.5-6_amd64.deb) ... Selecting previously unselected package python2.7. Unpacking python2.7 (from .../python2.7_2.7.5-6_amd64.deb) ... Selecting previously unselected package python-minimal. Unpacking python-minimal (from .../python-minimal_2.7.5-2_amd64.deb) ... Selecting previously unselected package libpython-stdlib:amd64. Unpacking libpython-stdlib:amd64 (from .../libpython-stdlib_2.7.5-2_amd64.deb) ... Selecting previously unselected package python. Unpacking python (from .../python_2.7.5-2_amd64.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_20130515.1_all.deb) ... Selecting previously unselected package automake. Unpacking automake (from .../automake_1%3a1.13.3-1_all.deb) ... Selecting previously unselected package autopoint. Unpacking autopoint (from .../autopoint_0.18.2.1-1_all.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.2.1-1_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. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_9.20130630_all.deb) ... Selecting previously unselected package libtool. Unpacking libtool (from .../libtool_2.4.2-1.3_amd64.deb) ... Selecting previously unselected package dh-autoreconf. Unpacking dh-autoreconf (from .../dh-autoreconf_9_all.deb) ... Selecting previously unselected package help2man. Unpacking help2man (from .../help2man_1.43.3_amd64.deb) ... Selecting previously unselected package libbam-dev. Unpacking libbam-dev (from .../libbam-dev_0.1.19-1_amd64.deb) ... Selecting previously unselected package libboost1.49-dev. Unpacking libboost1.49-dev (from .../libboost1.49-dev_1.49.0-4_amd64.deb) ... Selecting previously unselected package libboost-date-time1.49.0. Unpacking libboost-date-time1.49.0 (from .../libboost-date-time1.49.0_1.49.0-4_amd64.deb) ... Selecting previously unselected package libboost-serialization1.49.0. Unpacking libboost-serialization1.49.0 (from .../libboost-serialization1.49.0_1.49.0-4_amd64.deb) ... Selecting previously unselected package libboost-serialization1.49-dev. Unpacking libboost-serialization1.49-dev (from .../libboost-serialization1.49-dev_1.49.0-4_amd64.deb) ... Selecting previously unselected package libboost-date-time1.49-dev. Unpacking libboost-date-time1.49-dev (from .../libboost-date-time1.49-dev_1.49.0-4_amd64.deb) ... Selecting previously unselected package libboost-thread1.49.0. Unpacking libboost-thread1.49.0 (from .../libboost-thread1.49.0_1.49.0-4_amd64.deb) ... Selecting previously unselected package libboost-thread1.49-dev. Unpacking libboost-thread1.49-dev (from .../libboost-thread1.49-dev_1.49.0-4_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%3a1.2.8.dfsg-1_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+20130608-1) ... Setting up libpipeline1:amd64 (1.2.4-1) ... Setting up libssl1.0.0:amd64 (1.0.1e-3) ... Setting up groff-base (1.22.2-3) ... Setting up bsdmainutils (9.0.5) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up man-db (2.6.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libasprintf0c2:amd64 (0.18.2.1-1) ... Setting up libmagic1:amd64 (1:5.14-2) ... Setting up libsqlite3-0:amd64 (3.7.17-1) ... Setting up libxml2:amd64 (2.9.1+dfsg1-2) ... Setting up libglib2.0-0:amd64 (2.36.3-3) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.8-2) ... Setting up libexpat1:amd64 (2.1.0-4) ... Setting up libicu48:amd64 (4.8.1.1-12) ... Setting up libsigsegv2:amd64 (2.10-2) ... Setting up libunistring0:amd64 (0.9.3-5) ... Setting up libpython2.7-minimal (2.7.5-6) ... Setting up python2.7-minimal (2.7.5-6) ... Setting up file (1:5.14-2) ... Setting up gettext-base (0.18.2.1-1) ... Setting up m4 (1.4.16-5) ... Setting up mime-support (3.54) ... Setting up libpython2.7-stdlib (2.7.5-6) ... Setting up python2.7 (2.7.5-6) ... Setting up python-minimal (2.7.5-2) ... Setting up libpython-stdlib:amd64 (2.7.5-2) ... Setting up python (2.7.5-2) ... Setting up autoconf (2.69-1) ... Setting up autotools-dev (20130515.1) ... Setting up automake (1:1.13.3-1) ... update-alternatives: using /usr/bin/automake-1.13 to provide /usr/bin/automake (automake) in auto mode Setting up autopoint (0.18.2.1-1) ... Setting up gettext (0.18.2.1-1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20130630) ... Setting up libtool (2.4.2-1.3) ... Setting up dh-autoreconf (9) ... Setting up help2man (1.43.3) ... Setting up libbam-dev (0.1.19-1) ... Setting up libboost1.49-dev (1.49.0-4) ... Setting up libboost-date-time1.49.0 (1.49.0-4) ... Setting up libboost-serialization1.49.0 (1.49.0-4) ... Setting up libboost-serialization1.49-dev (1.49.0-4) ... Setting up libboost-date-time1.49-dev (1.49.0-4) ... Setting up libboost-thread1.49.0 (1.49.0-4) ... Setting up libboost-thread1.49-dev (1.49.0-4) ... Setting up libboost-thread-dev (1.49.0.1) ... Setting up seqan-dev (1.3.1-1) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-1) ... Setting up sbuild-build-depends-tophat-dummy (0.invalid.0) ... Processing triggers for libc-bin ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-xen-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.23.52.20130620-1 dpkg-dev_1.16.10 g++-4.6_4.6.4-4 g++-4.8_4.8.1-6 gcc-4.6_4.6.4-4 gcc-4.7_4.7.3-5 gcc-4.8_4.8.1-6 libc6-dev_2.17-7 libstdc++-4.8-dev_4.8.1-6 libstdc++6_4.8.1-6 libstdc++6-4.6-dev_4.6.4-4 libstdc++6-4.7-dev_4.7.3-5 linux-libc-dev_3.9.8-1 Package versions: apt_0.9.9.1 autoconf_2.69-1 automake_1:1.13.3-1 autopoint_0.18.2.1-1 autotools-dev_20130515.1 base-files_7.2 base-passwd_3.5.26 bash_4.2+dfsg-1 binutils_2.23.52.20130620-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.5 build-essential_11.6 bzip2_1.0.6-4 clang-3.3_1:3.3-3 coreutils_8.20-3 cpp_4:4.8.1-2 cpp-4.6_4.6.4-4 cpp-4.7_4.7.3-5 cpp-4.8_4.8.1-6 dash_0.5.7-3 debconf_1.5.50 debconf-i18n_1.5.50 debfoster_2.7-1.2 debhelper_9.20130630 debian-archive-keyring_2012.4 debianutils_4.3.4 dh-autoreconf_9 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.8-1 e2fsprogs_1.42.8-1 fakeroot_1.19-2 file_1:5.14-2 findutils_4.4.2-6 g++_4:4.8.1-2 g++-4.6_4.6.4-4 g++-4.8_4.8.1-6 gcc_4:4.8.1-2 gcc-4.4-base_4.4.7-4 gcc-4.5-base_4.5.4-1 gcc-4.6_4.6.4-4 gcc-4.6-base_4.6.4-4 gcc-4.7_4.7.3-5 gcc-4.7-base_4.7.3-5 gcc-4.8_4.8.1-6 gcc-4.8-base_4.8.1-6 gettext_0.18.2.1-1 gettext-base_0.18.2.1-1 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-2 groff-base_1.22.2-3 gzip_1.6-1 help2man_1.43.3 hostname_3.13 initscripts_2.88dsf-42 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.52-1 libapt-pkg4.12_0.9.9.1 libasan0_4.8.1-6 libasprintf0c2_0.18.2.1-1 libatomic1_4.8.1-6 libattr1_1:2.4.47-1 libbam-dev_0.1.19-1 libblkid1_2.20.1-5.5 libboost-date-time1.49-dev_1.49.0-4 libboost-date-time1.49.0_1.49.0-4 libboost-serialization1.49-dev_1.49.0-4 libboost-serialization1.49.0_1.49.0-4 libboost-thread-dev_1.49.0.1 libboost-thread1.49-dev_1.49.0-4 libboost-thread1.49.0_1.49.0-4 libboost1.49-dev_1.49.0-4 libbz2-1.0_1.0.6-4 libc-bin_2.17-7 libc-dev-bin_2.17-7 libc6_2.17-7 libc6-dev_2.17-7 libcap2_1:2.22-1.2 libclang-common-3.3-dev_1:3.3-3 libclang1-3.3_1:3.3-3 libclass-isa-perl_0.36-5 libcloog-isl4_0.18.0-2 libcloog-ppl1_0.16.1-3 libcomerr2_1.42.8-1 libcroco3_0.6.8-2 libdb5.1_5.1.29-6 libdpkg-perl_1.16.10 libexpat1_2.1.0-4 libffi6_3.0.13-4 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.2d-5 libgcc-4.7-dev_4.7.3-5 libgcc-4.8-dev_4.8.1-6 libgcc1_1:4.8.1-6 libgdbm3_1.8.3-12 libglib2.0-0_2.36.3-3 libgmp10_2:5.1.2+dfsg-2 libgmpxx4ldbl_2:5.1.2+dfsg-2 libgomp1_4.8.1-6 libgpm2_1.20.4-6.1 libicu48_4.8.1.1-12 libisl10_0.11.2-1 libitm1_4.8.1-6 libllvm3.3_1:3.3-3 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.14-2 libmount1_2.20.1-5.5 libmpc2_0.9-4 libmpc3_1.0.1-1 libmpfr4_3.1.1-1 libncurses5_5.9+20130608-1 libncursesw5_5.9+20130608-1 libobjc-4.7-dev_4.7.3-5 libobjc4_4.8.1-6 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.4-1 libppl-c4_1:1.0-7 libppl12_1:1.0-7 libpython-stdlib_2.7.5-2 libpython2.7-minimal_2.7.5-6 libpython2.7-stdlib_2.7.5-6 libquadmath0_4.8.1-6 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.13-2 libsemanage-common_2.1.10-2 libsemanage1_2.1.10-2 libsepol1_2.1.9-2 libsigsegv2_2.10-2 libslang2_2.2.4-15 libsqlite3-0_3.7.17-1 libss2_1.42.8-1 libssl1.0.0_1.0.1e-3 libstdc++-4.8-dev_4.8.1-6 libstdc++6_4.8.1-6 libstdc++6-4.6-dev_4.6.4-4 libstdc++6-4.7-dev_4.7.3-5 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+20130608-1 libtool_2.4.2-1.3 libtsan0_4.8.1-6 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.2 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.5 libxml2_2.9.1+dfsg1-2 linux-libc-dev_3.9.8-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian12 m4_1.4.16-5 make_3.81-8.2 man-db_2.6.5-2 mawk_1.3.3-17 mime-support_3.54 mount_2.20.1-5.5 multiarch-support_2.17-7 ncurses-base_5.9+20130608-1 ncurses-bin_5.9+20130608-1 passwd_1:4.1.5.1-1 patch_2.7.1-3 perl_5.14.2-21 perl-base_5.14.2-21 perl-modules_5.14.2-21 po-debconf_1.0.16+nmu2 python_2.7.5-2 python-minimal_2.7.5-2 python2.7_2.7.5-6 python2.7-minimal_2.7.5-6 readline-common_6.2+dfsg-0.1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-tophat-dummy_0.invalid.0 sed_4.2.2-1 sensible-utils_0.0.9 seqan-dev_1.3.1-1 sudo_1.8.5p2-1+nmu1 sysv-rc_2.88dsf-42 sysvinit_2.88dsf-42 sysvinit-utils_2.88dsf-42 tar_1.26+dfsg-6 tzdata_2013c-2 ucf_3.0027+nmu1 util-linux_2.20.1-5.5 vim_2:7.3.923-3 vim-common_2:7.3.923-3 vim-runtime_2:7.3.923-3 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1 zlib1g-dev_1:1.2.8.dfsg-1 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Thu Jul 4 15:05:07 2013 UTC using RSA key ID 1B5228B0 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./tophat_2.0.9-1.dsc dpkg-source: info: extracting tophat in tophat-2.0.9 dpkg-source: info: unpacking tophat_2.0.9.orig.tar.gz dpkg-source: info: unpacking tophat_2.0.9-1.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 Hack binNMU version ─────────────────── Created changelog entry for binNMU version 2.0.9-1clang1 User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=user PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=user SCHROOT_SESSION_ID=unstable-amd64-sbuild-28d3f931-d51b-48ec-80df-ef4db8dadeea SCHROOT_UID=1000 SCHROOT_USER=user SHELL=/bin/sh USER=user dpkg-buildpackage ───────────────── dpkg-buildpackage: source package tophat dpkg-buildpackage: source version 2.0.9-1clang1 dpkg-source --before-build tophat-2.0.9 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 debian/rules build-arch dh build-arch --with autoreconf dh_testdir -a dh_autoreconf -a 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.m4:33: 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.m4:33: 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.m4:33: 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.m4:33: 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.m4:33: AX_BOOST_THREAD is expanded from... configure.ac:35: the top level /usr/share/automake-1.13/am/library.am: warning: 'libgc.a': linking libraries using a non-POSIX /usr/share/automake-1.13/am/library.am: archiver requires 'AM_PROG_AR' in 'configure.ac' src/Makefile.am:561: while processing library 'libgc.a' /usr/share/automake-1.13/am/library.am: warning: 'libtophat.a': linking libraries using a non-POSIX /usr/share/automake-1.13/am/library.am: archiver requires 'AM_PROG_AR' in 'configure.ac' src/Makefile.am:561: while processing library 'libtophat.a' 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 -a ./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 whether make supports nested variables... 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 checking that generated files are newer than configure... done 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 2.0.9 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 3.3-3 (branches/release_33) (based on LLVM 3.3) 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 -a 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 In file included from reads.cpp:26: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 3 warnings generated. 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 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 In file included from bwt_map.cpp:27: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ ./bwt_map.h:950:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:951:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:952:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ ./bwt_map.h:1033:7: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:1034:7: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:1035:7: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ ./bwt_map.h:1053:8: warning: private field '_spliced' is not used [-Wunused-private-field] bool _spliced; ^ 10 warnings 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 common.o common.cpp 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 In file included from junctions.cpp:16: In file included from ./junctions.h:23: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 3 warnings 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 insertions.o insertions.cpp In file included from insertions.cpp:34: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 3 warnings 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 deletions.o deletions.cpp In file included from deletions.cpp:15: In file included from ./deletions.h:22: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 3 warnings 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 fusions.o fusions.cpp In file included from fusions.cpp:33: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 3 warnings 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 align_status.o align_status.cpp In file included from align_status.cpp:20: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 3 warnings 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 fragments.o fragments.cpp In file included from fragments.cpp:15: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 3 warnings 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 tokenize.o tokenize.cpp 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 In file included from inserts.cpp:17: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 3 warnings 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 qual.o qual.cpp 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 bam_merge_impl.o bam_merge_impl.cpp 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 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 In file included from coverage.cpp:15: In file included from ./coverage.h:17: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 3 warnings generated. 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 bam_merge_impl.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 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 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 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 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 In file included from GFaSeqGet.cpp:1: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: 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 In file included from gff.cpp:1: In file included from ./gff.h:7: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: 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 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 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 In file included from GTFToFasta.cpp:7: In file included from ./GTFToFasta.h:27: In file included from ./gff.h:7: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: 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 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 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 In file included from fix_map_ordering.cpp:18: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 3 warnings generated. 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 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 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 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 In file included from segment_juncs.cpp:39: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 3 warnings generated. 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 -L/usr/lib -Wl,-z,relro -o segment_juncs segment_juncs.o ../src/libtophat.a -lboost_thread-mt -lbam -lz 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 gtf_juncs.o gtf_juncs.cpp In file included from gtf_juncs.cpp:21: In file included from ./gff.h:7: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ In file included from gtf_juncs.cpp:24: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 4 warnings generated. 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_juncs gtf_juncs.o ../src/libtophat.a libgc.a -lbam -lz 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 juncs_db.o juncs_db.cpp juncs_db.cpp:85:22: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] if (insertion.left >= 0 && insertion.left <= ref_len) ~~~~~~~~~~~~~~ ^ ~ juncs_db.cpp:124:21: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] if (junction.left >= 0 && junction.left <= ref_len && ~~~~~~~~~~~~~ ^ ~ juncs_db.cpp:125:22: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] junction.right >= 0 && junction.right <= ref_len) ~~~~~~~~~~~~~~ ^ ~ juncs_db.cpp:168:19: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] if (fusion.left >= 0 && fusion.left < left_ref_len && ~~~~~~~~~~~ ^ ~ juncs_db.cpp:169:20: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] fusion.right >= 0 && fusion.right < right_ref_len) ~~~~~~~~~~~~ ^ ~ juncs_db.cpp:124:21: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] if (junction.left >= 0 && junction.left <= ref_len && ~~~~~~~~~~~~~ ^ ~ juncs_db.cpp:485:8: note: in instantiation of function template specialization 'print_splice, seqan::Packed > > >' requested here print_splice(itr->first, read_length, itr->first.antisense ? "GTAG|rev" : "GTAG|fwd", *ref_str, name, cout); ^ juncs_db.cpp:125:22: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] junction.right >= 0 && junction.right <= ref_len) ~~~~~~~~~~~~~~ ^ ~ juncs_db.cpp:85:22: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] if (insertion.left >= 0 && insertion.left <= ref_len) ~~~~~~~~~~~~~~ ^ ~ juncs_db.cpp:508:6: note: in instantiation of function template specialization 'print_insertion, seqan::Packed > > >' requested here print_insertion(*itr, read_length, *ref_str, name, cout); ^ juncs_db.cpp:168:19: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] if (fusion.left >= 0 && fusion.left < left_ref_len && ~~~~~~~~~~~ ^ ~ juncs_db.cpp:522:6: note: in instantiation of function template specialization 'print_fusion, seqan::Packed > > >' requested here print_fusion(*itr, read_length, *left_ref_str, *right_ref_str, left_ref_name, right_ref_name, cout); ^ juncs_db.cpp:169:20: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] fusion.right >= 0 && fusion.right < right_ref_len) ~~~~~~~~~~~~ ^ ~ In file included from juncs_db.cpp:33: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 13 warnings generated. 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 juncs_db juncs_db.o ../src/libtophat.a -lbam -lz 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 long_spanning_reads.o long_spanning_reads.cpp In file included from long_spanning_reads.cpp:38: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 3 warnings generated. 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 -L/usr/lib -Wl,-z,relro -o long_spanning_reads long_spanning_reads.o ../src/libtophat.a -lboost_thread-mt -lbam -lz 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 bam_merge.o bam_merge.cpp 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 bam_merge bam_merge.o ../src/libtophat.a ../src/libgc.a -lbam -lz 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 map2gtf.o map2gtf.cpp In file included from map2gtf.cpp:6: In file included from ./map2gtf.h:35: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ In file included from map2gtf.cpp:6: In file included from ./map2gtf.h:31: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 4 warnings generated. 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 map2gtf map2gtf.o ../src/libtophat.a libgc.a -lbam -lz 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 tophat_reports.o tophat_reports.cpp tophat_reports.cpp:2787:30: error: variable length array of non-POD element type 'JunctionSet' (aka 'map') JunctionSet vfinal_junctions[num_threads]; ^ tophat_reports.cpp:2788:32: error: variable length array of non-POD element type 'InsertionSet' (aka 'map') InsertionSet vfinal_insertions[num_threads]; ^ tophat_reports.cpp:2789:30: error: variable length array of non-POD element type 'DeletionSet' (aka 'map') DeletionSet vfinal_deletions[num_threads]; ^ tophat_reports.cpp:2790:26: error: variable length array of non-POD element type 'FusionSet' (aka 'map') FusionSet vfinal_fusions[num_threads]; ^ In file included from tophat_reports.cpp:38: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ tophat_reports.cpp:1956:13: warning: private field '_it' is not used [-Wunused-private-field] ReadTable& _it; ^ tophat_reports.cpp:1957:20: warning: private field '_rt' is not used [-Wunused-private-field] RefSequenceTable& _rt; ^ 5 warnings and 4 errors generated. make[3]: *** [tophat_reports.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[2]: Leaving directory `/«PKGBUILDDIR»' make[1]: Leaving directory `/«PKGBUILDDIR»' make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20130715-1339 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 47732 Build-Time: 103 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 18 Job: tophat_2.0.9-1 Machine Architecture: amd64 Package: tophat Package-Time: 170 Source-Version: 2.0.9-1 Space: 47732 Status: attempted Version: 2.0.9-1clang1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20130715-1339 Build needed 00:02:50, 47732k disc space DC-Status: Failed 171.255323886s DC-Time-Estimation: 171.255323886 versus expected 1 (r/m: 170.255323886 ; m: 1.0)