DC-Build-Header: tophat 2.0.12+dfsg-2 / 2014-09-04 15:38:39 +0000 DC-Task: source:tophat version:2.0.12+dfsg-2 architecture:any chroot:unstable esttime: logfile:/tmp/tophat_2.0.12+dfsg-2_unstable_clang.log modes:binary-only:parallel: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_2.0.12+dfsg-2' sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on ip-172-31-15-83.us-west-2.compute.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ tophat 2.0.12+dfsg-2clang1 (amd64) 04 Sep 2014 15:38 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: tophat Version: 2.0.12+dfsg-2clang1 Source Version: 2.0.12+dfsg-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/tophat-XvTLe3/tophat-2.0.12+dfsg' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/tophat-XvTLe3' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-2814fdcf-d0ca-42e4-921f-8170665f1a40' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Get:1 http://localhost:9999 unstable InRelease [233 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 2014-09-03-1436.55.pdiff [24.7 kB] Get:6 http://localhost:9999 unstable/main 2014-09-03-2030.01.pdiff [10.5 kB] Get:7 http://localhost:9999 unstable/main 2014-09-04-0229.22.pdiff [7545 B] Get:8 http://localhost:9999 unstable/main 2014-09-04-0831.05.pdiff [14.0 kB] Get:9 http://localhost:9999 unstable/main amd64 2014-09-03-1436.55.pdiff [26.7 kB] Get:10 http://localhost:9999 unstable/main 2014-09-04-0831.05.pdiff [14.0 kB] Get:11 http://localhost:9999 unstable/main amd64 2014-09-03-2030.01.pdiff [12.4 kB] Get:12 http://localhost:9999 unstable/main amd64 2014-09-04-0229.22.pdiff [5892 B] Get:13 http://localhost:9999 unstable/main amd64 2014-09-04-0831.05.pdiff [18.1 kB] Get:14 http://localhost:9999 unstable/main 2014-09-03-1436.55.pdiff [3960 B] Get:15 http://localhost:9999 unstable/main 2014-09-03-2030.01.pdiff [1010 B] Get:16 http://localhost:9999 unstable/main 2014-09-04-0229.22.pdiff [648 B] Get:17 http://localhost:9999 unstable/main 2014-09-04-0831.05.pdiff [61 B] Get:18 http://localhost:9999 unstable/main amd64 2014-09-04-0831.05.pdiff [18.1 kB] Get:19 http://localhost:9999 unstable/main 2014-09-04-0831.05.pdiff [61 B] Fetched 382 kB in 5s (69.1 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: binutils 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3310 kB of archives. After this operation, 50.2 kB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main binutils amd64 2.24.51.20140903-1 [3310 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3310 kB in 0s (29.9 MB/s) (Reading database ... 15135 files and directories currently installed.) Preparing to unpack .../binutils_2.24.51.20140903-1_amd64.deb ... Unpacking binutils (2.24.51.20140903-1) over (2.24.51.20140818-1) ... Setting up binutils (2.24.51.20140903-1) ... Processing triggers for libc-bin (2.19-10) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ 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 451 kB of source archives. Get:1 http://localhost:9999/debian/ unstable/main tophat 2.0.12+dfsg-2 (dsc) [2170 B] Get:2 http://localhost:9999/debian/ unstable/main tophat 2.0.12+dfsg-2 (tar) [441 kB] Get:3 http://localhost:9999/debian/ unstable/main tophat 2.0.12+dfsg-2 (diff) [7316 B] Fetched 451 kB in 1s (306 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... + CLANG_VERSION=3.5 + echo 'Install of clang-3.5' Install of clang-3.5 + apt-get update Hit http://localhost:9999 unstable InRelease Get:1 http://localhost:9999 unstable/main Sources/DiffIndex [7876 B] Get:2 http://localhost:9999 unstable/main amd64 Packages/DiffIndex [7876 B] Get:3 http://localhost:9999 unstable/main Translation-en/DiffIndex [7876 B] Fetched 23.6 kB in 1s (12.0 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-3.5 Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libbsd0 libclang-common-3.5-dev libclang1-3.5 libedit2 libffi6 libllvm3.5 libobjc-4.9-dev libobjc4 Suggested packages: gnustep gnustep-devel clang-3.5-doc Recommended packages: llvm-3.5-dev python The following NEW packages will be installed: clang-3.5 libbsd0 libclang-common-3.5-dev libclang1-3.5 libedit2 libffi6 libllvm3.5 libobjc-4.9-dev libobjc4 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. Need to get 33.3 MB of archives. After this operation, 132 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libbsd0 amd64 0.7.0-2 [67.9 kB] Get:2 http://localhost:9999/debian/ unstable/main libedit2 amd64 3.1-20140620-2 [85.1 kB] Get:3 http://localhost:9999/debian/ unstable/main libffi6 amd64 3.1-2 [19.8 kB] Get:4 http://localhost:9999/debian/ unstable/main libllvm3.5 amd64 1:3.5-1 [7609 kB] Get:5 http://localhost:9999/debian/ unstable/main libobjc4 amd64 4.9.1-12 [112 kB] Get:6 http://localhost:9999/debian/ unstable/main libobjc-4.9-dev amd64 4.9.1-12 [372 kB] Get:7 http://localhost:9999/debian/ unstable/main libclang1-3.5 amd64 1:3.5-1 [3628 kB] Get:8 http://localhost:9999/debian/ unstable/main libclang-common-3.5-dev amd64 1:3.5-1 [677 kB] Get:9 http://localhost:9999/debian/ unstable/main clang-3.5 amd64 1:3.5-1 [20.7 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 33.3 MB in 1s (30.9 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 15135 files and directories currently installed.) Preparing to unpack .../libbsd0_0.7.0-2_amd64.deb ... Unpacking libbsd0:amd64 (0.7.0-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../libedit2_3.1-20140620-2_amd64.deb ... Unpacking libedit2:amd64 (3.1-20140620-2) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../libffi6_3.1-2_amd64.deb ... Unpacking libffi6:amd64 (3.1-2) ... Selecting previously unselected package libllvm3.5:amd64. Preparing to unpack .../libllvm3.5_1%3a3.5-1_amd64.deb ... Unpacking libllvm3.5:amd64 (1:3.5-1) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../libobjc4_4.9.1-12_amd64.deb ... Unpacking libobjc4:amd64 (4.9.1-12) ... Selecting previously unselected package libobjc-4.9-dev:amd64. Preparing to unpack .../libobjc-4.9-dev_4.9.1-12_amd64.deb ... Unpacking libobjc-4.9-dev:amd64 (4.9.1-12) ... Selecting previously unselected package libclang1-3.5:amd64. Preparing to unpack .../libclang1-3.5_1%3a3.5-1_amd64.deb ... Unpacking libclang1-3.5:amd64 (1:3.5-1) ... Selecting previously unselected package libclang-common-3.5-dev. Preparing to unpack .../libclang-common-3.5-dev_1%3a3.5-1_amd64.deb ... Unpacking libclang-common-3.5-dev (1:3.5-1) ... Selecting previously unselected package clang-3.5. Preparing to unpack .../clang-3.5_1%3a3.5-1_amd64.deb ... Unpacking clang-3.5 (1:3.5-1) ... Setting up libbsd0:amd64 (0.7.0-2) ... Setting up libedit2:amd64 (3.1-20140620-2) ... Setting up libffi6:amd64 (3.1-2) ... Setting up libllvm3.5:amd64 (1:3.5-1) ... Setting up libobjc4:amd64 (4.9.1-12) ... Setting up libobjc-4.9-dev:amd64 (4.9.1-12) ... Setting up libclang1-3.5:amd64 (1:3.5-1) ... Setting up libclang-common-3.5-dev (1:3.5-1) ... Setting up clang-3.5 (1:3.5-1) ... Processing triggers for libc-bin (2.19-10) ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9' + cd /usr/bin + for VERSION in '$VERSIONS' + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-3.5 g++-4.6 + ln -s clang-3.5 gcc-4.6 + ln -s clang-3.5 cpp-4.6 + ln -s clang-3.5 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections + echo 'g++-4.6 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-3.5 g++-4.7 + ln -s clang-3.5 gcc-4.7 + ln -s clang-3.5 cpp-4.7 + ln -s clang-3.5 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections + echo 'g++-4.7 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-3.5 g++-4.8 + ln -s clang-3.5 gcc-4.8 + ln -s clang-3.5 cpp-4.8 + ln -s clang-3.5 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-3.5 g++-4.9 + ln -s clang-3.5 gcc-4.9 + ln -s clang-3.5 cpp-4.9 + ln -s clang-3.5 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections + echo 'g++-4.9 hold' + dpkg --set-selections + cd - /«BUILDDIR» + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang 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-PPUzUx/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/818 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 ... 15338 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... 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, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), autotools-dev, libbam-dev (>= 0.1.16), zlib1g-dev, dh-autoreconf, python, seqan-dev (>= 1.4), libboost-system-dev, libboost-thread-dev, help2man Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), autotools-dev, libbam-dev (>= 0.1.16), zlib1g-dev, dh-autoreconf, python, seqan-dev (>= 1.4), libboost-system-dev, libboost-thread-dev, help2man dpkg-deb: building package `sbuild-build-depends-tophat-dummy' in `/«BUILDDIR»/resolver-euuEVU/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-atomic1.55-dev libboost-atomic1.55.0 libboost-chrono1.55-dev libboost-chrono1.55.0 libboost-date-time1.55-dev libboost-date-time1.55.0 libboost-serialization1.55-dev libboost-serialization1.55.0 libboost-system-dev libboost-system1.55-dev libboost-system1.55.0 libboost-thread-dev libboost-thread1.55-dev libboost-thread1.55.0 libboost1.55-dev libcroco3 libglib2.0-0 libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libsqlite3-0 libssl1.0.0 libtool libtool-bin libunistring0 libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal seqan-dev zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican wordlist whois vacation dh-make gettext-doc groff libboost1.55-doc libboost-context1.55-dev libboost-coroutine1.55-dev libboost-exception1.55-dev libboost-filesystem1.55-dev libboost-graph1.55-dev libboost-graph-parallel1.55-dev libboost-iostreams1.55-dev libboost-locale1.55-dev libboost-log1.55-dev libboost-math1.55-dev libboost-mpi1.55-dev libboost-mpi-python1.55-dev libboost-program-options1.55-dev libboost-python1.55-dev libboost-random1.55-dev libboost-regex1.55-dev libboost-signals1.55-dev libboost-test1.55-dev libboost-timer1.55-dev libboost-wave1.55-dev libboost1.55-tools-dev libmpfrc++-dev libntl-dev libtool-doc automaken gfortran fortran95-compiler gcj-jdk 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-atomic1.55-dev libboost-atomic1.55.0 libboost-chrono1.55-dev libboost-chrono1.55.0 libboost-date-time1.55-dev libboost-date-time1.55.0 libboost-serialization1.55-dev libboost-serialization1.55.0 libboost-system-dev libboost-system1.55-dev libboost-system1.55.0 libboost-thread-dev libboost-thread1.55-dev libboost-thread1.55.0 libboost1.55-dev libcroco3 libglib2.0-0 libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libsqlite3-0 libssl1.0.0 libtool libtool-bin 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, 55 newly installed, 0 to remove and 0 not upgraded. Need to get 26.0 MB/26.0 MB of archives. After this operation, 180 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libpipeline1 amd64 1.3.0-1 [25.8 kB] Get:2 http://localhost:9999/debian/ unstable/main libssl1.0.0 amd64 1.0.1i-2 [1026 kB] Get:3 http://localhost:9999/debian/ unstable/main groff-base amd64 1.22.2-7 [1142 kB] Get:4 http://localhost:9999/debian/ unstable/main bsdmainutils amd64 9.0.5 [211 kB] Get:5 http://localhost:9999/debian/ unstable/main man-db amd64 2.6.7.1-1 [990 kB] Get:6 http://localhost:9999/debian/ unstable/main libasprintf0c2 amd64 0.19.2-2 [30.8 kB] Get:7 http://localhost:9999/debian/ unstable/main libmagic1 amd64 1:5.19-1 [237 kB] Get:8 http://localhost:9999/debian/ unstable/main libsqlite3-0 amd64 3.8.6-1 [431 kB] Get:9 http://localhost:9999/debian/ unstable/main libxml2 amd64 2.9.1+dfsg1-4 [797 kB] Get:10 http://localhost:9999/debian/ unstable/main libboost-atomic1.55.0 amd64 1.55.0+dfsg-2 [28.2 kB] Get:11 http://localhost:9999/debian/ unstable/main libboost-system1.55.0 amd64 1.55.0+dfsg-2 [30.2 kB] Get:12 http://localhost:9999/debian/ unstable/main libboost-chrono1.55.0 amd64 1.55.0+dfsg-2 [34.7 kB] Get:13 http://localhost:9999/debian/ unstable/main libboost-date-time1.55.0 amd64 1.55.0+dfsg-2 [40.8 kB] Get:14 http://localhost:9999/debian/ unstable/main libboost-serialization1.55.0 amd64 1.55.0+dfsg-2 [146 kB] Get:15 http://localhost:9999/debian/ unstable/main libboost-thread1.55.0 amd64 1.55.0+dfsg-2 [49.4 kB] Get:16 http://localhost:9999/debian/ unstable/main libglib2.0-0 amd64 2.40.0-5 [2421 kB] Get:17 http://localhost:9999/debian/ unstable/main libcroco3 amd64 0.6.8-3 [135 kB] Get:18 http://localhost:9999/debian/ unstable/main libsigsegv2 amd64 2.10-4 [28.8 kB] Get:19 http://localhost:9999/debian/ unstable/main libunistring0 amd64 0.9.3-5.2 [283 kB] Get:20 http://localhost:9999/debian/ unstable/main libpython2.7-minimal amd64 2.7.8-6 [349 kB] Get:21 http://localhost:9999/debian/ unstable/main python2.7-minimal amd64 2.7.8-6 [1374 kB] Get:22 http://localhost:9999/debian/ unstable/main file amd64 1:5.19-1 [58.0 kB] Get:23 http://localhost:9999/debian/ unstable/main gettext-base amd64 0.19.2-2 [120 kB] Get:24 http://localhost:9999/debian/ unstable/main m4 amd64 1.4.17-4 [254 kB] Get:25 http://localhost:9999/debian/ unstable/main mime-support all 3.56 [35.5 kB] Get:26 http://localhost:9999/debian/ unstable/main libpython2.7-stdlib amd64 2.7.8-6 [1883 kB] Get:27 http://localhost:9999/debian/ unstable/main python2.7 amd64 2.7.8-6 [244 kB] Get:28 http://localhost:9999/debian/ unstable/main python-minimal amd64 2.7.8-1 [39.7 kB] Get:29 http://localhost:9999/debian/ unstable/main libpython-stdlib amd64 2.7.8-1 [19.2 kB] Get:30 http://localhost:9999/debian/ unstable/main python amd64 2.7.8-1 [151 kB] Get:31 http://localhost:9999/debian/ unstable/main autoconf all 2.69-8 [340 kB] Get:32 http://localhost:9999/debian/ unstable/main autotools-dev all 20140510.1 [70.3 kB] Get:33 http://localhost:9999/debian/ unstable/main automake all 1:1.14.1-3 [725 kB] Get:34 http://localhost:9999/debian/ unstable/main autopoint all 0.19.2-2 [408 kB] Get:35 http://localhost:9999/debian/ unstable/main gettext amd64 0.19.2-2 [1237 kB] Get:36 http://localhost:9999/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:37 http://localhost:9999/debian/ unstable/main po-debconf all 1.0.16+nmu3 [220 kB] Get:38 http://localhost:9999/debian/ unstable/main debhelper all 9.20140817 [814 kB] Get:39 http://localhost:9999/debian/ unstable/main libtool-bin amd64 2.4.2-1.10 [81.6 kB] Get:40 http://localhost:9999/debian/ unstable/main libtool all 2.4.2-1.10 [190 kB] Get:41 http://localhost:9999/debian/ unstable/main dh-autoreconf all 9 [15.5 kB] Get:42 http://localhost:9999/debian/ unstable/main help2man amd64 1.46.1 [128 kB] Get:43 http://localhost:9999/debian/ unstable/main libbam-dev amd64 0.1.19-1 [123 kB] Get:44 http://localhost:9999/debian/ unstable/main libboost1.55-dev amd64 1.55.0+dfsg-2 [5812 kB] Get:45 http://localhost:9999/debian/ unstable/main libboost-atomic1.55-dev amd64 1.55.0+dfsg-2 [27.0 kB] Get:46 http://localhost:9999/debian/ unstable/main libboost-chrono1.55-dev amd64 1.55.0+dfsg-2 [36.4 kB] Get:47 http://localhost:9999/debian/ unstable/main libboost-serialization1.55-dev amd64 1.55.0+dfsg-2 [174 kB] Get:48 http://localhost:9999/debian/ unstable/main libboost-date-time1.55-dev amd64 1.55.0+dfsg-2 [47.5 kB] Get:49 http://localhost:9999/debian/ unstable/main libboost-system1.55-dev amd64 1.55.0+dfsg-2 [30.7 kB] Get:50 http://localhost:9999/debian/ unstable/main libboost-system-dev amd64 1.55.0.2 [3152 B] Get:51 http://localhost:9999/debian/ unstable/main libboost-thread1.55-dev amd64 1.55.0+dfsg-2 [49.1 kB] Get:52 http://localhost:9999/debian/ unstable/main libboost-thread-dev amd64 1.55.0.2 [3034 B] Get:53 http://localhost:9999/debian/ unstable/main seqan-dev all 1.4.1+dfsg-2 [2616 kB] Get:54 http://localhost:9999/debian/ unstable/main zlib1g-dev amd64 1:1.2.8.dfsg-2 [205 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 26.0 MB in 4s (6460 kB/s) Selecting previously unselected package libpipeline1:amd64. (Reading database ... 15338 files and directories currently installed.) Preparing to unpack .../libpipeline1_1.3.0-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.3.0-1) ... Selecting previously unselected package libssl1.0.0:amd64. Preparing to unpack .../libssl1.0.0_1.0.1i-2_amd64.deb ... Unpacking libssl1.0.0:amd64 (1.0.1i-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.2-7_amd64.deb ... Unpacking groff-base (1.22.2-7) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.5_amd64.deb ... Unpacking bsdmainutils (9.0.5) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.6.7.1-1_amd64.deb ... Unpacking man-db (2.6.7.1-1) ... Selecting previously unselected package libasprintf0c2:amd64. Preparing to unpack .../libasprintf0c2_0.19.2-2_amd64.deb ... Unpacking libasprintf0c2:amd64 (0.19.2-2) ... Selecting previously unselected package libmagic1:amd64. 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Processing triggers for libc-bin (2.19-10) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-xen-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.24.51.20140903-1 dpkg-dev_1.17.13 g++-4.6_4.6.4-7 g++-4.9_4.9.1-12 gcc-4.6_4.6.4-7 gcc-4.7_4.7.4-3 gcc-4.9_4.9.1-12 libc6-dev_2.19-10 libstdc++-4.9-dev_4.9.1-12 libstdc++6_4.9.1-12 libstdc++6-4.6-dev_4.6.4-7 linux-libc-dev_3.14.15-2 Package versions: acl_2.2.52-1.1 adduser_3.113+nmu3 apt_1.0.7 autoconf_2.69-8 automake_1:1.14.1-3 autopoint_0.19.2-2 autotools-dev_20140510.1 base-files_7.5 base-passwd_3.5.35 bash_4.3-9 binutils_2.24.51.20140903-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.7 bzip2_1.0.6-7 clang-3.5_1:3.5-1 coreutils_8.23-2 cpp_4:4.9.1-3 cpp-4.6_4.6.4-7 cpp-4.7_4.7.4-3 cpp-4.9_4.9.1-12 dash_0.5.7-4 dbus_1.8.6-2 debconf_1.5.53 debconf-i18n_1.5.53 debfoster_2.7-2 debhelper_9.20140817 debian-archive-keyring_2014.1 debianutils_4.4 dh-autoreconf_9 diffutils_1:3.3-1 dmsetup_2:1.02.88-1 dpkg_1.17.13 dpkg-dev_1.17.13 e2fslibs_1.42.12-1 e2fsprogs_1.42.12-1 fakeroot_1.20.1-1.1 file_1:5.19-1 findutils_4.4.2-9 g++_4:4.9.1-3 g++-4.6_4.6.4-7 g++-4.9_4.9.1-12 gcc_4:4.9.1-3 gcc-4.4-base_4.4.7-8 gcc-4.5-base_4.5.4-1 gcc-4.6_4.6.4-7 gcc-4.6-base_4.6.4-7 gcc-4.7_4.7.4-3 gcc-4.7-base_4.7.4-3 gcc-4.8-base_4.8.3-10 gcc-4.9_4.9.1-12 gcc-4.9-base_4.9.1-12 gettext_0.19.2-2 gettext-base_0.19.2-2 gnupg_1.4.18-3 gpgv_1.4.18-3 grep_2.20-2 groff-base_1.22.2-7 gzip_1.6-3 help2man_1.46.1 hostname_3.15 init_1.21 initscripts_2.88dsf-53.4 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.52-1.1 libalgorithm-c3-perl_0.09-1 libapt-pkg4.12_1.0.7 libarchive-extract-perl_0.72-1 libasan1_4.9.1-12 libasprintf0c2_0.19.2-2 libatomic1_4.9.1-12 libattr1_1:2.4.47-1 libaudit-common_1:2.3.7-1 libaudit1_1:2.3.7-1 libbam-dev_0.1.19-1 libblkid1_2.20.1-5.8 libboost-atomic1.55-dev_1.55.0+dfsg-2 libboost-atomic1.55.0_1.55.0+dfsg-2 libboost-chrono1.55-dev_1.55.0+dfsg-2 libboost-chrono1.55.0_1.55.0+dfsg-2 libboost-date-time1.55-dev_1.55.0+dfsg-2 libboost-date-time1.55.0_1.55.0+dfsg-2 libboost-serialization1.55-dev_1.55.0+dfsg-2 libboost-serialization1.55.0_1.55.0+dfsg-2 libboost-system-dev_1.55.0.2 libboost-system1.55-dev_1.55.0+dfsg-2 libboost-system1.55.0_1.55.0+dfsg-2 libboost-thread-dev_1.55.0.2 libboost-thread1.55-dev_1.55.0+dfsg-2 libboost-thread1.55.0_1.55.0+dfsg-2 libboost1.55-dev_1.55.0+dfsg-2 libbsd0_0.7.0-2 libbz2-1.0_1.0.6-7 libc-bin_2.19-10 libc-dev-bin_2.19-10 libc6_2.19-10 libc6-dev_2.19-10 libcap-ng0_0.7.4-2 libcap2_1:2.24-4 libcap2-bin_1:2.24-4 libcgi-fast-perl_1:2.02-1 libcgi-pm-perl_4.03-1 libcilkrts5_4.9.1-12 libclang-common-3.5-dev_1:3.5-1 libclang1-3.5_1:3.5-1 libclass-c3-perl_0.26-1 libclass-c3-xs-perl_0.13-2+b1 libclass-isa-perl_0.36-5 libcloog-isl4_0.18.2-1 libcloog-ppl1_0.16.1-5 libcomerr2_1.42.12-1 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-1 libdata-optlist-perl_0.109-1 libdata-section-perl_0.200006-1 libdb5.1_5.1.29-5 libdb5.3_5.3.28-6 libdbus-1-3_1.8.6-2 libdebconfclient0_0.191 libdevmapper1.02.1_2:1.02.88-1 libdpkg-perl_1.17.13 libedit2_3.1-20140620-2 libexpat1_2.1.0-6 libfakeroot_1.20.1-1.1 libfcgi-perl_0.77-1+b1 libffi6_3.1-2 libfile-fcntllock-perl_0.22-1+b1 libgc1c2_1:7.2d-6.3 libgcc-4.7-dev_4.7.4-3 libgcc-4.9-dev_4.9.1-12 libgcc1_1:4.9.1-12 libgcrypt11_1.5.4-3 libgcrypt20_1.6.2-3 libgdbm3_1.8.3-13 libglib2.0-0_2.40.0-5 libgmp10_2:6.0.0+dfsg-6 libgmpxx4ldbl_2:6.0.0+dfsg-6 libgomp1_4.9.1-12 libgpg-error0_1.13-4 libgpm2_1.20.4-6.1 libisl10_0.12.2-2 libitm1_4.9.1-12 libkmod2_18-1 libllvm3.5_1:3.5-1 liblocale-gettext-perl_1.05-8+b1 liblog-message-perl_0.8-1 liblog-message-simple-perl_0.10-2 liblsan0_4.9.1-12 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.19-1 libmodule-build-perl_0.420800-1 libmodule-pluggable-perl_5.1-1 libmodule-signature-perl_0.73-1 libmount1_2.20.1-5.8 libmpc2_0.9-4 libmpc3_1.0.2-1 libmpfr4_3.1.2-1 libmro-compat-perl_0.12-1 libncurses5_5.9+20140712-2 libncursesw5_5.9+20140712-2 libobjc-4.9-dev_4.9.1-12 libobjc4_4.9.1-12 libpackage-constants-perl_0.04-1 libpam-cap_1:2.24-4 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam-systemd_208-8 libpam0g_1.1.8-3.1 libparams-util-perl_1.07-2+b1 libpcre3_1:8.35-3 libpipeline1_1.3.0-1 libpod-latex-perl_0.61-1 libpod-readme-perl_0.11-1 libppl-c4_1:1.1-3 libppl13_1:1.1-3 libprocps3_1:3.3.9-7 libpython-stdlib_2.7.8-1 libpython2.7-minimal_2.7.8-6 libpython2.7-stdlib_2.7.8-6 libquadmath0_4.9.1-12 libreadline6_6.3-8 libregexp-common-perl_2013031301-1 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libsigsegv2_2.10-4 libslang2_2.2.4-17 libsoftware-license-perl_0.103010-1 libsqlite3-0_3.8.6-1 libss2_1.42.12-1 libssl1.0.0_1.0.1i-2 libstdc++-4.9-dev_4.9.1-12 libstdc++6_4.9.1-12 libstdc++6-4.6-dev_4.6.4-7 libsub-exporter-perl_0.986-1 libsub-install-perl_0.928-1 libswitch-perl_2.17-1 libsystemd-daemon0_208-8 libsystemd-journal0_208-8 libsystemd-login0_208-8 libterm-ui-perl_0.42-1 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b2 libtext-soundex-perl_3.4-1+b2 libtext-template-perl_1.46-1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140712-2 libtool_2.4.2-1.10 libtool-bin_2.4.2-1.10 libtsan0_4.9.1-12 libubsan0_4.9.1-12 libudev1_208-8 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-24 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.8 libwrap0_7.6.q-25 libxml2_2.9.1+dfsg1-4 linux-libc-dev_3.14.15-2 login_1:4.2-2+b1 lsb-base_4.1+Debian13 m4_1.4.17-4 make_4.0-8 man-db_2.6.7.1-1 mawk_1.3.3-17 mime-support_3.56 mount_2.20.1-5.8 multiarch-support_2.19-10 ncurses-base_5.9+20140712-2 ncurses-bin_5.9+20140712-2 passwd_1:4.2-2+b1 patch_2.7.1-6 perl_5.20.0-6 perl-base_5.20.0-6 perl-modules_5.20.0-6 po-debconf_1.0.16+nmu3 procps_1:3.3.9-7 psmisc_22.21-2 python_2.7.8-1 python-minimal_2.7.8-1 python2.7_2.7.8-6 python2.7-minimal_2.7.8-6 readline-common_6.3-8 rename_0.20-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-tophat-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 seqan-dev_1.4.1+dfsg-2 startpar_0.59-3 sudo_1.8.9p5-1 systemd_208-8 systemd-sysv_208-8 sysv-rc_2.88dsf-53.4 sysvinit_2.88dsf-53.4 sysvinit-utils_2.88dsf-53.4 tar_1.27.1-2 tcpd_7.6.q-25 tzdata_2014g-1 ucf_3.0030 udev_208-8 util-linux_2.20.1-5.8 vim_2:7.4.430-1 vim-common_2:7.4.430-1 vim-runtime_2:7.4.430-1 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-2 zlib1g-dev_1:1.2.8.dfsg-2 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Fri Aug 22 08:45:10 2014 UTC using RSA key ID D1C646D1 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./tophat_2.0.12+dfsg-2.dsc dpkg-source: info: extracting tophat in tophat-2.0.12+dfsg dpkg-source: info: unpacking tophat_2.0.12+dfsg.orig.tar.gz dpkg-source: info: unpacking tophat_2.0.12+dfsg-2.debian.tar.xz dpkg-source: info: applying fix_build_w_seqan1.4.patch 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 2.0.12+dfsg-2clang1 User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=10 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-2814fdcf-d0ca-42e4-921f-8170665f1a40 SCHROOT_UID=1000 SCHROOT_USER=user SHELL=/bin/sh USER=user dpkg-buildpackage ───────────────── dpkg-buildpackage: source package tophat dpkg-buildpackage: source version 2.0.12+dfsg-2clang1 dpkg-buildpackage: source distribution unstable dpkg-source --before-build tophat-2.0.12+dfsg 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 configure.ac:28: installing 'build-aux/compile' /usr/share/automake-1.14/am/library.am: warning: 'libgc.a': linking libraries using a non-POSIX /usr/share/automake-1.14/am/library.am: archiver requires 'AM_PROG_AR' in 'configure.ac' src/Makefile.am:561: while processing library 'libgc.a' /usr/share/automake-1.14/am/library.am: warning: 'libtophat.a': linking libraries using a non-POSIX /usr/share/automake-1.14/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 debian/rules override_dh_auto_configure make[1]: Entering directory '/«BUILDDIR»/tophat-2.0.12+dfsg' dh_auto_configure -- --with-boost-libdir=/usr/lib/x86_64-linux-gnu ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-boost-libdir=/usr/lib/x86_64-linux-gnu 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 whether gcc understands -c and -o together... yes 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... yes checking for exit in -lboost_system... 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 2.0.12 Configuration Results -- C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include Linker flags: -Wl,-z,relro GCC version: Debian clang version 3.5.0-1 (tags/RELEASE_350/final) (based on LLVM 3.5.0) 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. make[1]: Leaving directory '/«BUILDDIR»/tophat-2.0.12+dfsg' dh_auto_build -a make -j1 make[1]: Entering directory '/«BUILDDIR»/tophat-2.0.12+dfsg' make all-recursive make[2]: Entering directory '/«BUILDDIR»/tophat-2.0.12+dfsg' Making all in src make[3]: Entering directory '/«BUILDDIR»/tophat-2.0.12+dfsg/src' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -c -o alphabet.o 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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o prep_reads.o prep_reads.cpp g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o FastaTools.o FastaTools.cpp g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o bam2fastx.o bam2fastx.cpp g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o segment_juncs.o segment_juncs.cpp segment_juncs.cpp:61:18: warning: unused variable 'num_bowtie_mismatches' [-Wunused-const-variable] static const int num_bowtie_mismatches = 2; ^ segment_juncs.cpp:851:27: warning: unused function 'u32ToDna' [-Wunused-function] static inline std::string u32ToDna(uint32_t a, int len) { ^ 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; ^ 5 warnings generated. g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -o segment_juncs segment_juncs.o ../src/libtophat.a -lboost_thread -lboost_system -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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) ~~~~~~~~~~~~ ^ ~ 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; ^ 8 warnings generated. g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -o long_spanning_reads long_spanning_reads.o ../src/libtophat.a -lboost_thread -lboost_system -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o bam_merge.o bam_merge.cpp g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -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-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o tophat_reports.o tophat_reports.cpp tophat_reports.cpp:2857:30: error: variable length array of non-POD element type 'JunctionSet' (aka 'map') JunctionSet vfinal_junctions[num_threads]; ^ tophat_reports.cpp:2858:32: error: variable length array of non-POD element type 'InsertionSet' (aka 'map') InsertionSet vfinal_insertions[num_threads]; ^ tophat_reports.cpp:2859:30: error: variable length array of non-POD element type 'DeletionSet' (aka 'map') DeletionSet vfinal_deletions[num_threads]; ^ tophat_reports.cpp:2860:26: 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:1968:13: warning: private field '_it' is not used [-Wunused-private-field] ReadTable& _it; ^ tophat_reports.cpp:1969:20: 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 Makefile:1337: recipe for target 'tophat_reports.o' failed make[3]: Leaving directory '/«BUILDDIR»/tophat-2.0.12+dfsg/src' make[2]: *** [all-recursive] Error 1 Makefile:382: recipe for target 'all-recursive' failed make[2]: Leaving directory '/«BUILDDIR»/tophat-2.0.12+dfsg' make[1]: *** [all] Error 2 dh_auto_build: make -j1 returned exit code 2 Makefile:322: recipe for target 'all' failed make[1]: Leaving directory '/«BUILDDIR»/tophat-2.0.12+dfsg' make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 debian/rules:15: recipe for target 'build-arch' failed ──────────────────────────────────────────────────────────────────────────────── Build finished at 20140904-1541 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 54896 Build-Time: 105 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 20 Job: tophat_2.0.12+dfsg-2 Machine Architecture: amd64 Package: tophat Package-Time: 157 Source-Version: 2.0.12+dfsg-2 Space: 54896 Status: attempted Version: 2.0.12+dfsg-2clang1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20140904-1541 Build needed 00:02:37, 54896k disc space DC-Status: Failed 158.481673919s DC-Time-Estimation: 158.481673919 versus expected 1 (r/m: 157.481673919 ; m: 1.0)