DC-Build-Header: tophat 2.0.6-1 / Mon Jan 28 05:01:06 +0000 2013 DC-Task: logfile:/tmp/tophat_2.0.6-1_unstable_clang.log version:2.0.6-1 chroot:unstable modes:binary-only:clang source:tophat architecture:any esttime:133 DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/switch-to-clang tophat_2.0.6-1' Could not create '/sbuild-nonexistent/logs': No such file or directory Could not create '/sbuild-nonexistent/logs': No such file or directory sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on ip-10-157-4-166.ec2.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ tophat 2.0.6-1 (amd64) 28 Jan 2013 05:01 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: tophat Version: 2.0.6-1 Source Version: 2.0.6-1 Distribution: unstable Architecture: amd64 I: NOTICE: Log filtering will replace 'build/tophat-_Ic5k4/tophat-2.0.6' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/tophat-_Ic5k4' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-a4f54a46-f160-4c53-8358-1d4aa04f696e' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost unstable InRelease Get:1 http://localhost unstable Release.gpg [836 B] Get:2 http://localhost unstable Release [227 kB] Ign http://localhost unstable/main Sources/DiffIndex Ign http://localhost unstable/main amd64 Packages/DiffIndex Get:3 http://localhost unstable/main Translation-en/DiffIndex [7876 B] Get:4 http://localhost unstable/main 2013-01-27-2011.16.pdiff [737 B] Get:5 http://localhost unstable/main 2013-01-27-2011.16.pdiff [737 B] Get:6 http://localhost unstable/main Sources [8236 kB] Get:7 http://localhost unstable/main amd64 Packages [8284 kB] Get:8 http://localhost unstable/main 2013-01-28-0212.01.pdiff [43 B] Get:9 http://localhost unstable/main 2013-01-28-0212.01.pdiff [43 B] Fetched 16.8 MB in 3s (4694 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'tophat' packaging is maintained in the 'Git' version control system at: git://git.debian.org/debian-med/tophat.git Need to get 421 kB of source archives. Get:1 http://localhost/debian/ unstable/main tophat 2.0.6-1 (dsc) [2135 B] Get:2 http://localhost/debian/ unstable/main tophat 2.0.6-1 (tar) [414 kB] Get:3 http://localhost/debian/ unstable/main tophat 2.0.6-1 (diff) [5659 B] Fetched 421 kB in 0s (1215 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 'Add experimental as repository' Add experimental as repository + echo deb http://localhost:9999/debian experimental main + apt-get update Ign http://localhost unstable InRelease Ign http://localhost experimental InRelease Hit http://localhost unstable Release.gpg Get:1 http://localhost experimental Release.gpg [836 B] Hit http://localhost unstable Release Get:2 http://localhost experimental Release [161 kB] Ign http://localhost unstable/main Sources/DiffIndex Ign http://localhost unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Translation-en/DiffIndex Get:3 http://localhost experimental/main Translation-en [704 kB] Get:4 http://localhost experimental/main amd64 Packages [1605 kB] Hit http://localhost unstable/main Sources Hit http://localhost unstable/main amd64 Packages Fetched 2471 kB in 1s (1320 kB/s) Reading package lists... + echo 'Install of clang' Install of clang + apt-get update Ign http://localhost unstable InRelease Ign http://localhost experimental InRelease Hit http://localhost unstable Release.gpg Hit http://localhost experimental Release.gpg Hit http://localhost unstable Release Hit http://localhost experimental Release Ign http://localhost unstable/main Sources/DiffIndex Ign http://localhost unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Translation-en/DiffIndex Ign http://localhost experimental/main amd64 Packages/DiffIndex Get:1 http://localhost experimental/main Translation-en/DiffIndex [7819 B] Hit http://localhost unstable/main Sources Hit http://localhost unstable/main amd64 Packages Hit http://localhost experimental/main amd64 Packages Fetched 7819 B in 1s (3975 B/s) Reading package lists... + apt-get install --yes --no-install-recommends clang -t experimental Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: clang-3.2 compiler-rt cpp-4.7 g++-4.7 gcc-4.7 gcc-4.7-base gcc-4.8-base libc-dev-bin libc6 libc6-dev libclang-common-dev libexpat1 libffi5 libgcc-4.7-dev libgcc1 libgomp1 libitm1 libllvm3.2 libncurses5 libncursesw5 libobjc-4.7-dev libobjc4 libpython2.7-minimal libpython2.7-stdlib libquadmath0 libsqlite3-0 libssl1.0.0 libstdc++6 libstdc++6-4.7-dev libtinfo5 mime-support python python-minimal python2.7 python2.7-minimal Suggested packages: gcc-4.7-locales g++-4.7-multilib gcc-4.7-doc libstdc++6-4.7-dbg gcc-4.7-multilib libmudflap0-4.7-dev libgcc1-dbg libgomp1-dbg libitm1-dbg libquadmath0-dbg libmudflap0-dbg libcloog-ppl0 libppl-c2 libppl7 binutils-gold glibc-doc libstdc++6-4.7-doc python-doc python-tk python2.7-doc binfmt-support Recommended packages: llvm-3.2-dev manpages-dev file The following NEW packages will be installed: clang clang-3.2 compiler-rt gcc-4.8-base libclang-common-dev libexpat1 libffi5 libgcc-4.7-dev libllvm3.2 libncursesw5 libobjc-4.7-dev libobjc4 libpython2.7-minimal libpython2.7-stdlib libsqlite3-0 libssl1.0.0 mime-support python python-minimal python2.7 python2.7-minimal The following packages will be upgraded: cpp-4.7 g++-4.7 gcc-4.7 gcc-4.7-base libc-dev-bin libc6 libc6-dev libgcc1 libgomp1 libitm1 libncurses5 libquadmath0 libstdc++6 libstdc++6-4.7-dev libtinfo5 15 upgraded, 21 newly installed, 0 to remove and 24 not upgraded. Need to get 56.7 MB of archives. After this operation, 72.6 MB of additional disk space will be used. Get:1 http://localhost/debian/ experimental/main gcc-4.8-base amd64 4.8-20130127-1 [147 kB] Get:2 http://localhost/debian/ experimental/main libc6-dev amd64 2.16-0experimental1 [3086 kB] Get:3 http://localhost/debian/ experimental/main libc-dev-bin amd64 2.16-0experimental1 [226 kB] Get:4 http://localhost/debian/ experimental/main libc6 amd64 2.16-0experimental1 [4729 kB] Get:5 http://localhost/debian/ experimental/main libgcc1 amd64 1:4.8-20130127-1 [43.7 kB] Get:6 http://localhost/debian/ experimental/main libstdc++6 amd64 4.8-20130127-1 [335 kB] Get:7 http://localhost/debian/ experimental/main libtinfo5 amd64 5.9+20130119-1 [294 kB] Get:8 http://localhost/debian/ experimental/main libncurses5 amd64 5.9+20130119-1 [115 kB] Get:9 http://localhost/debian/ experimental/main libncursesw5 amd64 5.9+20130119-1 [142 kB] Get:10 http://localhost/debian/ unstable/main libssl1.0.0 amd64 1.0.1c-4 [1213 kB] Get:11 http://localhost/debian/ unstable/main libsqlite3-0 amd64 3.7.15.2-1 [463 kB] Get:12 http://localhost/debian/ experimental/main libexpat1 amd64 2.1.0-2 [138 kB] Get:13 http://localhost/debian/ unstable/main libffi5 amd64 3.0.10-3 [24.8 kB] Get:14 http://localhost/debian/ experimental/main libgomp1 amd64 4.8-20130127-1 [27.4 kB] Get:15 http://localhost/debian/ experimental/main libitm1 amd64 4.8-20130127-1 [37.7 kB] Get:16 http://localhost/debian/ unstable/main libllvm3.2 amd64 3.2-2 [7865 kB] Get:17 http://localhost/debian/ experimental/main libobjc4 amd64 4.8-20130127-1 [163 kB] Get:18 http://localhost/debian/ experimental/main libquadmath0 amd64 4.8-20130127-1 [139 kB] Get:19 http://localhost/debian/ experimental/main libstdc++6-4.7-dev amd64 4.7.2-19 [1678 kB] Get:20 http://localhost/debian/ experimental/main g++-4.7 amd64 4.7.2-19 [5877 kB] Get:21 http://localhost/debian/ experimental/main gcc-4.7 amd64 4.7.2-19 [5831 kB] Get:22 http://localhost/debian/ experimental/main cpp-4.7 amd64 4.7.2-19 [5416 kB] Get:23 http://localhost/debian/ experimental/main libgcc-4.7-dev amd64 4.7.2-19 [2465 kB] Get:24 http://localhost/debian/ experimental/main gcc-4.7-base amd64 4.7.2-19 [148 kB] Get:25 http://localhost/debian/ experimental/main mime-support all 3.53~experimental2 [36.5 kB] Get:26 http://localhost/debian/ experimental/main libpython2.7-minimal amd64 2.7.3-15 [531 kB] Get:27 http://localhost/debian/ experimental/main python2.7-minimal amd64 2.7.3-15 [1220 kB] Get:28 http://localhost/debian/ experimental/main libpython2.7-stdlib amd64 2.7.3-15 [2367 kB] Get:29 http://localhost/debian/ experimental/main python2.7 amd64 2.7.3-15 [326 kB] Get:30 http://localhost/debian/ experimental/main python-minimal amd64 2.7.3-10 [41.8 kB] Get:31 http://localhost/debian/ experimental/main python amd64 2.7.3-10 [184 kB] Get:32 http://localhost/debian/ experimental/main libobjc-4.7-dev amd64 4.7.2-19 [717 kB] Get:33 http://localhost/debian/ experimental/main libclang-common-dev amd64 3.2-1~exp5 [303 kB] Get:34 http://localhost/debian/ experimental/main compiler-rt amd64 3.2-1~exp5 [315 kB] Get:35 http://localhost/debian/ experimental/main clang-3.2 amd64 3.2-1~exp5 [10.1 MB] Get:36 http://localhost/debian/ experimental/main clang all 3.2-1~exp5 [9506 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 56.7 MB in 1s (33.9 MB/s) Selecting previously unselected package gcc-4.8-base:amd64. (Reading database ... 13484 files and directories currently installed.) Unpacking gcc-4.8-base:amd64 (from .../gcc-4.8-base_4.8-20130127-1_amd64.deb) ... Setting up gcc-4.8-base:amd64 (4.8-20130127-1) ... (Reading database ... 13491 files and directories currently installed.) Preparing to replace libc6-dev:amd64 2.13-38 (using .../libc6-dev_2.16-0experimental1_amd64.deb) ... Unpacking replacement libc6-dev:amd64 ... Preparing to replace libc-dev-bin 2.13-38 (using .../libc-dev-bin_2.16-0experimental1_amd64.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libc6:amd64 2.13-38 (using .../libc6_2.16-0experimental1_amd64.deb) ... debconf: unable to initialize frontend: Dialog debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype Checking for services that may need to be restarted... Checking init scripts... Unpacking replacement libc6:amd64 ... Setting up libc6:amd64 (2.16-0experimental1) ... debconf: unable to initialize frontend: Dialog debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype Checking for services that may need to be restarted... Checking init scripts... Nothing to restart. (Reading database ... 13509 files and directories currently installed.) Preparing to replace libgcc1:amd64 1:4.7.2-5 (using .../libgcc1_1%3a4.8-20130127-1_amd64.deb) ... Unpacking replacement libgcc1:amd64 ... Setting up libgcc1:amd64 (1:4.8-20130127-1) ... (Reading database ... 13509 files and directories currently installed.) Preparing to replace libstdc++6:amd64 4.7.2-5 (using .../libstdc++6_4.8-20130127-1_amd64.deb) ... Unpacking replacement libstdc++6:amd64 ... Setting up libstdc++6:amd64 (4.8-20130127-1) ... (Reading database ... 13509 files and directories currently installed.) Preparing to replace libtinfo5:amd64 5.9-10 (using .../libtinfo5_5.9+20130119-1_amd64.deb) ... Unpacking replacement libtinfo5:amd64 ... Setting up libtinfo5:amd64 (5.9+20130119-1) ... (Reading database ... 13509 files and directories currently installed.) Preparing to replace libncurses5:amd64 5.9-10 (using .../libncurses5_5.9+20130119-1_amd64.deb) ... Unpacking replacement libncurses5:amd64 ... Setting up libncurses5:amd64 (5.9+20130119-1) ... Selecting previously unselected package libncursesw5:amd64. (Reading database ... 13509 files and directories currently installed.) Unpacking libncursesw5:amd64 (from .../libncursesw5_5.9+20130119-1_amd64.deb) ... Selecting previously unselected package libssl1.0.0:amd64. Unpacking libssl1.0.0:amd64 (from .../libssl1.0.0_1.0.1c-4_amd64.deb) ... Selecting previously unselected package libsqlite3-0:amd64. Unpacking libsqlite3-0:amd64 (from .../libsqlite3-0_3.7.15.2-1_amd64.deb) ... Selecting previously unselected package libexpat1:amd64. Unpacking libexpat1:amd64 (from .../libexpat1_2.1.0-2_amd64.deb) ... Selecting previously unselected package libffi5:amd64. Unpacking libffi5:amd64 (from .../libffi5_3.0.10-3_amd64.deb) ... Preparing to replace libgomp1:amd64 4.7.2-5 (using .../libgomp1_4.8-20130127-1_amd64.deb) ... Unpacking replacement libgomp1:amd64 ... Preparing to replace libitm1:amd64 4.7.2-5 (using .../libitm1_4.8-20130127-1_amd64.deb) ... Unpacking replacement libitm1:amd64 ... Selecting previously unselected package libllvm3.2:amd64. Unpacking libllvm3.2:amd64 (from .../libllvm3.2_3.2-2_amd64.deb) ... Selecting previously unselected package libobjc4:amd64. Unpacking libobjc4:amd64 (from .../libobjc4_4.8-20130127-1_amd64.deb) ... Preparing to replace libquadmath0:amd64 4.7.2-5 (using .../libquadmath0_4.8-20130127-1_amd64.deb) ... Unpacking replacement libquadmath0:amd64 ... Preparing to replace libstdc++6-4.7-dev 4.7.2-5 (using .../libstdc++6-4.7-dev_4.7.2-19_amd64.deb) ... Unpacking replacement libstdc++6-4.7-dev:amd64 ... Preparing to replace g++-4.7 4.7.2-5 (using .../g++-4.7_4.7.2-19_amd64.deb) ... Unpacking replacement g++-4.7 ... Preparing to replace gcc-4.7 4.7.2-5 (using .../gcc-4.7_4.7.2-19_amd64.deb) ... Unpacking replacement gcc-4.7 ... Preparing to replace cpp-4.7 4.7.2-5 (using .../cpp-4.7_4.7.2-19_amd64.deb) ... Unpacking replacement cpp-4.7 ... Selecting previously unselected package libgcc-4.7-dev:amd64. Unpacking libgcc-4.7-dev:amd64 (from .../libgcc-4.7-dev_4.7.2-19_amd64.deb) ... Preparing to replace gcc-4.7-base:amd64 4.7.2-5 (using .../gcc-4.7-base_4.7.2-19_amd64.deb) ... Unpacking replacement gcc-4.7-base:amd64 ... Selecting previously unselected package mime-support. Unpacking mime-support (from .../mime-support_3.53~experimental2_all.deb) ... Selecting previously unselected package libpython2.7-minimal:amd64. Unpacking libpython2.7-minimal:amd64 (from .../libpython2.7-minimal_2.7.3-15_amd64.deb) ... Selecting previously unselected package python2.7-minimal. Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3-15_amd64.deb) ... Selecting previously unselected package libpython2.7-stdlib:amd64. Unpacking libpython2.7-stdlib:amd64 (from .../libpython2.7-stdlib_2.7.3-15_amd64.deb) ... Selecting previously unselected package python2.7. Unpacking python2.7 (from .../python2.7_2.7.3-15_amd64.deb) ... Selecting previously unselected package python-minimal. Unpacking python-minimal (from .../python-minimal_2.7.3-10_amd64.deb) ... Selecting previously unselected package python. Unpacking python (from .../python_2.7.3-10_amd64.deb) ... Selecting previously unselected package libobjc-4.7-dev:amd64. Unpacking libobjc-4.7-dev:amd64 (from .../libobjc-4.7-dev_4.7.2-19_amd64.deb) ... Selecting previously unselected package libclang-common-dev. Unpacking libclang-common-dev (from .../libclang-common-dev_3.2-1~exp5_amd64.deb) ... Selecting previously unselected package compiler-rt. Unpacking compiler-rt (from .../compiler-rt_3.2-1~exp5_amd64.deb) ... Selecting previously unselected package clang-3.2. Unpacking clang-3.2 (from .../clang-3.2_3.2-1~exp5_amd64.deb) ... Selecting previously unselected package clang. Unpacking clang (from .../clang_3.2-1~exp5_all.deb) ... Setting up libc-dev-bin (2.16-0experimental1) ... Setting up libc6-dev:amd64 (2.16-0experimental1) ... Setting up libncursesw5:amd64 (5.9+20130119-1) ... Setting up libssl1.0.0:amd64 (1.0.1c-4) ... debconf: unable to initialize frontend: Dialog debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype Setting up libsqlite3-0:amd64 (3.7.15.2-1) ... Setting up libexpat1:amd64 (2.1.0-2) ... Setting up libffi5:amd64 (3.0.10-3) ... Setting up libgomp1:amd64 (4.8-20130127-1) ... Setting up libitm1:amd64 (4.8-20130127-1) ... Setting up libllvm3.2:amd64 (3.2-2) ... Setting up libobjc4:amd64 (4.8-20130127-1) ... Setting up libquadmath0:amd64 (4.8-20130127-1) ... Setting up gcc-4.7-base:amd64 (4.7.2-19) ... Setting up libgcc-4.7-dev:amd64 (4.7.2-19) ... Setting up libstdc++6-4.7-dev:amd64 (4.7.2-19) ... Setting up cpp-4.7 (4.7.2-19) ... Setting up gcc-4.7 (4.7.2-19) ... Setting up g++-4.7 (4.7.2-19) ... Setting up mime-support (3.53~experimental2) ... Setting up libpython2.7-minimal:amd64 (2.7.3-15) ... Setting up python2.7-minimal (2.7.3-15) ... Linking and byte-compiling packages for runtime python2.7... Setting up libpython2.7-stdlib:amd64 (2.7.3-15) ... Setting up python2.7 (2.7.3-15) ... Setting up python-minimal (2.7.3-10) ... Setting up python (2.7.3-10) ... Setting up libobjc-4.7-dev:amd64 (4.7.2-19) ... Setting up libclang-common-dev (3.2-1~exp5) ... Setting up compiler-rt (3.2-1~exp5) ... Setting up clang-3.2 (3.2-1~exp5) ... Setting up clang (3.2-1~exp5) ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7' + cd /usr/bin + for VERSION in '$VERSIONS' + rm g++-4.6 gcc-4.6 cpp-4.6 + ln -s clang++ g++-4.6 + ln -s clang gcc-4.6 + ln -s clang cpp-4.6 + for VERSION in '$VERSIONS' + rm g++-4.7 gcc-4.7 cpp-4.7 + ln -s clang++ g++-4.7 + ln -s clang gcc-4.7 + ln -s clang cpp-4.7 + cd - /«BUILDDIR» + echo 'Block the installation of new gcc version' Block the installation of new gcc version + 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 '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-vBD3Ie/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/710 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 ... 14674 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-VU_M7b/apt_archive/sbuild-build-depends-tophat-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install tophat build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: autoconf automake autotools-dev bsdmainutils debhelper dh-autoreconf file gettext gettext-base groff-base help2man html2text intltool-debian libasprintf-dev 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 libgettextpo-dev libgettextpo0 libglib2.0-0 libicu48 libmagic1 libpcre3 libpipeline1 libsigsegv2 libtool libunistring0 libxml2 m4 man-db po-debconf 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 Recommended packages: autopoint curl wget lynx-cur libglib2.0-data shared-mime-info libltdl-dev xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autotools-dev bsdmainutils debhelper dh-autoreconf file gettext gettext-base groff-base help2man html2text intltool-debian libasprintf-dev 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 libgettextpo-dev libgettextpo0 libglib2.0-0 libicu48 libmagic1 libpcre3 libpipeline1 libsigsegv2 libtool libunistring0 libxml2 m4 man-db po-debconf sbuild-build-depends-tophat-dummy seqan-dev zlib1g-dev 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. Need to get 28.9 MB/28.9 MB of archives. After this operation, 171 MB of additional disk space will be used. Get:1 http://localhost/debian/ unstable/main libpipeline1 amd64 1.2.2-1 [39.9 kB] Get:2 http://localhost/debian/ unstable/main groff-base amd64 1.22.1-2 [741 kB] Get:3 http://localhost/debian/ unstable/main bsdmainutils amd64 9.0.4 [210 kB] Get:4 http://localhost/debian/ unstable/main man-db amd64 2.6.3-3 [898 kB] Get:5 http://localhost/debian/ unstable/main libasprintf0c2 amd64 0.18.1.1-10 [27.2 kB] Get:6 http://localhost/debian/ unstable/main libmagic1 amd64 5.11-2 [202 kB] Get:7 http://localhost/debian/ unstable/main libpcre3 amd64 1:8.31-2 [247 kB] Get:8 http://localhost/debian/ unstable/main libxml2 amd64 2.8.0+dfsg1-7 [903 kB] Get:9 http://localhost/debian/ unstable/main libglib2.0-0 amd64 2.33.12+really2.32.4-5 [1838 kB] Get:10 http://localhost/debian/ unstable/main libcroco3 amd64 0.6.6-2 [134 kB] Get:11 http://localhost/debian/ unstable/main libunistring0 amd64 0.9.3-5 [434 kB] Get:12 http://localhost/debian/ unstable/main libgettextpo0 amd64 0.18.1.1-10 [145 kB] Get:13 http://localhost/debian/ unstable/main libicu48 amd64 4.8.1.1-10 [4741 kB] Get:14 http://localhost/debian/ unstable/main file amd64 5.11-2 [51.8 kB] Get:15 http://localhost/debian/ unstable/main gettext-base amd64 0.18.1.1-10 [154 kB] Get:16 http://localhost/debian/ unstable/main libsigsegv2 amd64 2.9-4 [28.9 kB] Get:17 http://localhost/debian/ unstable/main m4 amd64 1.4.16-4 [260 kB] Get:18 http://localhost/debian/ unstable/main autoconf all 2.69-1 [589 kB] Get:19 http://localhost/debian/ unstable/main autotools-dev all 20120608.1 [73.0 kB] Get:20 http://localhost/debian/ unstable/main automake all 1:1.11.6-1 [607 kB] Get:21 http://localhost/debian/ unstable/main html2text amd64 1.3.2a-15 [103 kB] Get:22 http://localhost/debian/ unstable/main libasprintf-dev amd64 0.18.1.1-10 [26.8 kB] Get:23 http://localhost/debian/ unstable/main libgettextpo-dev amd64 0.18.1.1-10 [184 kB] Get:24 http://localhost/debian/ unstable/main gettext amd64 0.18.1.1-10 [1815 kB] Get:25 http://localhost/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:26 http://localhost/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB] Get:27 http://localhost/debian/ unstable/main debhelper all 9.20120909 [705 kB] Get:28 http://localhost/debian/ unstable/main libtool amd64 2.4.2-1.2 [621 kB] Get:29 http://localhost/debian/ unstable/main dh-autoreconf all 7 [15.3 kB] Get:30 http://localhost/debian/ unstable/main help2man amd64 1.41.1 [101 kB] Get:31 http://localhost/debian/ unstable/main libbam-dev amd64 0.1.18-4 [156 kB] Get:32 http://localhost/debian/ unstable/main libboost1.49-dev amd64 1.49.0-3.1 [9203 kB] Get:33 http://localhost/debian/ unstable/main libboost-date-time1.49.0 amd64 1.49.0-3.1 [46.7 kB] Get:34 http://localhost/debian/ unstable/main libboost-serialization1.49.0 amd64 1.49.0-3.1 [212 kB] Get:35 http://localhost/debian/ unstable/main libboost-serialization1.49-dev amd64 1.49.0-3.1 [316 kB] Get:36 http://localhost/debian/ unstable/main libboost-date-time1.49-dev amd64 1.49.0-3.1 [49.5 kB] Get:37 http://localhost/debian/ unstable/main libboost-thread1.49.0 amd64 1.49.0-3.1 [61.0 kB] Get:38 http://localhost/debian/ unstable/main libboost-thread1.49-dev amd64 1.49.0-3.1 [67.1 kB] Get:39 http://localhost/debian/ unstable/main libboost-thread-dev amd64 1.49.0.1 [2736 B] Get:40 http://localhost/debian/ unstable/main seqan-dev all 1.3.1-1 [2442 kB] Get:41 http://localhost/debian/ unstable/main zlib1g-dev amd64 1:1.2.7.dfsg-13 [215 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 28.9 MB in 1s (20.0 MB/s) Selecting previously unselected package libpipeline1:amd64. (Reading database ... 14674 files and directories currently installed.) Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.2-1_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.22.1-2_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.3-3_amd64.deb) ... Selecting previously unselected package libasprintf0c2:amd64. Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.1.1-10_amd64.deb) ... Selecting previously unselected package libmagic1:amd64. Unpacking libmagic1:amd64 (from .../libmagic1_5.11-2_amd64.deb) ... Selecting previously unselected package libpcre3:amd64. Unpacking libpcre3:amd64 (from .../libpcre3_1%3a8.31-2_amd64.deb) ... Selecting previously unselected package libxml2:amd64. 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Unpacking libboost1.49-dev (from .../libboost1.49-dev_1.49.0-3.1_amd64.deb) ... Selecting previously unselected package libboost-date-time1.49.0. Unpacking libboost-date-time1.49.0 (from .../libboost-date-time1.49.0_1.49.0-3.1_amd64.deb) ... Selecting previously unselected package libboost-serialization1.49.0. Unpacking libboost-serialization1.49.0 (from .../libboost-serialization1.49.0_1.49.0-3.1_amd64.deb) ... Selecting previously unselected package libboost-serialization1.49-dev. Unpacking libboost-serialization1.49-dev (from .../libboost-serialization1.49-dev_1.49.0-3.1_amd64.deb) ... Selecting previously unselected package libboost-date-time1.49-dev. Unpacking libboost-date-time1.49-dev (from .../libboost-date-time1.49-dev_1.49.0-3.1_amd64.deb) ... Selecting previously unselected package libboost-thread1.49.0. Unpacking libboost-thread1.49.0 (from .../libboost-thread1.49.0_1.49.0-3.1_amd64.deb) ... Selecting previously unselected package libboost-thread1.49-dev. Unpacking libboost-thread1.49-dev (from .../libboost-thread1.49-dev_1.49.0-3.1_amd64.deb) ... Selecting previously unselected package libboost-thread-dev. Unpacking libboost-thread-dev (from .../libboost-thread-dev_1.49.0.1_amd64.deb) ... Selecting previously unselected package seqan-dev. Unpacking seqan-dev (from .../seqan-dev_1.3.1-1_all.deb) ... Selecting previously unselected package zlib1g-dev:amd64. Unpacking zlib1g-dev:amd64 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_amd64.deb) ... Selecting previously unselected package sbuild-build-depends-tophat-dummy. Unpacking sbuild-build-depends-tophat-dummy (from .../sbuild-build-depends-tophat-dummy.deb) ... Processing triggers for mime-support ... Setting up libpipeline1:amd64 (1.2.2-1) ... Setting up groff-base (1.22.1-2) ... Setting up bsdmainutils (9.0.4) ... 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 (2.6.3-3) ... Building database of manual pages ... Setting up libasprintf0c2:amd64 (0.18.1.1-10) ... Setting up libmagic1:amd64 (5.11-2) ... Setting up libpcre3:amd64 (1:8.31-2) ... Setting up libxml2:amd64 (2.8.0+dfsg1-7) ... Setting up libglib2.0-0:amd64 (2.33.12+really2.32.4-5) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.6-2) ... Setting up libunistring0:amd64 (0.9.3-5) ... Setting up libgettextpo0:amd64 (0.18.1.1-10) ... Setting up libicu48:amd64 (4.8.1.1-10) ... Setting up file (5.11-2) ... Setting up gettext-base (0.18.1.1-10) ... Setting up libsigsegv2 (2.9-4) ... Setting up m4 (1.4.16-4) ... Setting up autoconf (2.69-1) ... Setting up autotools-dev (20120608.1) ... Setting up automake (1:1.11.6-1) ... update-alternatives: using /usr/bin/automake-1.11 to provide /usr/bin/automake (automake) in auto mode Setting up html2text (1.3.2a-15) ... Setting up libasprintf-dev:amd64 (0.18.1.1-10) ... Setting up libgettextpo-dev:amd64 (0.18.1.1-10) ... Setting up gettext (0.18.1.1-10) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120909) ... Setting up libtool (2.4.2-1.2) ... Setting up dh-autoreconf (7) ... Setting up help2man (1.41.1) ... Setting up libbam-dev (0.1.18-4) ... Setting up libboost1.49-dev (1.49.0-3.1) ... Setting up libboost-date-time1.49.0 (1.49.0-3.1) ... Setting up libboost-serialization1.49.0 (1.49.0-3.1) ... Setting up libboost-serialization1.49-dev (1.49.0-3.1) ... Setting up libboost-date-time1.49-dev (1.49.0-3.1) ... Setting up libboost-thread1.49.0 (1.49.0-3.1) ... Setting up libboost-thread1.49-dev (1.49.0-3.1) ... Setting up libboost-thread-dev (1.49.0.1) ... Setting up seqan-dev (1.3.1-1) ... Setting up zlib1g-dev:amd64 (1:1.2.7.dfsg-13) ... Setting up sbuild-build-depends-tophat-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-xen-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-15 g++-4.7_4.7.2-19 gcc-4.6_4.6.3-15 gcc-4.7_4.7.2-19 libc6-dev_2.16-0experimental1 libstdc++6_4.8-20130127-1 libstdc++6-4.6-dev_4.6.3-15 libstdc++6-4.7-dev_4.7.2-19 linux-libc-dev_3.2.35-2 Package versions: apt_0.9.7.7 autoconf_2.69-1 automake_1:1.11.6-1 autotools-dev_20120608.1 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 binutils_2.22-7.1 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 clang_3.2-1~exp5 clang-3.2_3.2-1~exp5 compiler-rt_3.2-1~exp5 coreutils_8.20-3 cpp_4:4.7.2-1 cpp-4.6_4.6.3-15 cpp-4.7_4.7.2-19 dash_0.5.7-3 debconf_1.5.49 debconf-i18n_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 dh-autoreconf_7 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 g++_4:4.7.2-1 g++-4.6_4.6.3-15 g++-4.7_4.7.2-19 gcc_4:4.7.2-1 gcc-4.4-base_4.4.7-3 gcc-4.5-base_4.5.4-1 gcc-4.6_4.6.3-15 gcc-4.6-base_4.6.3-15 gcc-4.7_4.7.2-19 gcc-4.7-base_4.7.2-19 gcc-4.8-base_4.8-20130127-1 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-1 groff-base_1.22.1-2 gzip_1.5-1.1 help2man_1.41.1 hostname_3.12 html2text_1.3.2a-15 initscripts_2.88dsf-39 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.7 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libbam-dev_0.1.18-4 libblkid1_2.20.1-5.3 libboost-date-time1.49-dev_1.49.0-3.1 libboost-date-time1.49.0_1.49.0-3.1 libboost-serialization1.49-dev_1.49.0-3.1 libboost-serialization1.49.0_1.49.0-3.1 libboost-thread-dev_1.49.0.1 libboost-thread1.49-dev_1.49.0-3.1 libboost-thread1.49.0_1.49.0-3.1 libboost1.49-dev_1.49.0-3.1 libbz2-1.0_1.0.6-4 libc-bin_2.13-38 libc-dev-bin_2.16-0experimental1 libc6_2.16-0experimental1 libc6-dev_2.16-0experimental1 libclang-common-dev_3.2-1~exp5 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libexpat1_2.1.0-2 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9.1 libgcc-4.7-dev_4.7.2-19 libgcc1_1:4.8-20130127-1 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.8-20130127-1 libgpm2_1.20.4-6 libicu48_4.8.1.1-10 libitm1_4.8-20130127-1 libllvm3.2_3.2-2 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_5.11-2 libmount1_2.20.1-5.3 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9+20130119-1 libncursesw5_5.9+20130119-1 libobjc-4.7-dev_4.7.2-19 libobjc4_4.8-20130127-1 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-2 libpipeline1_1.2.2-1 libpython2.7-minimal_2.7.3-15 libpython2.7-stdlib_2.7.3-15 libquadmath0_4.8-20130127-1 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libsigsegv2_2.9-4 libslang2_2.2.4-15 libsqlite3-0_3.7.15.2-1 libss2_1.42.5-1 libssl1.0.0_1.0.1c-4 libstdc++6_4.8-20130127-1 libstdc++6-4.6-dev_4.6.3-15 libstdc++6-4.7-dev_4.7.2-19 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+20130119-1 libtool_2.4.2-1.2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.35-2 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 m4_1.4.16-4 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mime-support_3.53~experimental2 mount_2.20.1-5.3 multiarch-support_2.13-38 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-17 perl-base_5.14.2-17 perl-modules_5.14.2-17 po-debconf_1.0.16+nmu2 python_2.7.3-10 python-minimal_2.7.3-10 python2.7_2.7.3-15 python2.7-minimal_2.7.3-15 readline-common_6.2+dfsg-0.1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-tophat-dummy_0.invalid.0 sed_4.2.1-10 sensible-utils_0.0.7 seqan-dev_1.3.1-1 sudo_1.8.5p2-1 sysv-rc_2.88dsf-39 sysvinit_2.88dsf-39 sysvinit-utils_2.88dsf-39 tar_1.26+dfsg-0.1 tzdata_2012j-1 ucf_3.0025+nmu3 util-linux_2.20.1-5.3 vim_2:7.3.547-6 vim-common_2:7.3.547-6 vim-runtime_2:7.3.547-6 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Tue Nov 6 08:52:03 2012 UTC using RSA key ID 2295D502 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./tophat_2.0.6-1.dsc dpkg-source: info: extracting tophat in tophat-2.0.6 dpkg-source: info: unpacking tophat_2.0.6.orig.tar.gz dpkg-source: info: unpacking tophat_2.0.6-1.debian.tar.gz dpkg-source: info: applying fix_includes_path.patch dpkg-source: info: applying bashism_in_shell_script.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=user PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=user SCHROOT_SESSION_ID=unstable-amd64-sbuild-a4f54a46-f160-4c53-8358-1d4aa04f696e SCHROOT_UID=1000 SCHROOT_USER=user SHELL=/bin/sh USER=user dpkg-buildpackage ───────────────── dpkg-buildpackage: source package tophat dpkg-buildpackage: source version 2.0.6-1 dpkg-buildpackage: source changed by Charles Plessy dpkg-source --before-build tophat-2.0.6 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 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 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 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 configure: error: We could not detect the bam libraries (version or higher). If you have a staged bam library (still not installed) please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option. checking for bamlib... "tail -v -n +0 config.log" ==> config.log <== This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by tophat configure 2.0.6, which was generated by GNU Autoconf 2.69. Invocation command line was $ ./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 ## --------- ## ## Platform. ## ## --------- ## hostname = ip-10-157-4-166 uname -m = x86_64 uname -r = 2.6.32-5-xen-amd64 uname -s = Linux uname -v = #1 SMP Sun Sep 23 13:49:30 UTC 2012 /usr/bin/uname -p = unknown /bin/uname -X = unknown /bin/arch = unknown /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /usr/local/sbin PATH: /usr/local/bin PATH: /usr/sbin PATH: /usr/bin PATH: /sbin PATH: /bin PATH: /usr/games ## ----------- ## ## Core tests. ## ## ----------- ## configure:2358: checking for a BSD-compatible install configure:2426: result: /usr/bin/install -c configure:2437: checking whether build environment is sane configure:2487: result: yes configure:2628: checking for a thread-safe mkdir -p configure:2667: result: /bin/mkdir -p configure:2680: checking for gawk configure:2710: result: no configure:2680: checking for mawk configure:2696: found /usr/bin/mawk configure:2707: result: mawk configure:2718: checking whether make sets $(MAKE) configure:2740: result: yes configure:2841: checking for gawk configure:2868: result: mawk configure:2937: checking for g++ configure:2953: found /usr/bin/g++ configure:2964: result: g++ configure:2991: checking for C++ compiler version configure:3000: g++ --version >&5 Debian clang version 3.2-1~exp5 (tags/RELEASE_32/final) (based on LLVM 3.2) Target: x86_64-pc-linux-gnu Thread model: posix configure:3011: $? = 0 configure:3000: g++ -v >&5 Debian clang version 3.2-1~exp5 (tags/RELEASE_32/final) (based on LLVM 3.2) Target: x86_64-pc-linux-gnu Thread model: posix configure:3011: $? = 0 configure:3000: g++ -V >&5 clang: error: argument to '-V' is missing (expected 1 value) clang: error: no input files configure:3011: $? = 1 configure:3000: g++ -qversion >&5 clang: error: no input files configure:3011: $? = 1 configure:3031: checking whether the C++ compiler works configure:3053: g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro conftest.cpp >&5 configure:3057: $? = 0 configure:3105: result: yes configure:3108: checking for C++ compiler default output file name configure:3110: result: a.out configure:3116: checking for suffix of executables configure:3123: g++ -o conftest -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro conftest.cpp >&5 configure:3127: $? = 0 configure:3149: result: configure:3171: checking whether we are cross compiling configure:3179: g++ -o conftest -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro conftest.cpp >&5 configure:3183: $? = 0 configure:3190: ./conftest configure:3194: $? = 0 configure:3209: result: no configure:3214: checking for suffix of object files configure:3236: g++ -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.cpp >&5 configure:3240: $? = 0 configure:3261: result: o configure:3265: checking whether we are using the GNU C++ compiler configure:3284: g++ -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.cpp >&5 configure:3284: $? = 0 configure:3293: result: yes configure:3302: checking whether g++ accepts -g configure:3322: g++ -c -g -D_FORTIFY_SOURCE=2 conftest.cpp >&5 configure:3322: $? = 0 configure:3363: result: yes configure:3397: checking for style of include used by make configure:3425: result: GNU configure:3451: checking dependency style of g++ configure:3562: result: none configure:3625: checking for gcc configure:3641: found /usr/bin/gcc configure:3652: result: gcc configure:3881: checking for C compiler version configure:3890: gcc --version >&5 Debian clang version 3.2-1~exp5 (tags/RELEASE_32/final) (based on LLVM 3.2) Target: x86_64-pc-linux-gnu Thread model: posix configure:3901: $? = 0 configure:3890: gcc -v >&5 Debian clang version 3.2-1~exp5 (tags/RELEASE_32/final) (based on LLVM 3.2) Target: x86_64-pc-linux-gnu Thread model: posix configure:3901: $? = 0 configure:3890: gcc -V >&5 clang: error: argument to '-V' is missing (expected 1 value) clang: error: no input files configure:3901: $? = 1 configure:3890: gcc -qversion >&5 clang: error: no input files configure:3901: $? = 1 configure:3905: checking whether we are using the GNU C compiler configure:3924: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:3924: $? = 0 configure:3933: result: yes configure:3942: checking whether gcc accepts -g configure:3962: gcc -c -g -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:3962: $? = 0 configure:4003: result: yes configure:4020: checking for gcc option to accept ISO C89 configure:4083: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:4083: $? = 0 configure:4096: result: none needed configure:4118: checking dependency style of gcc configure:4229: result: none configure:4244: checking whether make sets $(MAKE) configure:4266: result: yes configure:4318: checking for ranlib configure:4334: found /usr/bin/ranlib configure:4345: result: ranlib configure:4401: checking for a Python interpreter with version >= 2.4 configure:4418: python -c import sys # split strings by '.' and convert to numeric. Append some zeros # because we need at least 4 digits for the hex conversion. # map returns an iterator in Python 3.0 and a list in 2.x minver = list(map(int, '2.4'.split('.'))) + [0, 0, 0] minverhex = 0 # xrange is not present in Python 3.0 and range returns an iterator for i in list(range(0, 4)): minverhex = (minverhex << 8) + minver[i] sys.exit(sys.hexversion < minverhex) configure:4421: $? = 0 configure:4427: result: python configure:4435: checking for python configure:4453: found /usr/bin/python configure:4465: result: /usr/bin/python configure:4483: checking for python version configure:4490: result: 2.7 configure:4502: checking for python platform configure:4509: result: linux2 configure:4516: checking for python script directory configure:4544: result: ${prefix}/lib/python2.7/dist-packages configure:4553: checking for python extension module directory configure:4581: result: ${exec_prefix}/lib/python2.7/dist-packages configure:4643: checking for boostlib >= 1.38.0 configure:4697: g++ -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include conftest.cpp >&5 configure:4697: $? = 0 configure:4699: result: yes configure:4882: checking for bamlib configure:4931: g++ -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.cpp >&5 In file included from conftest.cpp:14: In file included from /usr/include/samtools/bam.h:46: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:36:1: error: unknown type name '__extern_always_inline' __fortify_function __wur char * ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:143:28: note: expanded from macro '__fortify_function' #define __fortify_function __extern_always_inline __attribute_artificial__ ^ In file included from conftest.cpp:14: In file included from /usr/include/samtools/bam.h:46: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:36:20: error: expected unqualified-id __fortify_function __wur char * ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:297:17: note: expanded from macro '__wur' # define __wur __attribute_warn_unused_result__ ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:295:4: note: expanded from macro '__attribute_warn_unused_result__' __attribute__ ((__warn_unused_result__)) ^ In file included from conftest.cpp:14: In file included from /usr/include/samtools/bam.h:46: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:63:1: error: unknown type name '__extern_always_inline' __fortify_function int ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:143:28: note: expanded from macro '__fortify_function' #define __fortify_function __extern_always_inline __attribute_artificial__ ^ In file included from conftest.cpp:14: In file included from /usr/include/samtools/bam.h:46: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:63:20: error: expected unqualified-id __fortify_function int ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:82:1: error: unknown type name '__extern_always_inline' __fortify_function __wur int ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:143:28: note: expanded from macro '__fortify_function' #define __fortify_function __extern_always_inline __attribute_artificial__ ^ In file included from conftest.cpp:14: In file included from /usr/include/samtools/bam.h:46: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:82:20: error: expected unqualified-id __fortify_function __wur int ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:297:17: note: expanded from macro '__wur' # define __wur __attribute_warn_unused_result__ ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:295:4: note: expanded from macro '__attribute_warn_unused_result__' __attribute__ ((__warn_unused_result__)) ^ In file included from conftest.cpp:14: In file included from /usr/include/samtools/bam.h:46: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:112:1: error: unknown type name '__extern_always_inline' __fortify_function size_t ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:143:28: note: expanded from macro '__fortify_function' #define __fortify_function __extern_always_inline __attribute_artificial__ ^ In file included from conftest.cpp:14: In file included from /usr/include/samtools/bam.h:46: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:112:26: error: expected ';' after top level declarator __fortify_function size_t ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:133:8: error: reference to 'size_t' is ambiguous extern size_t __REDIRECT_NTH (__wcstombs_alias, ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:112:20: note: candidate found by name lookup is 'size_t' __fortify_function size_t ^ /usr/include/clang/3.2/include/stddef.h:35:33: note: candidate found by name lookup is 'size_t' typedef __typeof__(sizeof(int)) size_t; ^ In file included from conftest.cpp:14: In file included from /usr/include/samtools/bam.h:46: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:136:11: error: reference to 'size_t' is ambiguous size_t __len), wcstombs); ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:190:11: note: expanded from macro '__REDIRECT_NTH' name proto __THROW __asm__ (__ASMNAME (#alias)) ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:112:20: note: candidate found by name lookup is 'size_t' __fortify_function size_t ^ /usr/include/clang/3.2/include/stddef.h:35:33: note: candidate found by name lookup is 'size_t' typedef __typeof__(sizeof(int)) size_t; ^ In file included from conftest.cpp:14: In file included from /usr/include/samtools/bam.h:46: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:137:8: error: reference to 'size_t' is ambiguous extern size_t __REDIRECT_NTH (__wcstombs_chk_warn, ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:112:20: note: candidate found by name lookup is 'size_t' __fortify_function size_t ^ /usr/include/clang/3.2/include/stddef.h:35:33: note: candidate found by name lookup is 'size_t' typedef __typeof__(sizeof(int)) size_t; ^ In file included from conftest.cpp:14: In file included from /usr/include/samtools/bam.h:46: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:140:11: error: reference to 'size_t' is ambiguous size_t __len, size_t __dstlen), __wcstombs_chk) ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:190:11: note: expanded from macro '__REDIRECT_NTH' name proto __THROW __asm__ (__ASMNAME (#alias)) ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:112:20: note: candidate found by name lookup is 'size_t' __fortify_function size_t ^ /usr/include/clang/3.2/include/stddef.h:35:33: note: candidate found by name lookup is 'size_t' typedef __typeof__(sizeof(int)) size_t; ^ In file included from conftest.cpp:14: In file included from /usr/include/samtools/bam.h:46: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:140:25: error: reference to 'size_t' is ambiguous size_t __len, size_t __dstlen), __wcstombs_chk) ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:190:11: note: expanded from macro '__REDIRECT_NTH' name proto __THROW __asm__ (__ASMNAME (#alias)) ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:112:20: note: candidate found by name lookup is 'size_t' __fortify_function size_t ^ /usr/include/clang/3.2/include/stddef.h:35:33: note: candidate found by name lookup is 'size_t' typedef __typeof__(sizeof(int)) size_t; ^ In file included from conftest.cpp:14: In file included from /usr/include/samtools/bam.h:46: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:143:1: error: unknown type name '__extern_always_inline' __fortify_function size_t ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:143:28: note: expanded from macro '__fortify_function' #define __fortify_function __extern_always_inline __attribute_artificial__ ^ In file included from conftest.cpp:14: In file included from /usr/include/samtools/bam.h:46: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:143:26: error: expected ';' after top level declarator __fortify_function size_t ^ In file included from conftest.cpp:14: In file included from /usr/include/samtools/bam.h:47: /usr/include/string.h:43:8: error: reference to 'size_t' is ambiguous size_t __n) __THROW __nonnull ((1, 2)); ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:143:20: note: candidate found by name lookup is 'size_t' __fortify_function size_t ^ /usr/include/clang/3.2/include/stddef.h:35:33: note: candidate found by name lookup is 'size_t' typedef __typeof__(sizeof(int)) size_t; ^ In file included from conftest.cpp:14: In file included from /usr/include/samtools/bam.h:47: /usr/include/string.h:46:56: error: reference to 'size_t' is ambiguous extern void *memmove (void *__dest, const void *__src, size_t __n) ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:143:20: note: candidate found by name lookup is 'size_t' __fortify_function size_t ^ /usr/include/clang/3.2/include/stddef.h:35:33: note: candidate found by name lookup is 'size_t' typedef __typeof__(sizeof(int)) size_t; ^ In file included from conftest.cpp:14: In file included from /usr/include/samtools/bam.h:47: /usr/include/string.h:55:18: error: reference to 'size_t' is ambiguous int __c, size_t __n) ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:143:20: note: candidate found by name lookup is 'size_t' __fortify_function size_t ^ /usr/include/clang/3.2/include/stddef.h:35:33: note: candidate found by name lookup is 'size_t' typedef __typeof__(sizeof(int)) size_t; ^ In file included from conftest.cpp:14: In file included from /usr/include/samtools/bam.h:47: /usr/include/string.h:62:42: error: reference to 'size_t' is ambiguous extern void *memset (void *__s, int __c, size_t __n) __THROW __nonnull ((1)); ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:143:20: note: candidate found by name lookup is 'size_t' __fortify_function size_t ^ /usr/include/clang/3.2/include/stddef.h:35:33: note: candidate found by name lookup is 'size_t' typedef __typeof__(sizeof(int)) size_t; ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. configure:4931: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "tophat" | #define PACKAGE_TARNAME "tophat" | #define PACKAGE_VERSION "2.0.6" | #define PACKAGE_STRING "tophat 2.0.6" | #define PACKAGE_BUGREPORT "cole@cs.umd.edu, infphilo@umiacs.umd.edu" | #define PACKAGE_URL "" | #define SVN_REVISION "" | #define PACKAGE "tophat" | #define VERSION "2.0.6" | #define HAVE_BOOST /**/ | /* end confdefs.h. */ | | #include | | int | main () | { | | | ; | return 0; | } configure:5023: g++ -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/include/bam-0 conftest.cpp >&5 conftest.cpp:14:12: fatal error: 'bam/version.hpp' file not found #include ^ 1 error generated. configure:5023: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "tophat" | #define PACKAGE_TARNAME "tophat" | #define PACKAGE_VERSION "2.0.6" | #define PACKAGE_STRING "tophat 2.0.6" | #define PACKAGE_BUGREPORT "cole@cs.umd.edu, infphilo@umiacs.umd.edu" | #define PACKAGE_URL "" | #define SVN_REVISION "" | #define PACKAGE "tophat" | #define VERSION "2.0.6" | #define HAVE_BOOST /**/ | /* end confdefs.h. */ | | #include | | int | main () | { | | | ; | return 0; | } configure:5042: error: We could not detect the bam libraries (version or higher). If you have a staged bam library (still not installed) please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option. ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_c_compiler_gnu=yes ac_cv_cxx_compiler_gnu=yes ac_cv_env_CCC_set= ac_cv_env_CCC_value= ac_cv_env_CC_set= ac_cv_env_CC_value= ac_cv_env_CFLAGS_set=set ac_cv_env_CFLAGS_value='-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security' ac_cv_env_CPPFLAGS_set=set ac_cv_env_CPPFLAGS_value=-D_FORTIFY_SOURCE=2 ac_cv_env_CPP_set= ac_cv_env_CPP_value= ac_cv_env_CXXFLAGS_set=set ac_cv_env_CXXFLAGS_value='-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security' ac_cv_env_CXX_set= ac_cv_env_CXX_value= ac_cv_env_LDFLAGS_set=set ac_cv_env_LDFLAGS_value=-Wl,-z,relro ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_PYTHON_set= ac_cv_env_PYTHON_value= ac_cv_env_build_alias_set=set ac_cv_env_build_alias_value=x86_64-linux-gnu ac_cv_env_host_alias_set= ac_cv_env_host_alias_value= ac_cv_env_target_alias_set= ac_cv_env_target_alias_value= ac_cv_objext=o ac_cv_path_PYTHON=/usr/bin/python ac_cv_path_install='/usr/bin/install -c' ac_cv_path_mkdir=/bin/mkdir ac_cv_prog_AWK=mawk ac_cv_prog_ac_ct_CC=gcc ac_cv_prog_ac_ct_CXX=g++ dh_auto_configure: ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=${prefix}/include --mandir=${prefix}/share/man --infodir=${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --libdir=${prefix}/lib/x86_64-linux-gnu --libexecdir=${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking returned exit code 1 ac_cv_prog_ac_ct_RANLIB=ranlib ac_cv_prog_cc_c89= ac_cv_prog_cc_g=yes ac_cv_prog_cxx_g=yes ac_cv_prog_make_make_set=yes am_cv_CC_dependencies_compiler_type=none am_cv_CXX_dependencies_compiler_type=none am_cv_pathless_PYTHON=python am_cv_python_platform=linux2 am_cv_python_pyexecdir='${exec_prefix}/lib/python2.7/dist-packages' am_cv_python_pythondir='${prefix}/lib/python2.7/dist-packages' am_cv_python_version=2.7 ## ----------------- ## ## Output variables. ## ## ----------------- ## ACLOCAL='${SHELL} /«PKGBUILDDIR»/build-aux/missing --run aclocal-1.11' AMDEPBACKSLASH='' AMDEP_FALSE='' AMDEP_TRUE='#' AMTAR='$${TAR-tar}' AUTOCONF='${SHELL} /«PKGBUILDDIR»/build-aux/missing --run autoconf' AUTOHEADER='${SHELL} /«PKGBUILDDIR»/build-aux/missing --run autoheader' AUTOMAKE='${SHELL} /«PKGBUILDDIR»/build-aux/missing --run automake-1.11' AWK='mawk' BAM_CPPFLAGS='-I/include/bam-0' BAM_LDFLAGS='-L/lib' BAM_LIB='' BOOST_CPPFLAGS='-I/usr/include' BOOST_LDFLAGS='-L/usr/lib' BOOST_SYSTEM_LIB='' BOOST_THREAD_LIB='' CC='gcc' CCDEPMODE='depmode=none' CFLAGS='-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security' CPP='' CPPFLAGS='-D_FORTIFY_SOURCE=2 -I/include/bam-0' CXX='g++' CXXDEPMODE='depmode=none' CXXFLAGS='-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security' CYGPATH_W='echo' DEFS='' DEPDIR='.deps' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='' EXEEXT='' GREP='' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' LDFLAGS='-Wl,-z,relro -L/lib' LIBOBJS='' LIBS='' LTLIBOBJS='' MAKEINFO='${SHELL} /«PKGBUILDDIR»/build-aux/missing --run makeinfo' MKDIR_P='/bin/mkdir -p' OBJEXT='o' PACKAGE='tophat' PACKAGE_BUGREPORT='cole@cs.umd.edu, infphilo@umiacs.umd.edu' PACKAGE_NAME='tophat' PACKAGE_STRING='tophat 2.0.6' PACKAGE_TARNAME='tophat' PACKAGE_URL='' PACKAGE_VERSION='2.0.6' PATH_SEPARATOR=':' PYTHON='/usr/bin/python' PYTHON_EXEC_PREFIX='${exec_prefix}' PYTHON_PLATFORM='linux2' PYTHON_PREFIX='${prefix}' PYTHON_VERSION='2.7' RANLIB='ranlib' SET_MAKE='' SHELL='/bin/bash' STRIP='' VERSION='2.0.6' ac_ct_CC='gcc' ac_ct_CXX='g++' am__EXEEXT_FALSE='' am__EXEEXT_TRUE='' am__fastdepCC_FALSE='' am__fastdepCC_TRUE='#' am__fastdepCXX_FALSE='' am__fastdepCXX_TRUE='#' am__include='include' am__isrc='' am__leading_dot='.' am__nodep='' am__quote='' am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -' bindir='${exec_prefix}/bin' build='x86_64-linux-gnu' build_alias='x86_64-linux-gnu' build_cpu='' build_os='' build_vendor='' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' exec_prefix='NONE' host='' host_alias='' host_cpu='' host_os='' host_vendor='' htmldir='${docdir}' includedir='${prefix}/include' infodir='${prefix}/share/info' install_sh='${SHELL} /«PKGBUILDDIR»/build-aux/install-sh' libdir='${prefix}/lib/x86_64-linux-gnu' libexecdir='${prefix}/lib/x86_64-linux-gnu' localedir='${datarootdir}/locale' localstatedir='/var' mandir='${prefix}/share/man' mkdir_p='/bin/mkdir -p' oldincludedir='/usr/include' pdfdir='${docdir}' pkgpyexecdir='${pyexecdir}/tophat' pkgpythondir='${pythondir}/tophat' prefix='/usr' program_transform_name='s,x,x,' psdir='${docdir}' pyexecdir='${exec_prefix}/lib/python2.7/dist-packages' pythondir='${prefix}/lib/python2.7/dist-packages' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' sysconfdir='/etc' target_alias='' ## ----------- ## ## confdefs.h. ## ## ----------- ## /* confdefs.h */ #define PACKAGE_NAME "tophat" #define PACKAGE_TARNAME "tophat" #define PACKAGE_VERSION "2.0.6" #define PACKAGE_STRING "tophat 2.0.6" #define PACKAGE_BUGREPORT "cole@cs.umd.edu, infphilo@umiacs.umd.edu" #define PACKAGE_URL "" #define SVN_REVISION "" #define PACKAGE "tophat" #define VERSION "2.0.6" #define HAVE_BOOST /**/ configure: exit 1 make: *** [build-arch] Error 255 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20130128-0501 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 2928 Build-Time: 9 Distribution: unstable Fail-Stage: build Install-Time: 11 Job: tophat_2.0.6-1 Package: tophat Package-Time: 49 Source-Version: 2.0.6-1 Space: 2928 Status: attempted Version: 2.0.6-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20130128-0501 Build needed 00:00:49, 2928k disc space DC-Status: Failed 49.376121s DC-Time-Estimation: 49.376121 versus expected 133 (r/m: 1.69360973090616 ; m: 49.376121)