DC-Build-Header: hhsuite 2.0.15-1 / Tue Jan 29 14:14:36 +0000 2013 DC-Task: logfile:/tmp/hhsuite_2.0.15-1_unstable_clang.log version:2.0.15-1 modes:binary-only:clang chroot:unstable source:hhsuite esttime:123 architecture:any DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/switch-to-clang hhsuite_2.0.15-1' 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-10-159-4-134.ec2.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ hhsuite 2.0.15-1 (amd64) 29 Jan 2013 14:14 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: hhsuite Version: 2.0.15-1 Source Version: 2.0.15-1 Distribution: unstable Architecture: amd64 I: NOTICE: Log filtering will replace 'build/hhsuite-_W5FU7/hhsuite-2.0.15' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/hhsuite-_W5FU7' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-7982bd7b-0fb9-4837-b7a5-33b2817bb992' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost unstable InRelease Hit http://localhost unstable Release.gpg Hit http://localhost unstable Release Ign http://localhost unstable/main Sources/DiffIndex Ign http://localhost unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Translation-en/DiffIndex Hit http://localhost unstable/main Sources Hit http://localhost unstable/main amd64 Packages 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: 'hhsuite' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/hhsuite/trunk/ Need to get 3925 kB of source archives. Get:1 http://localhost/debian/ unstable/main hhsuite 2.0.15-1 (dsc) [2128 B] Get:2 http://localhost/debian/ unstable/main hhsuite 2.0.15-1 (tar) [3914 kB] Get:3 http://localhost/debian/ unstable/main hhsuite 2.0.15-1 (diff) [9178 B] Fetched 3925 kB in 0s (6369 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 [709 kB] Get:4 http://localhost experimental/main amd64 Packages [1615 kB] Hit http://localhost unstable/main Sources Hit http://localhost unstable/main amd64 Packages Fetched 2486 kB in 1s (1329 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 (3959 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 56.6 MB of archives. After this operation, 72.5 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 2.17-0experimental0 [3111 kB] Get:3 http://localhost/debian/ experimental/main libc-dev-bin amd64 2.17-0experimental0 [230 kB] Get:4 http://localhost/debian/ experimental/main libc6 amd64 2.17-0experimental0 [4604 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 56.6 MB in 1s (35.0 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_2.17-0experimental0_amd64.deb) ... Unpacking replacement libc6-dev:amd64 ... Preparing to replace libc-dev-bin 2.13-38 (using .../libc-dev-bin_2.17-0experimental0_amd64.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libc6:amd64 2.13-38 (using .../libc6_2.17-0experimental0_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 (2.17-0experimental0) ... 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 ... 13512 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 ... 13512 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 ... 13512 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 ... 13512 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 ... 13512 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 (2.17-0experimental0) ... Setting up libc6-dev:amd64 (2.17-0experimental0) ... 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-0t3vW8/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/708 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14677 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 (>= 8.0.0), libffindex0-dev (>= 0.9.6.1), help2man, libpng12-dev 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 (>= 8.0.0), libffindex0-dev (>= 0.9.6.1), help2man, libpng12-dev dpkg-deb: building package `sbuild-build-depends-hhsuite-dummy' in `/«BUILDDIR»/resolver-WwWFdP/apt_archive/sbuild-build-depends-hhsuite-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install hhsuite build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils debhelper file gettext gettext-base groff-base help2man html2text intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffindex0 libffindex0-dev libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libpng12-0 libpng12-dev libunistring0 libxml2 man-db po-debconf zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper file gettext gettext-base groff-base help2man html2text intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffindex0 libffindex0-dev libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libpng12-0 libpng12-dev libunistring0 libxml2 man-db po-debconf sbuild-build-depends-hhsuite-dummy zlib1g-dev 0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded. Need to get 9921 kB/9922 kB of archives. After this operation, 28.0 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 libpng12-0 amd64 1.2.49-3 [190 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 html2text amd64 1.3.2a-15 [103 kB] Get:17 http://localhost/debian/ unstable/main libasprintf-dev amd64 0.18.1.1-10 [26.8 kB] Get:18 http://localhost/debian/ unstable/main libgettextpo-dev amd64 0.18.1.1-10 [184 kB] Get:19 http://localhost/debian/ unstable/main gettext amd64 0.18.1.1-10 [1815 kB] Get:20 http://localhost/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:21 http://localhost/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB] Get:22 http://localhost/debian/ unstable/main debhelper all 9.20120909 [705 kB] Get:23 http://localhost/debian/ unstable/main help2man amd64 1.41.1 [101 kB] Get:24 http://localhost/debian/ unstable/main zlib1g-dev amd64 1:1.2.7.dfsg-13 [215 kB] Get:25 http://localhost/debian/ unstable/main libpng12-dev amd64 1.2.49-3 [267 kB] Get:26 http://localhost/debian/ unstable/main libffindex0 amd64 0.9.9-2 [17.0 kB] Get:27 http://localhost/debian/ unstable/main libffindex0-dev amd64 0.9.9-2 [16.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 9921 kB in 0s (13.3 MB/s) Selecting previously unselected package libpipeline1:amd64. (Reading database ... 14677 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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Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously unselected package libasprintf-dev:amd64. Unpacking libasprintf-dev:amd64 (from .../libasprintf-dev_0.18.1.1-10_amd64.deb) ... Selecting previously unselected package libgettextpo-dev:amd64. Unpacking libgettextpo-dev:amd64 (from .../libgettextpo-dev_0.18.1.1-10_amd64.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-10_amd64.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ... Selecting previously unselected package help2man. Unpacking help2man (from .../help2man_1.41.1_amd64.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 libpng12-dev. Unpacking libpng12-dev (from .../libpng12-dev_1.2.49-3_amd64.deb) ... Selecting previously unselected package libffindex0. Unpacking libffindex0 (from .../libffindex0_0.9.9-2_amd64.deb) ... Selecting previously unselected package libffindex0-dev. Unpacking libffindex0-dev (from .../libffindex0-dev_0.9.9-2_amd64.deb) ... Selecting previously unselected package sbuild-build-depends-hhsuite-dummy. Unpacking sbuild-build-depends-hhsuite-dummy (from .../sbuild-build-depends-hhsuite-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 libpng12-0:amd64 (1.2.49-3) ... Setting up file (5.11-2) ... Setting up gettext-base (0.18.1.1-10) ... 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 help2man (1.41.1) ... Setting up zlib1g-dev:amd64 (1:1.2.7.dfsg-13) ... Setting up libpng12-dev (1.2.49-3) ... Setting up libffindex0 (0.9.9-2) ... Setting up libffindex0-dev (0.9.9-2) ... Setting up sbuild-build-depends-hhsuite-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_2.17-0experimental0 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 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 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 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-38 libc-dev-bin_2.17-0experimental0 libc6_2.17-0experimental0 libc6-dev_2.17-0experimental0 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 libffindex0_0.9.9-2 libffindex0-dev_0.9.9-2 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 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 libpng12-0_1.2.49-3 libpng12-dev_1.2.49-3 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 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 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 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-hhsuite-dummy_0.invalid.0 sed_4.2.1-10 sensible-utils_0.0.7 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 Thu Jun 28 11:45:44 2012 UTC using RSA key ID 9A0C52FA gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./hhsuite_2.0.15-1.dsc dpkg-source: info: extracting hhsuite in hhsuite-2.0.15 dpkg-source: info: unpacking hhsuite_2.0.15.orig.tar.gz dpkg-source: info: unpacking hhsuite_2.0.15-1.debian.tar.gz dpkg-source: info: applying Makefile dpkg-source: info: applying paths dpkg-source: info: applying help dpkg-source: info: applying rest1 dpkg-source: info: applying hardening dpkg-source: info: applying unused_variables_warning dpkg-source: info: applying unnecessary_libz 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-7982bd7b-0fb9-4837-b7a5-33b2817bb992 SCHROOT_UID=1000 SCHROOT_USER=user SHELL=/bin/sh USER=user dpkg-buildpackage ───────────────── dpkg-buildpackage: source package hhsuite dpkg-buildpackage: source version 2.0.15-1 dpkg-buildpackage: source changed by Laszlo Kajan dpkg-source --before-build hhsuite-2.0.15 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --parallel dh_testdir -O--parallel dh_auto_clean -O--parallel make[1]: Entering directory `/«PKGBUILDDIR»' make -C src clean make[2]: Entering directory `/«PKGBUILDDIR»/src' rm -f *.o cs/*.o rm -f hhconsensus hhconsensus_valgrind hhfilter_valgrind hhfilter hhalign_valgrind hhalign hhmake hhblits_valgrind hhblits hhsearch_valgrind hhsearch cstranslate make[2]: Leaving directory `/«PKGBUILDDIR»/src' make[1]: Leaving directory `/«PKGBUILDDIR»' debian/rules override_dh_clean make[1]: Entering directory `/«PKGBUILDDIR»' rm -f hhalign.1 hhblits.1 hhconsensus.1 hhfilter.1 hhmake.1 hhsearch.1 dh_clean make[1]: Leaving directory `/«PKGBUILDDIR»' debian/rules build-arch dh build-arch --parallel dh_testdir -a -O--parallel dh_auto_configure -a -O--parallel dh_auto_build -a -O--parallel make[1]: Entering directory `/«PKGBUILDDIR»' make -C data all make[2]: Entering directory `/«PKGBUILDDIR»/data' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/«PKGBUILDDIR»/data' make -C src all make[2]: Entering directory `/«PKGBUILDDIR»/src' g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/aa.cc -o cs/aa.o clang: warning: -Wl,-z,relro: 'linker' input unused clang: warning: argument unused during compilation: '-fopenmp' g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/application.cc -o cs/application.o clang: warning: -Wl,-z,relro: 'linker' input unused clang: warning: argument unused during compilation: '-fopenmp' g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/as.cc -o cs/as.o clang: warning: -Wl,-z,relro: 'linker' input unused clang: warning: argument unused during compilation: '-fopenmp' g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/assert_helpers.cc -o cs/assert_helpers.o clang: warning: -Wl,-z,relro: 'linker' input unused clang: warning: argument unused during compilation: '-fopenmp' g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/blosum_matrix.cc -o cs/blosum_matrix.o clang: warning: -Wl,-z,relro: 'linker' input unused clang: warning: argument unused during compilation: '-fopenmp' g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/getopt_pp.cc -o cs/getopt_pp.o clang: warning: -Wl,-z,relro: 'linker' input unused clang: warning: argument unused during compilation: '-fopenmp' g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/log.cc -o cs/log.o clang: warning: -Wl,-z,relro: 'linker' input unused clang: warning: argument unused during compilation: '-fopenmp' g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -DHH_SSE3 -msse3 -Wl,-z,relro hhblits.C -o hhblits cs/aa.o cs/application.o cs/as.o cs/assert_helpers.o cs/blosum_matrix.o cs/getopt_pp.o cs/log.o -lpthread -fopenmp -lrt -lffindex In file included from hhblits.C:123: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:6: In file included from cs/count_profile.h:6: cs/alignment.h:93:56: error: reference to non-static member function must be called; did you mean to call it with no arguments? void set_name(const std::string& header) { name_ = name; } ^~~~ () In file included from hhblits.C:123: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:8: cs/alignment-inl.h:827:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from hhblits.C:123: In file included from cs/context_library.h:9: cs/pseudocounts.h:14:1: warning: class template 'CountProfile' was previously declared as a struct template [-Wmismatched-tags] class CountProfile; ^ cs/count_profile.h:14:8: note: previous use is here struct CountProfile { ^ cs/pseudocounts.h:14:1: note: did you mean struct here? class CountProfile; ^~~~~ struct In file included from hhblits.C:132: ./hhutil.C:478:49: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhutil.C:483:45: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ In file included from hhblits.C:142: ./hhhmm.C:169:23: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(q.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:174:21: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:360:39: warning: when type is in parentheses, array cannot have dynamic size seq[k-1]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:367:40: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ~ ^~~~~~~~~~~~~~~~ ~ ./hhhmm.C:468:29: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:719:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:740:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:761:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:835:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1009:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1011:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1014:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1032:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1034:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1182:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1203:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1224:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1295:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1471:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1473:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1476:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1494:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1496:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:2177:28: warning: when type is in parentheses, array cannot have dynamic size char** lines = new(char*[3*L+100000]); ~ ^~~~~~~~~~ ~ ./hhhmm.C:2205:29: warning: when type is in parentheses, array cannot have dynamic size lines[nline]=new(char[strlen(line)+1]); ~ ^~~~~~~~~~~~~~ ~ ./hhhmm.C:2329:30: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:2336:30: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf]=new(char[L+2]); ~ ^~~ ~ In file included from hhblits.C:143: ./hhalignment.C:47:21: warning: when type is in parentheses, array cannot have dynamic size sname = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:48:19: warning: when type is in parentheses, array cannot have dynamic size seq = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:49:15: warning: when type is in parentheses, array cannot have dynamic size l = new(int[maxres]); ~ ^~~~~~ ~ ./hhalignment.C:50:17: warning: when type is in parentheses, array cannot have dynamic size X = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:51:31: warning: when type is in parentheses, array cannot have dynamic size I = new(short unsigned int*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:52:19: warning: when type is in parentheses, array cannot have dynamic size keep = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:53:22: warning: when type is in parentheses, array cannot have dynamic size display = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:54:18: warning: when type is in parentheses, array cannot have dynamic size wg = new(float[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:55:19: warning: when type is in parentheses, array cannot have dynamic size nseqs = new(int[maxres+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:144:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:150:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(ali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:156:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(ali.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:162:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:167:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:252:31: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:254:29: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:256:43: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:313:31: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(cur_name)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:429:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:431:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:433:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:647:31: warning: when type is in parentheses, array cannot have dynamic size if (nres==NULL) nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:921:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:924:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:926:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:947:27: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(q->sname[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:970:26: warning: when type is in parentheses, array cannot have dynamic size char *dummy = new(char[N_in+1]); ~ ^~~~~~ ~ ./hhalignment.C:1029:21: warning: when type is in parentheses, array cannot have dynamic size char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted; in[k]=0: seq k has not yet been accepted at current seqid ~ ^~~~~~ ~ ./hhalignment.C:1030:23: warning: when type is in parentheses, array cannot have dynamic size char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ~ ^~~~~~ ~ ./hhalignment.C:1031:21: warning: when type is in parentheses, array cannot have dynamic size int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering? (variable used in former version was idmax) ~ ^~~ ~ ./hhalignment.C:1032:25: warning: when type is in parentheses, array cannot have dynamic size int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ~ ^~~ ~ ./hhalignment.C:1033:27: warning: when type is in parentheses, array cannot have dynamic size int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid) ~ ^~~~~~ ~ ./hhalignment.C:1034:18: warning: when type is in parentheses, array cannot have dynamic size int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ~ ^~~ ~ ./hhalignment.C:1062:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1063:21: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1077:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:1093:21: warning: when type is in parentheses, array cannot have dynamic size ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences ~ ^~~~ ~ ./hhalignment.C:1301:30: warning: when type is in parentheses, array cannot have dynamic size float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore ~ ^~~ ~ ./hhalignment.C:1310:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1311:21: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1324:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:1596:37: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->ncons]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:1603:40: warning: when type is in parentheses, array cannot have dynamic size q->sname[q->nfirst]=new(char[strlen(name)+11]); ~ ^~~~~~~~~~~~~~~ ~ ./hhalignment.C:1607:38: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->nfirst]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:1659:33: warning: when type is in parentheses, array cannot have dynamic size q->sname[nn]=new(char[strlen(sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1662:31: warning: when type is in parentheses, array cannot have dynamic size q->seq[nn]=new(char[strlen(seq[k])+1]); ~ ^~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1762:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C:1824:57: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]0) wi[k]=wg[k]; else wi[k]=0.0; ^ ./hhalignment.C:2171:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C:2241:58: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]==GAP) wi[k]=wg[k]; else wi[k]=0.0; ^ ./hhalignment.C:2417:28: warning: when type is in parentheses, array cannot have dynamic size char* cur_seq = new(char[par.maxcol]); // Sequence currently read in ~ ^~~~~~~~~~ ~ ./hhalignment.C:2432:23: warning: when type is in parentheses, array cannot have dynamic size int* imatch=new(int[hit.j2+1]); ~ ^~~~~~~~ ~ ./hhalignment.C:2564:38: warning: when type is in parentheses, array cannot have dynamic size char* new_seq=new(char[2*maxcol]); ~ ^~~~~~~~ ~ ./hhalignment.C:2577:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[h]); ~ ^ ~ ./hhalignment.C:2580:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[h]); ~ ^ ~ ./hhalignment.C:2582:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[h]); ~ ^ ~ ./hhalignment.C:2584:28: warning: when type is in parentheses, array cannot have dynamic size sname[N_in]=new(char[strlen(Tali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:2615:20: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2653:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2655:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2657:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C:2676:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2678:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2680:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C:2733:20: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ In file included from hhblits.C:144: ./hhhit.C:141:17: warning: when type is in parentheses, array cannot have dynamic size bMM=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:142:17: warning: when type is in parentheses, array cannot have dynamic size bMI=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:143:17: warning: when type is in parentheses, array cannot have dynamic size bIM=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:144:17: warning: when type is in parentheses, array cannot have dynamic size bDG=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:145:17: warning: when type is in parentheses, array cannot have dynamic size bGD=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:146:22: warning: when type is in parentheses, array cannot have dynamic size cell_off=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:149:23: warning: when type is in parentheses, array cannot have dynamic size bMM[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:150:23: warning: when type is in parentheses, array cannot have dynamic size bMI[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:151:23: warning: when type is in parentheses, array cannot have dynamic size bIM[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:152:23: warning: when type is in parentheses, array cannot have dynamic size bGD[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:153:23: warning: when type is in parentheses, array cannot have dynamic size bDG[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:154:28: warning: when type is in parentheses, array cannot have dynamic size cell_off[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:192:20: warning: when type is in parentheses, array cannot have dynamic size F_MM=new(double*[Nq]); ~ ^~ ~ ./hhhit.C:199:20: warning: when type is in parentheses, array cannot have dynamic size scale=new(double[Nq+1]); // need Nq+3? ~ ^~~~ ~ ./hhhit.C:202:28: warning: when type is in parentheses, array cannot have dynamic size F_MM[i] = new(double[Nt]); ~ ^~ ~ ./hhhit.C:252:20: warning: when type is in parentheses, array cannot have dynamic size B_MM=new(double*[Nq]); ~ ^~ ~ ./hhhit.C:261:28: warning: when type is in parentheses, array cannot have dynamic size B_MM[i] = new(double[Nt]); ~ ^~ ~ ./hhhit.C:291:15: warning: when type is in parentheses, array cannot have dynamic size i = new(int[len]); ~ ^~~ ~ ./hhhit.C:292:15: warning: when type is in parentheses, array cannot have dynamic size j = new(int[len]); ~ ^~~ ~ ./hhhit.C:1147:21: warning: when type is in parentheses, array cannot have dynamic size S = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1148:21: warning: when type is in parentheses, array cannot have dynamic size S_ss = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1487:21: warning: when type is in parentheses, array cannot have dynamic size S = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1488:21: warning: when type is in parentheses, array cannot have dynamic size S_ss = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1489:28: warning: when type is in parentheses, array cannot have dynamic size P_posterior = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1795:21: warning: when type is in parentheses, array cannot have dynamic size longname=new(char[strlen(t->longname)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1796:21: warning: when type is in parentheses, array cannot have dynamic size name =new(char[strlen(t->name)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1797:21: warning: when type is in parentheses, array cannot have dynamic size file =new(char[strlen(t->file)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1808:22: warning: when type is in parentheses, array cannot have dynamic size this->i = new( int[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C:1809:22: warning: when type is in parentheses, array cannot have dynamic size this->j = new( int[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C:1810:23: warning: when type is in parentheses, array cannot have dynamic size states = new( char[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C:1813:19: warning: when type is in parentheses, array cannot have dynamic size sname=new(char*[t->n_display]); ~ ^~~~~~~~~~~~ ~ ./hhhit.C:1814:19: warning: when type is in parentheses, array cannot have dynamic size seq =new(char*[t->n_display]); ~ ^~~~~~~~~~~~ ~ ./hhhit.C:1833:24: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(t->sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1834:24: warning: when type is in parentheses, array cannot have dynamic size seq[k] = new(char[strlen(t->seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1840:20: warning: when type is in parentheses, array cannot have dynamic size dbfile = new(char[strlen(ptr)+1]); ~ ^~~~~~~~~~~~~ ~ In file included from hhblits.C:145: ./hhhalfalignment.C:46:15: warning: when type is in parentheses, array cannot have dynamic size h = new(int[maxseqdis]); //h[k] = next position of sequence k to be written ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:47:17: warning: when type is in parentheses, array cannot have dynamic size s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k of output alignment ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:48:16: warning: when type is in parentheses, array cannot have dynamic size l = new(int*[maxseqdis]); //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:49:16: warning: when type is in parentheses, array cannot have dynamic size m = new(int*[maxseqdis]); //counts positions: m[k][i] = position of match state i in string seq[k] ~ ^~~~~~~~~ ~ In file included from hhblits.C:262: ./hhprefilter.C:794:34: warning: when type is in parentheses, array cannot have dynamic size dbfiles_new[ndb_new]=new(char[strlen(db_name)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhprefilter.C:846:30: warning: when type is in parentheses, array cannot have dynamic size dbnames[num_dbs]=new(char[strlen(word)+1]); ~ ^~~~~~~~~~~~~~ ~ ./hhprefilter.C:1044:38: warning: when type is in parentheses, array cannot have dynamic size __m128i** workspace = new(__m128i*[cpu]); ~ ^~~ ~ ./hhprefilter.C:1062:9: warning: unknown pragma ignored [-Wunknown-pragmas] #pragma omp parallel for schedule(static) private(score, thread_id) ^ ./hhprefilter.C:1076:9: warning: unknown pragma ignored [-Wunknown-pragmas] #pragma omp critical ^ ./hhprefilter.C:1090:9: warning: unknown pragma ignored [-Wunknown-pragmas] #pragma omp parallel for schedule(static) private(evalue, score, thread_id) ^ ./hhprefilter.C:1104:9: warning: unknown pragma ignored [-Wunknown-pragmas] #pragma omp critical ^ ./hhprefilter.C:1143:38: warning: when type is in parentheses, array cannot have dynamic size dbfiles_old[ndb_old]=new(char[strlen(db_name)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhprefilter.C:1149:38: warning: when type is in parentheses, array cannot have dynamic size dbfiles_new[ndb_new]=new(char[strlen(db_name)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhprefilter.C:1174:9: warning: unknown pragma ignored [-Wunknown-pragmas] #pragma omp parallel for schedule(static) private(block, block_count, thread_id) ^ ./hhprefilter.C:1204:9: warning: unknown pragma ignored [-Wunknown-pragmas] #pragma omp critical ^ hhblits.C:782:32: warning: when type is in parentheses, array cannot have dynamic size Qali.longname = new(char[strlen(q->longname)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~ ~ hhblits.C:915:32: warning: when type is in parentheses, array cannot have dynamic size hit[bin]->dbfile = new(char[strlen(dbfiles[idb])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ hhblits.C:1121:26: warning: when type is in parentheses, array cannot have dynamic size dbfiles[ndb]=new(char[strlen(hit_cur.dbfile)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~ ~ hhblits.C:1407:32: warning: when type is in parentheses, array cannot have dynamic size hit[bin]->dbfile = new(char[strlen(hit_cur.dbfile)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~ ~ hhblits.C:1717:36: warning: when type is in parentheses, array cannot have dynamic size hit[bin]->dbfile = new(char[strlen(dbfiles[idb])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ hhblits.C:2143:20: warning: when type is in parentheses, array cannot have dynamic size format = new(int[bins]); ~ ^~~~ ~ hhblits.C:2241:33: warning: when type is in parentheses, array cannot have dynamic size dbfiles_new[ndb_new]=new(char[strlen(dbfiles_old[a])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~ ~ 155 warnings and 1 error generated. make[2]: *** [hhblits] Error 1 make[1]: *** [all] Error 2 make[2]: Leaving directory `/«PKGBUILDDIR»/src' make[1]: Leaving directory `/«PKGBUILDDIR»' dh_auto_build: make -j1 returned exit code 2 make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20130129-1415 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 12020 Build-Time: 8 Distribution: unstable Fail-Stage: build Install-Time: 7 Job: hhsuite_2.0.15-1 Package: hhsuite Package-Time: 43 Source-Version: 2.0.15-1 Space: 12020 Status: attempted Version: 2.0.15-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20130129-1415 Build needed 00:00:43, 12020k disc space DC-Status: Failed 43.67093s DC-Time-Estimation: 43.67093 versus expected 123 (r/m: 1.81651890628388 ; m: 43.67093)