DC-Build-Header: hhsuite 2.0.14-1 / Sat Jun 23 16:31:04 +0000 2012 DC-Task: logfile:/tmp/hhsuite_2.0.14-1_unstable_clang.log version:2.0.14-1 chroot:unstable modes:binary-only:clang source:hhsuite architecture:any esttime:123 DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/switch-to-clang hhsuite_2.0.14-1' sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on ip-10-28-205-240.ec2.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ hhsuite 2.0.14-1 (amd64) 23 Jun 2012 16:31 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: hhsuite Version: 2.0.14-1 Source Version: 2.0.14-1 Distribution: unstable Architecture: amd64 I: NOTICE: Log filtering will replace 'build/hhsuite-226z36/hhsuite-2.0.14' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/hhsuite-226z36' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-99991d3e-02f4-4660-b363-1f084c770e1f' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost unstable InRelease Get:1 http://localhost unstable Release.gpg [836 B] Get:2 http://localhost unstable Release [233 kB] Get:3 http://localhost unstable/main Sources/DiffIndex [7876 B] Get:4 http://localhost unstable/main amd64 Packages/DiffIndex [7876 B] Get:5 http://localhost unstable/main Translation-en/DiffIndex [7876 B] Get:6 http://localhost unstable/main 2012-06-23-0814.36.pdiff [8967 B] Get:7 http://localhost unstable/main 2012-06-23-0814.36.pdiff [8967 B] Get:8 http://localhost unstable/main amd64 2012-06-23-0814.36.pdiff [6101 B] Get:9 http://localhost unstable/main 2012-06-23-0814.36.pdiff [1297 B] Get:10 http://localhost unstable/main amd64 2012-06-23-0814.36.pdiff [6101 B] Get:11 http://localhost unstable/main 2012-06-23-1414.42.pdiff [10.6 kB] Get:12 http://localhost unstable/main 2012-06-23-0814.36.pdiff [1297 B] Get:13 http://localhost unstable/main amd64 2012-06-23-1414.42.pdiff [11.3 kB] Get:14 http://localhost unstable/main 2012-06-23-1414.42.pdiff [10.6 kB] Get:15 http://localhost unstable/main 2012-06-23-1414.42.pdiff [696 B] Get:16 http://localhost unstable/main amd64 2012-06-23-1414.42.pdiff [11.3 kB] Get:17 http://localhost unstable/main 2012-06-23-1414.42.pdiff [696 B] Fetched 296 kB in 7s (41.1 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: base-passwd bsdutils libblkid1 libmount1 libuuid1 mount util-linux 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1300 kB of archives. After this operation, 308 kB disk space will be freed. Get:1 http://localhost/debian/ unstable/main mount amd64 2.20.1-5.1 [213 kB] Get:2 http://localhost/debian/ unstable/main util-linux amd64 2.20.1-5.1 [659 kB] Get:3 http://localhost/debian/ unstable/main base-passwd amd64 3.5.26 [46.3 kB] Get:4 http://localhost/debian/ unstable/main bsdutils amd64 1:2.20.1-5.1 [85.3 kB] Get:5 http://localhost/debian/ unstable/main libuuid1 amd64 2.20.1-5.1 [56.9 kB] Get:6 http://localhost/debian/ unstable/main libblkid1 amd64 2.20.1-5.1 [120 kB] Get:7 http://localhost/debian/ unstable/main libmount1 amd64 2.20.1-5.1 [120 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1300 kB in 0s (13.5 MB/s) (Reading database ... 11730 files and directories currently installed.) Preparing to replace mount 2.20.1-5 (using .../mount_2.20.1-5.1_amd64.deb) ... Unpacking replacement mount ... Setting up mount (2.20.1-5.1) ... (Reading database ... 11730 files and directories currently installed.) Preparing to replace util-linux 2.20.1-5 (using .../util-linux_2.20.1-5.1_amd64.deb) ... Unpacking replacement util-linux ... Setting up util-linux (2.20.1-5.1) ... (Reading database ... 11730 files and directories currently installed.) Preparing to replace base-passwd 3.5.25 (using .../base-passwd_3.5.26_amd64.deb) ... Unpacking replacement base-passwd ... Setting up base-passwd (3.5.26) ... (Reading database ... 11730 files and directories currently installed.) Preparing to replace bsdutils 1:2.20.1-5 (using .../bsdutils_1%3a2.20.1-5.1_amd64.deb) ... Unpacking replacement bsdutils ... Setting up bsdutils (1:2.20.1-5.1) ... (Reading database ... 11730 files and directories currently installed.) Preparing to replace libuuid1:amd64 2.20.1-5 (using .../libuuid1_2.20.1-5.1_amd64.deb) ... Unpacking replacement libuuid1:amd64 ... Setting up libuuid1:amd64 (2.20.1-5.1) ... (Reading database ... 11730 files and directories currently installed.) Preparing to replace libblkid1:amd64 2.20.1-5 (using .../libblkid1_2.20.1-5.1_amd64.deb) ... Unpacking replacement libblkid1:amd64 ... Setting up libblkid1:amd64 (2.20.1-5.1) ... (Reading database ... 11730 files and directories currently installed.) Preparing to replace libmount1 2.20.1-5 (using .../libmount1_2.20.1-5.1_amd64.deb) ... Unpacking replacement libmount1 ... Setting up libmount1 (2.20.1-5.1) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ 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 3526 kB of source archives. Get:1 http://localhost/debian/ unstable/main hhsuite 2.0.14-1 (dsc) [2115 B] Get:2 http://localhost/debian/ unstable/main hhsuite 2.0.14-1 (tar) [3515 kB] Get:3 http://localhost/debian/ unstable/main hhsuite 2.0.14-1 (diff) [8700 B] Fetched 3526 kB in 0s (4352 kB/s) Download complete and in download only mode Check arch ────────── ┌──────────────────────────────────────────────────────────────────────────────┐ │ Chroot Setup Commands │ └──────────────────────────────────────────────────────────────────────────────┘ /tmp/switch-to-clang ──────────────────── + echo 'Entering customization script...' Entering customization script... + apt-get update Ign http://localhost unstable InRelease Hit http://localhost unstable Release.gpg Hit http://localhost unstable Release Hit http://localhost unstable/main Sources/DiffIndex Hit http://localhost unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Translation-en/DiffIndex Reading package lists... + echo 'Install of clang' Install of clang + apt-get update Ign http://localhost unstable InRelease Hit http://localhost unstable Release.gpg Hit http://localhost unstable Release Hit http://localhost unstable/main Sources/DiffIndex Hit http://localhost unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Translation-en/DiffIndex Reading package lists... + apt-get install --yes --no-install-recommends clang -t unstable Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libclang-common-dev libffi5 libllvm3.1 Recommended packages: llvm-3.1-dev python The following NEW packages will be installed: clang libclang-common-dev libffi5 libllvm3.1 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 13.1 MB of archives. After this operation, 35.6 MB of additional disk space will be used. Get:1 http://localhost/debian/ unstable/main libffi5 amd64 3.0.10-3 [24.8 kB] Get:2 http://localhost/debian/ unstable/main libllvm3.1 amd64 3.1-1 [7276 kB] Get:3 http://localhost/debian/ unstable/main libclang-common-dev amd64 3.1-6 [84.0 kB] Get:4 http://localhost/debian/ unstable/main clang amd64 3.1-6 [5755 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 13.1 MB in 0s (29.2 MB/s) Selecting previously unselected package libffi5:amd64. (Reading database ... 11730 files and directories currently installed.) Unpacking libffi5:amd64 (from .../libffi5_3.0.10-3_amd64.deb) ... Selecting previously unselected package libllvm3.1:amd64. Unpacking libllvm3.1:amd64 (from .../libllvm3.1_3.1-1_amd64.deb) ... Selecting previously unselected package libclang-common-dev. Unpacking libclang-common-dev (from .../libclang-common-dev_3.1-6_amd64.deb) ... Selecting previously unselected package clang. Unpacking clang (from .../archives/clang_3.1-6_amd64.deb) ... Setting up libffi5:amd64 (3.0.10-3) ... Setting up libllvm3.1:amd64 (3.1-1) ... Setting up libclang-common-dev (3.1-6) ... Setting up clang (3.1-6) ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSION=4.7 + cd /usr/bin + rm g++-4.7 gcc-4.7 cpp-4.7 + ln -s clang++ g++-4.7 + ln -s clang gcc-4.7 + ln -s clang cpp-4.7 + cd - /«BUILDDIR» + echo 'Block the installation of new gcc version' Block the installation of new gcc version + dpkg --set-selections + echo 'gcc-4.6 hold' + dpkg --set-selections + echo 'cpp-4.6 hold' + dpkg --set-selections + echo 'g++-4.6 hold' + dpkg --set-selections + echo 'gcc-4.7 hold' + dpkg --set-selections + echo 'cpp-4.7 hold' + dpkg --set-selections + echo 'g++-4.7 hold' + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + grep clang + gcc --version I: Finished running '/tmp/switch-to-clang'. Finished processing commands. ──────────────────────────────────────────────────────────────────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-URD7Kn/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/706 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 11810 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.0.0), libffindex0-dev, help2man, libpng12-dev Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.0.0), libffindex0-dev, help2man, libpng12-dev dpkg-deb: building package `sbuild-build-depends-hhsuite-dummy' in `/«BUILDDIR»/resolver-l2Mg0k/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 libasprintf0c2 libcroco3 libffindex0 libffindex0-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 libasprintf0c2 libcroco3 libffindex0 libffindex0-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, 26 newly installed, 0 to remove and 0 not upgraded. Need to get 10.7 MB/10.7 MB of archives. After this operation, 27.3 MB of additional disk space will be used. Get:1 http://localhost/debian/ unstable/main libpipeline1 amd64 1.2.1-1 [39.2 kB] Get:2 http://localhost/debian/ unstable/main libasprintf0c2 amd64 0.18.1.1-9 [26.8 kB] Get:3 http://localhost/debian/ unstable/main libmagic1 amd64 5.11-1 [250 kB] Get:4 http://localhost/debian/ unstable/main libpcre3 amd64 1:8.30-5 [242 kB] Get:5 http://localhost/debian/ unstable/main libxml2 amd64 2.8.0+dfsg1-4 [903 kB] Get:6 http://localhost/debian/ unstable/main libglib2.0-0 amd64 2.32.3-1 [2081 kB] Get:7 http://localhost/debian/ unstable/main libcroco3 amd64 0.6.5-1 [151 kB] Get:8 http://localhost/debian/ unstable/main libunistring0 amd64 0.9.3-5 [434 kB] Get:9 http://localhost/debian/ unstable/main libgettextpo0 amd64 0.18.1.1-9 [145 kB] Get:10 http://localhost/debian/ unstable/main libpng12-0 amd64 1.2.49-1 [190 kB] Get:11 http://localhost/debian/ unstable/main bsdmainutils amd64 9.0.3 [209 kB] Get:12 http://localhost/debian/ unstable/main groff-base amd64 1.21-8 [1152 kB] Get:13 http://localhost/debian/ unstable/main man-db amd64 2.6.2-1 [1061 kB] Get:14 http://localhost/debian/ unstable/main file amd64 5.11-1 [53.2 kB] Get:15 http://localhost/debian/ unstable/main gettext-base amd64 0.18.1.1-9 [154 kB] Get:16 http://localhost/debian/ unstable/main html2text amd64 1.3.2a-15 [103 kB] Get:17 http://localhost/debian/ unstable/main gettext amd64 0.18.1.1-9 [1975 kB] Get:18 http://localhost/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:19 http://localhost/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB] Get:20 http://localhost/debian/ unstable/main debhelper all 9.20120608 [700 kB] Get:21 http://localhost/debian/ unstable/main help2man amd64 1.40.10 [96.2 kB] Get:22 http://localhost/debian/ unstable/main zlib1g-dev amd64 1:1.2.7.dfsg-13 [215 kB] Get:23 http://localhost/debian/ unstable/main libpng12-dev amd64 1.2.49-1 [266 kB] Get:24 http://localhost/debian/ unstable/main libffindex0 amd64 0.9.3-2 [15.2 kB] Get:25 http://localhost/debian/ unstable/main libffindex0-dev amd64 0.9.3-2 [14.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 10.7 MB in 0s (17.2 MB/s) Selecting previously unselected package libpipeline1:amd64. (Reading database ... 11810 files and directories currently installed.) Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.1-1_amd64.deb) ... Selecting previously unselected package libasprintf0c2:amd64. Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.1.1-9_amd64.deb) ... Selecting previously unselected package libmagic1:amd64. Unpacking libmagic1:amd64 (from .../libmagic1_5.11-1_amd64.deb) ... Selecting previously unselected package libpcre3:amd64. Unpacking libpcre3:amd64 (from .../libpcre3_1%3a8.30-5_amd64.deb) ... Selecting previously unselected package libxml2:amd64. Unpacking libxml2:amd64 (from .../libxml2_2.8.0+dfsg1-4_amd64.deb) ... Selecting previously unselected package libglib2.0-0:amd64. Unpacking libglib2.0-0:amd64 (from .../libglib2.0-0_2.32.3-1_amd64.deb) ... Selecting previously unselected package libcroco3:amd64. Unpacking libcroco3:amd64 (from .../libcroco3_0.6.5-1_amd64.deb) ... Selecting previously unselected package libunistring0:amd64. Unpacking libunistring0:amd64 (from .../libunistring0_0.9.3-5_amd64.deb) ... Selecting previously unselected package libgettextpo0:amd64. Unpacking libgettextpo0:amd64 (from .../libgettextpo0_0.18.1.1-9_amd64.deb) ... Selecting previously unselected package libpng12-0:amd64. Unpacking libpng12-0:amd64 (from .../libpng12-0_1.2.49-1_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-8_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.2-1_amd64.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.11-1_amd64.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_amd64.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-9_amd64.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ... Selecting previously unselected package help2man. Unpacking help2man (from .../help2man_1.40.10_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_1.2.49-1_amd64.deb) ... Selecting previously unselected package libffindex0. Unpacking libffindex0 (from .../libffindex0_0.9.3-2_amd64.deb) ... Selecting previously unselected package libffindex0-dev. Unpacking libffindex0-dev (from .../libffindex0-dev_0.9.3-2_amd64.deb) ... Selecting previously unselected package sbuild-build-depends-hhsuite-dummy. Unpacking sbuild-build-depends-hhsuite-dummy (from .../sbuild-build-depends-hhsuite-dummy.deb) ... Setting up libpipeline1:amd64 (1.2.1-1) ... Setting up libasprintf0c2:amd64 (0.18.1.1-9) ... Setting up libmagic1:amd64 (5.11-1) ... Setting up libpcre3:amd64 (1:8.30-5) ... Setting up libxml2:amd64 (2.8.0+dfsg1-4) ... Setting up libglib2.0-0:amd64 (2.32.3-1) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.5-1) ... Setting up libunistring0:amd64 (0.9.3-5) ... Setting up libgettextpo0:amd64 (0.18.1.1-9) ... Setting up libpng12-0:amd64 (1.2.49-1) ... Setting up bsdmainutils (9.0.3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode. Setting up groff-base (1.21-8) ... Setting up man-db (2.6.2-1) ... Building database of manual pages ... Setting up file (5.11-1) ... Setting up gettext-base (0.18.1.1-9) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-9) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120608) ... Setting up help2man (1.40.10) ... Setting up zlib1g-dev:amd64 (1:1.2.7.dfsg-13) ... Setting up libpng12-dev (1.2.49-1) ... Setting up libffindex0 (0.9.3-2) ... Setting up libffindex0-dev (0.9.3-2) ... 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_2.22-6.1 dpkg-dev_1.16.4.3 g++-4.6_4.6.3-7 g++-4.7_4.7.1-1 gcc-4.6_4.6.3-7 gcc-4.7_4.7.1-1 libc6-dev_2.13-33 libstdc++6_4.7.1-1 libstdc++6-4.6-dev_4.6.3-7 libstdc++6-4.7-dev_4.7.1-1 linux-libc-dev_3.2.20-1 Package versions: apt_0.9.7 base-files_6.11 base-passwd_3.5.26 bash_4.2-2 binutils_2.22-6.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 clang_3.1-6 coreutils_8.13-3.2 cpp_4:4.7.0-6 cpp-4.6_4.6.3-7 cpp-4.7_4.7.1-1 dash_0.5.7-3 debconf_1.5.44 debconf-i18n_1.5.44 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.1 diffutils_1:3.2-6 dpkg_1.16.4.3 dpkg-dev_1.16.4.3 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-1 findutils_4.4.2-4 g++_4:4.7.0-6 g++-4.6_4.6.3-7 g++-4.7_4.7.1-1 gcc_4:4.7.0-6 gcc-4.4-base_4.4.7-1 gcc-4.5-base_4.5.3-12 gcc-4.6_4.6.3-7 gcc-4.6-base_4.6.3-7 gcc-4.7_4.7.1-1 gcc-4.7-base_4.7.1-1 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.12-2 groff-base_1.21-8 gzip_1.5-1.1 help2man_1.40.10 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-27 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-33 libc-dev-bin_2.13-33 libc6_2.13-33 libc6-dev_2.13-33 libclang-common-dev_3.1-6 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-4 libdpkg-perl_1.16.4.3 libffi5_3.0.10-3 libffindex0_0.9.3-2 libffindex0-dev_0.9.3-2 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-8 libgcc1_1:4.7.1-1 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-1 libitm1_4.7.1-1 libllvm3.1_3.1-1 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-1 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-9 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libpng12-0_1.2.49-1 libpng12-dev_1.2.49-1 libquadmath0_4.7.1-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-13 libss2_1.42.4-3 libstdc++6_4.7.1-1 libstdc++6-4.6-dev_4.6.3-7 libstdc++6-4.7-dev_4.7.1-1 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_5.9-9 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-4 linux-libc-dev_3.2.20-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-33 ncurses-base_5.9-9 ncurses-bin_5.9-9 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 readline-common_6.2-8 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 sysv-rc_2.88dsf-27 sysvinit_2.88dsf-27 sysvinit-utils_2.88dsf-27 tar_1.26-4 tzdata_2012c-1 ucf_3.0025+nmu3 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Wed May 23 14:05:37 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_2.0.14-1.dsc dpkg-source: info: extracting hhsuite in hhsuite-2.0.14 dpkg-source: info: unpacking hhsuite_2.0.14.orig.tar.gz dpkg-source: info: unpacking hhsuite_2.0.14-1.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 Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=root PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/bin/X11 SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=0 SCHROOT_GROUP=root SCHROOT_SESSION_ID=unstable-amd64-sbuild-99991d3e-02f4-4660-b363-1f084c770e1f SCHROOT_UID=0 SCHROOT_USER=root SHELL=/bin/sh USER=root dpkg-buildpackage ───────────────── dpkg-buildpackage: warning: using a gain-root-command while being root dpkg-buildpackage: source package hhsuite dpkg-buildpackage: source version 2.0.14-1 dpkg-buildpackage: source changed by Laszlo Kajan dpkg-source --before-build hhsuite-2.0.14 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --parallel dh_testdir -O--parallel dh_auto_clean -O--parallel make -j1 distclean 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 rm -f debian/hhsuite.substvars rm -f debian/hhsuite.*.debhelper rm -rf debian/hhsuite/ rm -f debian/hhsuite-data.substvars rm -f debian/hhsuite-data.*.debhelper rm -rf debian/hhsuite-data/ rm -f debian/hhsuite-dbg.substvars rm -f debian/hhsuite-dbg.*.debhelper rm -rf debian/hhsuite-dbg/ 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 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 -j1 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 when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' 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 when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' 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 when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' 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 when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' 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 when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' 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 when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' 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 when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' 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 clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' 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:142:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:149:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(ali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:153:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(ali.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:157:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:159:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:241:31: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:243:29: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:245:43: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:302:31: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(cur_name)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:418:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:420:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:422:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:636:31: warning: when type is in parentheses, array cannot have dynamic size if (nres==NULL) nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:903:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:906:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:908:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:929:27: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(q->sname[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:952:26: warning: when type is in parentheses, array cannot have dynamic size char *dummy = new(char[N_in+1]); ~ ^~~~~~ ~ ./hhalignment.C:1011:21: 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:1012:23: 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:1013:21: 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:1014:25: 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:1015:27: 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:1016:18: 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:1044:21: 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:1045:21: 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:1059:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:1075:21: 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:1283:30: 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:1292:21: 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:1293:21: 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:1306:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:1578:37: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->ncons]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:1585:40: warning: when type is in parentheses, array cannot have dynamic size q->sname[q->nfirst]=new(char[strlen(name)+11]); ~ ^~~~~~~~~~~~~~~ ~ ./hhalignment.C:1589:38: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->nfirst]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:1641:33: warning: when type is in parentheses, array cannot have dynamic size q->sname[nn]=new(char[strlen(sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1644:31: warning: when type is in parentheses, array cannot have dynamic size q->seq[nn]=new(char[strlen(seq[k])+1]); ~ ^~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1744:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C:1806:57: 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:2153:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C:2223:58: 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:2400:28: warning: when type is in parentheses, array cannot have dynamic size char* cur_seq = new(char[par.maxcol]); // Sequence currently read in ~ ^~~~~~~~~~ ~ ./hhalignment.C:2423:23: warning: when type is in parentheses, array cannot have dynamic size int* imatch=new(int[hit.j2+1]); ~ ^~~~~~~~ ~ ./hhalignment.C:2555:38: warning: when type is in parentheses, array cannot have dynamic size char* new_seq=new(char[2*maxcol]); ~ ^~~~~~~~ ~ ./hhalignment.C:2568:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[h]); ~ ^ ~ ./hhalignment.C:2571:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[h]); ~ ^ ~ ./hhalignment.C:2573:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[h]); ~ ^ ~ ./hhalignment.C:2575:28: warning: when type is in parentheses, array cannot have dynamic size sname[N_in]=new(char[strlen(Tali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:2606:20: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2644:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2646:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2648:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C:2667:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2669:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2671:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C:2724:20: 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:783:32: warning: when type is in parentheses, array cannot have dynamic size Qali.longname = new(char[strlen(q->longname)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~ ~ hhblits.C:916:32: warning: when type is in parentheses, array cannot have dynamic size hit[bin]->dbfile = new(char[strlen(dbfiles[idb])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ hhblits.C:1122:26: warning: when type is in parentheses, array cannot have dynamic size dbfiles[ndb]=new(char[strlen(hit_cur.dbfile)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~ ~ hhblits.C:1408:32: warning: when type is in parentheses, array cannot have dynamic size hit[bin]->dbfile = new(char[strlen(hit_cur.dbfile)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~ ~ hhblits.C:1704:36: warning: when type is in parentheses, array cannot have dynamic size hit[bin]->dbfile = new(char[strlen(dbfiles[idb])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ hhblits.C:2117:20: warning: when type is in parentheses, array cannot have dynamic size format = new(int[bins]); ~ ^~~~ ~ hhblits.C:2246:33: 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[2]: Leaving directory `/«PKGBUILDDIR»/src' make[1]: *** [all] Error 2 dh_auto_build: make -j1 returned exit code 2 make[1]: Leaving directory `/«PKGBUILDDIR»' make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120623-1631 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 11012 Build-Time: 10 Distribution: unstable Fail-Stage: build Install-Time: 8 Job: hhsuite_2.0.14-1 Package: hhsuite Package-Time: 46 Source-Version: 2.0.14-1 Space: 11012 Status: attempted Version: 2.0.14-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120623-1631 Build needed 00:00:46, 11012k disc space DC-Status: Failed 46.699896s DC-Time-Estimation: 46.699896 versus expected 123 (r/m: 1.63383884195374 ; m: 46.699896)