DC-Build-Header: disulfinder 1.2.11-2 / Sat Jun 23 16:33:58 +0000 2012 DC-Task: logfile:/tmp/disulfinder_1.2.11-2_unstable_clang.log version:1.2.11-2 chroot:unstable modes:binary-only:clang source:disulfinder architecture:any esttime:95 DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/switch-to-clang disulfinder_1.2.11-2' sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on ip-10-28-74-239.ec2.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ disulfinder 1.2.11-2 (amd64) 23 Jun 2012 16:33 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: disulfinder Version: 1.2.11-2 Source Version: 1.2.11-2 Distribution: unstable Architecture: amd64 I: NOTICE: Log filtering will replace 'build/disulfinder-icypi8/disulfinder-1.2.11' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/disulfinder-icypi8' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-8699425f-3cb3-4257-932b-f47b5ed0d4b0' 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 (41.6 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 (22.3 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: 'disulfinder' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/svn/debian-med/trunk/packages/rostlab/disulfinder/trunk/ Need to get 2486 kB of source archives. Get:1 http://localhost/debian/ unstable/main disulfinder 1.2.11-2 (dsc) [1456 B] Get:2 http://localhost/debian/ unstable/main disulfinder 1.2.11-2 (tar) [2481 kB] Get:3 http://localhost/debian/ unstable/main disulfinder 1.2.11-2 (diff) [3527 B] Fetched 2486 kB in 0s (4734 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 (30.3 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-weRqNp/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 ... 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 (>= 7.0.50~), libboost-dev, libboost-graph-dev, libf2c2-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 (>= 7.0.50~), libboost-dev, libboost-graph-dev, libf2c2-dev dpkg-deb: building package `sbuild-build-depends-disulfinder-dummy' in `/«BUILDDIR»/resolver-nuqhQL/apt_archive/sbuild-build-depends-disulfinder-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install disulfinder 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 html2text intltool-debian libasprintf0c2 libboost-dev libboost-graph-dev libboost-graph1.49-dev libboost-serialization1.49-dev libboost-serialization1.49.0 libboost-test1.49-dev libboost-test1.49.0 libboost1.49-dev libcroco3 libf2c2 libf2c2-dev libgettextpo0 libglib2.0-0 libicu48 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff libboost-doc libboost1.49-doc libboost-chrono1.49-dev libboost-date-time1.49-dev libboost-filesystem1.49-dev libboost-graph-parallel1.49-dev libboost-iostreams1.49-dev libboost-locale1.49-dev libboost-math1.49-dev libboost-mpi1.49-dev libboost-program-options1.49-dev libboost-python1.49-dev libboost-random1.49-dev libboost-regex1.49-dev libboost-signals1.49-dev libboost-system1.49-dev libboost-thread1.49-dev libboost-timer1.49-dev libboost-wave1.49-dev xsltproc doxygen docbook-xml docbook-xsl default-jdk fop less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur autopoint libboost-graph1.49.0 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 html2text intltool-debian libasprintf0c2 libboost-dev libboost-graph-dev libboost-graph1.49-dev libboost-serialization1.49-dev libboost-serialization1.49.0 libboost-test1.49-dev libboost-test1.49.0 libboost1.49-dev libcroco3 libf2c2 libf2c2-dev libgettextpo0 libglib2.0-0 libicu48 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf sbuild-build-depends-disulfinder-dummy 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 29.6 MB/29.6 MB of archives. After this operation, 151 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 libicu48 amd64 4.8.1.1-8 [8138 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 libboost1.49-dev amd64 1.49.0-3 [9266 kB] Get:22 http://localhost/debian/ unstable/main libboost-dev amd64 1.49.0.1 [3022 B] Get:23 http://localhost/debian/ unstable/main libboost-serialization1.49.0 amd64 1.49.0-3 [209 kB] Get:24 http://localhost/debian/ unstable/main libboost-serialization1.49-dev amd64 1.49.0-3 [305 kB] Get:25 http://localhost/debian/ unstable/main libboost-test1.49.0 amd64 1.49.0-3 [265 kB] Get:26 http://localhost/debian/ unstable/main libboost-test1.49-dev amd64 1.49.0-3 [657 kB] Get:27 http://localhost/debian/ unstable/main libboost-graph1.49-dev amd64 1.49.0-3 [166 kB] Get:28 http://localhost/debian/ unstable/main libboost-graph-dev amd64 1.49.0.1 [2812 B] Get:29 http://localhost/debian/ unstable/main libf2c2 amd64 20090411-2 [159 kB] Get:30 http://localhost/debian/ unstable/main libf2c2-dev amd64 20090411-2 [478 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 29.6 MB in 1s (16.7 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 libicu48:amd64. Unpacking libicu48:amd64 (from .../libicu48_4.8.1.1-8_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 libboost1.49-dev. Unpacking libboost1.49-dev (from .../libboost1.49-dev_1.49.0-3_amd64.deb) ... Selecting previously unselected package libboost-dev. Unpacking libboost-dev (from .../libboost-dev_1.49.0.1_amd64.deb) ... Selecting previously unselected package libboost-serialization1.49.0. Unpacking libboost-serialization1.49.0 (from .../libboost-serialization1.49.0_1.49.0-3_amd64.deb) ... Selecting previously unselected package libboost-serialization1.49-dev. Unpacking libboost-serialization1.49-dev (from .../libboost-serialization1.49-dev_1.49.0-3_amd64.deb) ... Selecting previously unselected package libboost-test1.49.0. Unpacking libboost-test1.49.0 (from .../libboost-test1.49.0_1.49.0-3_amd64.deb) ... Selecting previously unselected package libboost-test1.49-dev. Unpacking libboost-test1.49-dev (from .../libboost-test1.49-dev_1.49.0-3_amd64.deb) ... Selecting previously unselected package libboost-graph1.49-dev. Unpacking libboost-graph1.49-dev (from .../libboost-graph1.49-dev_1.49.0-3_amd64.deb) ... Selecting previously unselected package libboost-graph-dev. Unpacking libboost-graph-dev (from .../libboost-graph-dev_1.49.0.1_amd64.deb) ... Selecting previously unselected package libf2c2. Unpacking libf2c2 (from .../libf2c2_20090411-2_amd64.deb) ... Selecting previously unselected package libf2c2-dev. Unpacking libf2c2-dev (from .../libf2c2-dev_20090411-2_amd64.deb) ... Selecting previously unselected package sbuild-build-depends-disulfinder-dummy. Unpacking sbuild-build-depends-disulfinder-dummy (from .../sbuild-build-depends-disulfinder-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 libicu48:amd64 (4.8.1.1-8) ... 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 libboost1.49-dev (1.49.0-3) ... Setting up libboost-dev (1.49.0.1) ... Setting up libboost-serialization1.49.0 (1.49.0-3) ... Setting up libboost-serialization1.49-dev (1.49.0-3) ... Setting up libboost-test1.49.0 (1.49.0-3) ... Setting up libboost-test1.49-dev (1.49.0-3) ... Setting up libboost-graph1.49-dev (1.49.0-3) ... Setting up libboost-graph-dev (1.49.0.1) ... Setting up libf2c2 (20090411-2) ... Setting up libf2c2-dev (20090411-2) ... Setting up sbuild-build-depends-disulfinder-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 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 libboost-dev_1.49.0.1 libboost-graph-dev_1.49.0.1 libboost-graph1.49-dev_1.49.0-3 libboost-serialization1.49-dev_1.49.0-3 libboost-serialization1.49.0_1.49.0-3 libboost-test1.49-dev_1.49.0-3 libboost-test1.49.0_1.49.0-3 libboost1.49-dev_1.49.0-3 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 libf2c2_20090411-2 libf2c2-dev_20090411-2 libffi5_3.0.10-3 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 libicu48_4.8.1.1-8 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 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-disulfinder-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 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Thu Sep 1 12:45:13 2011 UTC using DSA key ID BE9D5339 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./disulfinder_1.2.11-2.dsc dpkg-source: info: extracting disulfinder in disulfinder-1.2.11 dpkg-source: info: unpacking disulfinder_1.2.11.orig.tar.gz dpkg-source: info: unpacking disulfinder_1.2.11-2.debian.tar.gz 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-8699425f-3cb3-4257-932b-f47b5ed0d4b0 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 disulfinder dpkg-buildpackage: source version 1.2.11-2 dpkg-buildpackage: source changed by Laszlo Kajan dpkg-source --before-build disulfinder-1.2.11 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean make -j1 distclean make[1]: Entering directory `/«PKGBUILDDIR»' if [ -e "disulfind/src/Makefile" ]; then make -C disulfind/src clean; fi make[2]: Entering directory `/«PKGBUILDDIR»/disulfind/src' make -C NN clean make[3]: Entering directory `/«PKGBUILDDIR»/disulfind/src/NN' rm -f *~ *.o brnn-train brnn-test make[3]: Leaving directory `/«PKGBUILDDIR»/disulfind/src/NN' make -C Common clean make[3]: Entering directory `/«PKGBUILDDIR»/disulfind/src/Common' make -C eig clean make[4]: Entering directory `/«PKGBUILDDIR»/disulfind/src/Common/eig' rm *.o libeig.a *~ -f make[4]: Leaving directory `/«PKGBUILDDIR»/disulfind/src/Common/eig' rm *.o libCommon.a Eig Norm *~ -f make[3]: Leaving directory `/«PKGBUILDDIR»/disulfind/src/Common' make -C SVM clean make[3]: Entering directory `/«PKGBUILDDIR»/disulfind/src/SVM' rm *~ *.o *.a *.exe SVMClassifier -f make[3]: Leaving directory `/«PKGBUILDDIR»/disulfind/src/SVM' cd SVM && make clean make[3]: Entering directory `/«PKGBUILDDIR»/disulfind/src/SVM' rm *~ *.o *.a *.exe SVMClassifier -f make[3]: Leaving directory `/«PKGBUILDDIR»/disulfind/src/SVM' cd Input && make clean make[3]: Entering directory `/«PKGBUILDDIR»/disulfind/src/Input' rm *.o makeWindow makeSparseVector globalDescriptor createKernelDataset createBRNNDataset buildXfolds *~ -f make[3]: Leaving directory `/«PKGBUILDDIR»/disulfind/src/Input' cd Output && make clean make[3]: Entering directory `/«PKGBUILDDIR»/disulfind/src/Output' rm *.o makeASCIIOutput makeHTMLOutput *~ -f make[3]: Leaving directory `/«PKGBUILDDIR»/disulfind/src/Output' cd FSA-Alignment && make clean make[3]: Entering directory `/«PKGBUILDDIR»/disulfind/src/FSA-Alignment' rm *.o fold_automata viterbi_aligner timed_transitions *~ -f make[3]: Leaving directory `/«PKGBUILDDIR»/disulfind/src/FSA-Alignment' cd BRNN && make clean make[3]: Entering directory `/«PKGBUILDDIR»/disulfind/src/BRNN' rm -f *.o core rm -f ./RNNs/*.o ./RNNs/core disulfind-conn make[3]: Leaving directory `/«PKGBUILDDIR»/disulfind/src/BRNN' rm disulfinder disultrainer *.o *~ -f make[2]: Leaving directory `/«PKGBUILDDIR»/disulfind/src' rm -f *.[12345678] *.[12345678].gz #if [ -d "disulfind" ]; then rm -rf disulfind; fi if [ -d "disulfinder-1.2.11" ]; then rm -rf "disulfinder-1.2.11"; fi rm -rf patch-stamp \ initial-clean-stamp \ "disulfinder-1.2.11.tar.gz" \ .pc make[1]: Leaving directory `/«PKGBUILDDIR»' dh_clean rm -f debian/disulfinder.substvars rm -f debian/disulfinder.*.debhelper rm -rf debian/disulfinder/ rm -f debian/disulfinder-data.substvars rm -f debian/disulfinder-data.*.debhelper rm -rf debian/disulfinder-data/ rm -f debian/*.debhelper.log rm -f debian/files find . \( \( -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} \; \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \) rm -f *-stamp debian/rules build-arch dh_testdir /usr/bin/make prefix=/usr make[1]: Entering directory `/«PKGBUILDDIR»' /usr/bin/make -C disulfind/src disulfinder make[2]: Entering directory `/«PKGBUILDDIR»/disulfind/src' g++ -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/GlobalDescriptor.cpp -o Input/GlobalDescriptor.o In file included from Input/GlobalDescriptor.cpp:3: In file included from Input/utils.h:2: Input/Protein.h:16:20: warning: unused variable 'aa_codes' [-Wunused-variable] static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered in profile files ^ Input/Protein.h:17:20: warning: unused variable 'tdb_aa_codes' [-Wunused-variable] static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files ^ Input/Protein.h:19:20: warning: unused variable 'aa_three_codes' [-Wunused-variable] static const char *aa_three_codes[23] = { ^ 3 warnings generated. g++ -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/createBRNNDataset.cpp -o Input/createBRNNDataset.o In file included from Input/createBRNNDataset.cpp:2: In file included from Input/createBRNNDataset.h:1: In file included from Input/utils.h:2: Input/Protein.h:16:20: warning: unused variable 'aa_codes' [-Wunused-variable] static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered in profile files ^ Input/Protein.h:17:20: warning: unused variable 'tdb_aa_codes' [-Wunused-variable] static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files ^ Input/Protein.h:19:20: warning: unused variable 'aa_three_codes' [-Wunused-variable] static const char *aa_three_codes[23] = { ^ 3 warnings generated. g++ -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/createKernelDataset.cpp -o Input/createKernelDataset.o In file included from Input/createKernelDataset.cpp:2: In file included from Input/createKernelDataset.h:1: In file included from Input/utils.h:2: Input/Protein.h:17:20: warning: unused variable 'tdb_aa_codes' [-Wunused-variable] static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files ^ Input/Protein.h:19:20: warning: unused variable 'aa_three_codes' [-Wunused-variable] static const char *aa_three_codes[23] = { ^ 2 warnings generated. g++ -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/makeWindow.cpp -o Input/makeWindow.o g++ -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/makeSparseVector.cpp -o Input/makeSparseVector.o g++ -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/Protein.cpp -o Input/Protein.o g++ -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/buildXfolds.cpp -o Input/buildXfolds.o Input/buildXfolds.cpp:16:41: error: variable length array of non-POD element type 'std::vector' std::vector fold_examples[folds_number]; ^ 1 error generated. make[2]: *** [Input/buildXfolds.o] Error 1 make[2]: Leaving directory `/«PKGBUILDDIR»/disulfind/src' make[1]: *** [disulfinder] Error 2 make: *** [build-stamp] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 make[1]: Leaving directory `/«PKGBUILDDIR»' ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120623-1634 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 15720 Build-Time: 7 Distribution: unstable Fail-Stage: build Install-Time: 12 Job: disulfinder_1.2.11-2 Package: disulfinder Package-Time: 45 Source-Version: 1.2.11-2 Space: 15720 Status: attempted Version: 1.2.11-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120623-1634 Build needed 00:00:45, 15720k disc space DC-Status: Failed 46.380372s DC-Time-Estimation: 46.380372 versus expected 95 (r/m: 1.04828025096478 ; m: 46.380372)