DC-Build-Header: disulfinder 1.2.11-2 / Sun Sep 11 11:10:07 +0200 2011 sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on talc-118.nancy.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ disulfinder 1.2.11-2 (amd64) 11 Sep 2011 11:10 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: disulfinder Version: 1.2.11-2 Source Version: 1.2.11-2 Distribution: lsid64c Architecture: amd64 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost sid InRelease Hit http://localhost sid Release.gpg Hit http://localhost sid Release Ign http://localhost sid/main Sources/DiffIndex Ign http://localhost sid/main amd64 Packages/DiffIndex Ign http://localhost sid/main TranslationIndex Hit http://localhost sid/main Sources Hit http://localhost sid/main amd64 Packages Ign http://localhost sid/main Translation-en Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: binutils cpp-4.6 g++-4.6 gcc-4.6 gcc-4.6-base libc-bin libc-dev-bin libc6 libc6-dev libgcc1 libgomp1 libquadmath0 libstdc++6 libstdc++6-4.6-dev multiarch-support 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 34.4 MB of archives. After this operation, 1073 kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libc6-dev libc-dev-bin libgomp1 gcc-4.6-base libgcc1 cpp-4.6 libquadmath0 libstdc++6-4.6-dev g++-4.6 gcc-4.6 libstdc++6 binutils libc-bin libc6 multiarch-support Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libc6-dev amd64 2.13-20 [2637 kB] Get:2 http://localhost/debian/ sid/main libc-dev-bin amd64 2.13-20 [217 kB] Get:3 http://localhost/debian/ sid/main libgomp1 amd64 4.6.1-10 [25.7 kB] Get:4 http://localhost/debian/ sid/main gcc-4.6-base amd64 4.6.1-10 [135 kB] Get:5 http://localhost/debian/ sid/main libgcc1 amd64 1:4.6.1-10 [42.9 kB] Get:6 http://localhost/debian/ sid/main cpp-4.6 amd64 4.6.1-10 [4816 kB] Get:7 http://localhost/debian/ sid/main libquadmath0 amd64 4.6.1-10 [126 kB] Get:8 http://localhost/debian/ sid/main libstdc++6-4.6-dev amd64 4.6.1-10 [1660 kB] Get:9 http://localhost/debian/ sid/main g++-4.6 amd64 4.6.1-10 [6952 kB] Get:10 http://localhost/debian/ sid/main gcc-4.6 amd64 4.6.1-10 [7303 kB] Get:11 http://localhost/debian/ sid/main libstdc++6 amd64 4.6.1-10 [337 kB] Get:12 http://localhost/debian/ sid/main binutils amd64 2.21.53.20110910-1 [4844 kB] Get:13 http://localhost/debian/ sid/main libc-bin amd64 2.13-20 [819 kB] Get:14 http://localhost/debian/ sid/main libc6 amd64 2.13-20 [4323 kB] Get:15 http://localhost/debian/ sid/main multiarch-support amd64 2.13-20 [141 kB] Preconfiguring packages ... Fetched 34.4 MB in 0s (63.6 MB/s) (Reading database ... 10788 files and directories currently installed.) Preparing to replace libc6-dev 2.13-18 (using .../libc6-dev_2.13-20_amd64.deb) ... Unpacking replacement libc6-dev ... Preparing to replace libc-dev-bin 2.13-18 (using .../libc-dev-bin_2.13-20_amd64.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libgomp1 4.6.1-9 (using .../libgomp1_4.6.1-10_amd64.deb) ... Unpacking replacement libgomp1 ... Preparing to replace gcc-4.6-base 4.6.1-9 (using .../gcc-4.6-base_4.6.1-10_amd64.deb) ... Unpacking replacement gcc-4.6-base ... Setting up gcc-4.6-base (4.6.1-10) ... (Reading database ... 10788 files and directories currently installed.) Preparing to replace libgcc1 1:4.6.1-9 (using .../libgcc1_1%3a4.6.1-10_amd64.deb) ... Unpacking replacement libgcc1 ... Setting up libgcc1 (1:4.6.1-10) ... (Reading database ... 10788 files and directories currently installed.) Preparing to replace cpp-4.6 4.6.1-9 (using .../cpp-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement cpp-4.6 ... Preparing to replace libquadmath0 4.6.1-9 (using .../libquadmath0_4.6.1-10_amd64.deb) ... Unpacking replacement libquadmath0 ... Preparing to replace libstdc++6-4.6-dev 4.6.1-9 (using .../libstdc++6-4.6-dev_4.6.1-10_amd64.deb) ... Unpacking replacement libstdc++6-4.6-dev ... Preparing to replace g++-4.6 4.6.1-9 (using .../g++-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement g++-4.6 ... Preparing to replace gcc-4.6 4.6.1-9 (using .../gcc-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement gcc-4.6 ... Preparing to replace libstdc++6 4.6.1-9 (using .../libstdc++6_4.6.1-10_amd64.deb) ... Unpacking replacement libstdc++6 ... Setting up libstdc++6 (4.6.1-10) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace binutils 2.21.53.20110823-3 (using .../binutils_2.21.53.20110910-1_amd64.deb) ... Unpacking replacement binutils ... Preparing to replace libc-bin 2.13-18 (using .../libc-bin_2.13-20_amd64.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.13-20) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace libc6 2.13-18 (using .../libc6_2.13-20_amd64.deb) ... Unpacking replacement libc6 ... Setting up libc6 (2.13-20) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace multiarch-support 2.13-18 (using .../multiarch-support_2.13-20_amd64.deb) ... Unpacking replacement multiarch-support ... Setting up multiarch-support (2.13-20) ... Setting up libc-dev-bin (2.13-20) ... Setting up libc6-dev (2.13-20) ... Setting up libgomp1 (4.6.1-10) ... Setting up cpp-4.6 (4.6.1-10) ... Setting up libquadmath0 (4.6.1-10) ... Setting up binutils (2.21.53.20110910-1) ... Setting up gcc-4.6 (4.6.1-10) ... Setting up libstdc++6-4.6-dev (4.6.1-10) ... Setting up g++-4.6 (4.6.1-10) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: '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/ sid/main disulfinder 1.2.11-2 (dsc) [1456 B] Get:2 http://localhost/debian/ sid/main disulfinder 1.2.11-2 (tar) [2481 kB] Get:3 http://localhost/debian/ sid/main disulfinder 1.2.11-2 (diff) [3527 B] Fetched 2486 kB in 0s (15.5 MB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/build/disulfinder-tCZhDr/resolver-LlkB0U/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 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/702 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Selecting previously deselected package sbuild-build-depends-core-dummy. (Reading database ... 10801 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) ... Cannot open /var/lib/schroot/mount/lsid64c-79563d06-236c-4172-a4f9-2ee4bf691563/etc/lsb-release: No such file or directory 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 `/build/disulfinder-tCZhDr/resolver-tJT8RT/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 libboost-dev libboost-graph-dev libboost-graph1.46-dev libboost-serialization1.46-dev libboost-serialization1.46.1 libboost-test1.46-dev libboost-test1.46.1 libboost1.46-dev libcroco3 libf2c2 libf2c2-dev libglib2.0-0 libicu44 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff libboost1.46-doc libboost-date-time1.46-dev libboost-filesystem1.46-dev libboost-graph-parallel1.46-dev libboost-iostreams1.46-dev libboost-math1.46-dev libboost-mpi1.46-dev libboost-program-options1.46-dev libboost-python1.46-dev libboost-random1.46-dev libboost-regex1.46-dev libboost-signals1.46-dev libboost-system1.46-dev libboost-thread1.46-dev libboost-wave1.46-dev xsltproc doxygen docbook-xml docbook-xsl default-jdk fop www-browser libmail-box-perl Recommended packages: curl wget lynx-cur autopoint libboost-graph1.46.1 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 libboost-dev libboost-graph-dev libboost-graph1.46-dev libboost-serialization1.46-dev libboost-serialization1.46.1 libboost-test1.46-dev libboost-test1.46.1 libboost1.46-dev libcroco3 libf2c2 libf2c2-dev libglib2.0-0 libicu44 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf sbuild-build-depends-disulfinder-dummy 0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 26.3 MB/26.3 MB of archives. After this operation, 134 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libpcre3 bsdmainutils groff-base man-db libmagic1 file gettext-base libxml2 html2text libglib2.0-0 libcroco3 libunistring0 gettext intltool-debian po-debconf debhelper libicu44 libboost1.46-dev libboost-dev libboost-serialization1.46.1 libboost-serialization1.46-dev libboost-test1.46.1 libboost-test1.46-dev libboost-graph1.46-dev libboost-graph-dev libf2c2 libf2c2-dev sbuild-build-depends-disulfinder-dummy Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libpipeline1 amd64 1.2.0-3 [37.9 kB] Get:2 http://localhost/debian/ sid/main libpcre3 amd64 8.12-4 [225 kB] Get:3 http://localhost/debian/ sid/main bsdmainutils amd64 8.2.3 [208 kB] Get:4 http://localhost/debian/ sid/main groff-base amd64 1.21-6 [1150 kB] Get:5 http://localhost/debian/ sid/main man-db amd64 2.6.0.2-2 [1023 kB] Get:6 http://localhost/debian/ sid/main libmagic1 amd64 5.08-1 [246 kB] Get:7 http://localhost/debian/ sid/main file amd64 5.08-1 [51.7 kB] Get:8 http://localhost/debian/ sid/main gettext-base amd64 0.18.1.1-4 [154 kB] Get:9 http://localhost/debian/ sid/main libxml2 amd64 2.7.8.dfsg-4 [892 kB] Get:10 http://localhost/debian/ sid/main html2text amd64 1.3.2a-15 [103 kB] Get:11 http://localhost/debian/ sid/main libglib2.0-0 amd64 2.28.6-1 [1648 kB] Get:12 http://localhost/debian/ sid/main libcroco3 amd64 0.6.2-1 [125 kB] Get:13 http://localhost/debian/ sid/main libunistring0 amd64 0.9.3-4 [437 kB] Get:14 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-4 [2079 kB] Get:15 http://localhost/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:16 http://localhost/debian/ sid/main po-debconf all 1.0.16+nmu1 [223 kB] Get:17 http://localhost/debian/ sid/main debhelper all 8.9.6 [562 kB] Get:18 http://localhost/debian/ sid/main libicu44 amd64 4.4.2-2 [7065 kB] Get:19 http://localhost/debian/ sid/main libboost1.46-dev amd64 1.46.1-7 [7832 kB] Get:20 http://localhost/debian/ sid/main libboost-dev amd64 1.46.1.1 [2610 B] Get:21 http://localhost/debian/ sid/main libboost-serialization1.46.1 amd64 1.46.1-7 [209 kB] Get:22 http://localhost/debian/ sid/main libboost-serialization1.46-dev amd64 1.46.1-7 [304 kB] Get:23 http://localhost/debian/ sid/main libboost-test1.46.1 amd64 1.46.1-7 [259 kB] Get:24 http://localhost/debian/ sid/main libboost-test1.46-dev amd64 1.46.1-7 [646 kB] Get:25 http://localhost/debian/ sid/main libboost-graph1.46-dev amd64 1.46.1-7 [165 kB] Get:26 http://localhost/debian/ sid/main libboost-graph-dev amd64 1.46.1.1 [2582 B] Get:27 http://localhost/debian/ sid/main libf2c2 amd64 20090411-2 [159 kB] Get:28 http://localhost/debian/ sid/main libf2c2-dev amd64 20090411-2 [478 kB] Preconfiguring packages ... Fetched 26.3 MB in 0s (47.7 MB/s) Selecting previously deselected package libpipeline1. (Reading database ... 10801 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_amd64.deb) ... Selecting previously deselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ... Selecting previously deselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_amd64.deb) ... Selecting previously deselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ... Selecting previously deselected package man-db. Unpacking man-db (from .../man-db_2.6.0.2-2_amd64.deb) ... Selecting previously deselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.08-1_amd64.deb) ... Selecting previously deselected package file. Unpacking file (from .../archives/file_5.08-1_amd64.deb) ... Selecting previously deselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_amd64.deb) ... Selecting previously deselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_amd64.deb) ... Selecting previously deselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously deselected package libglib2.0-0. Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_amd64.deb) ... Selecting previously deselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.2-1_amd64.deb) ... Selecting previously deselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-4_amd64.deb) ... Selecting previously deselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-4_amd64.deb) ... Selecting previously deselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously deselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ... Selecting previously deselected package debhelper. Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ... Selecting previously deselected package libicu44. Unpacking libicu44 (from .../libicu44_4.4.2-2_amd64.deb) ... Selecting previously deselected package libboost1.46-dev. Unpacking libboost1.46-dev (from .../libboost1.46-dev_1.46.1-7_amd64.deb) ... Selecting previously deselected package libboost-dev. Unpacking libboost-dev (from .../libboost-dev_1.46.1.1_amd64.deb) ... Selecting previously deselected package libboost-serialization1.46.1. Unpacking libboost-serialization1.46.1 (from .../libboost-serialization1.46.1_1.46.1-7_amd64.deb) ... Selecting previously deselected package libboost-serialization1.46-dev. Unpacking libboost-serialization1.46-dev (from .../libboost-serialization1.46-dev_1.46.1-7_amd64.deb) ... Selecting previously deselected package libboost-test1.46.1. Unpacking libboost-test1.46.1 (from .../libboost-test1.46.1_1.46.1-7_amd64.deb) ... Selecting previously deselected package libboost-test1.46-dev. Unpacking libboost-test1.46-dev (from .../libboost-test1.46-dev_1.46.1-7_amd64.deb) ... Selecting previously deselected package libboost-graph1.46-dev. Unpacking libboost-graph1.46-dev (from .../libboost-graph1.46-dev_1.46.1-7_amd64.deb) ... Selecting previously deselected package libboost-graph-dev. Unpacking libboost-graph-dev (from .../libboost-graph-dev_1.46.1.1_amd64.deb) ... Selecting previously deselected package libf2c2. Unpacking libf2c2 (from .../libf2c2_20090411-2_amd64.deb) ... Selecting previously deselected package libf2c2-dev. Unpacking libf2c2-dev (from .../libf2c2-dev_20090411-2_amd64.deb) ... Selecting previously deselected package sbuild-build-depends-disulfinder-dummy. Unpacking sbuild-build-depends-disulfinder-dummy (from .../sbuild-build-depends-disulfinder-dummy.deb) ... Processing triggers for install-info ... Setting up libpipeline1 (1.2.0-3) ... Setting up libpcre3 (8.12-4) ... Setting up bsdmainutils (8.2.3) ... 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 (1.21-6) ... Setting up man-db (2.6.0.2-2) ... Building database of manual pages ... Setting up libmagic1 (5.08-1) ... Setting up file (5.08-1) ... Setting up gettext-base (0.18.1.1-4) ... Setting up libxml2 (2.7.8.dfsg-4) ... Setting up html2text (1.3.2a-15) ... Setting up libglib2.0-0 (2.28.6-1) ... No schema files found: doing nothing. Setting up libcroco3 (0.6.2-1) ... Setting up libunistring0 (0.9.3-4) ... Setting up gettext (0.18.1.1-4) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu1) ... Setting up debhelper (8.9.6) ... Setting up libicu44 (4.4.2-2) ... Setting up libboost1.46-dev (1.46.1-7) ... Setting up libboost-dev (1.46.1.1) ... Setting up libboost-serialization1.46.1 (1.46.1-7) ... Setting up libboost-serialization1.46-dev (1.46.1-7) ... Setting up libboost-test1.46.1 (1.46.1-7) ... Setting up libboost-test1.46-dev (1.46.1-7) ... Setting up libboost-graph1.46-dev (1.46.1-7) ... Setting up libboost-graph-dev (1.46.1.1) ... 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-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-10 gcc-4.6_4.6.1-10 libc6-dev_2.13-20 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 linux-libc-dev_3.0.0-3 Package versions: apt_0.8.15.6 apt-utils_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 clang_2.9-11 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-10 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-10 gcc_4:4.6.1-2 gcc-4.6_4.6.1-10 gcc-4.6-base_4.6.1-10 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 less_444-1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libboost-dev_1.46.1.1 libboost-graph-dev_1.46.1.1 libboost-graph1.46-dev_1.46.1-7 libboost-serialization1.46-dev_1.46.1-7 libboost-serialization1.46.1_1.46.1-7 libboost-test1.46-dev_1.46.1-7 libboost-test1.46.1_1.46.1-7 libboost1.46-dev_1.46.1-7 libbz2-1.0_1.0.5-7 libc-bin_2.13-20 libc-dev-bin_2.13-20 libc6_2.13-20 libc6-dev_2.13-20 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libf2c2_20090411-2 libf2c2-dev_20090411-2 libffi5_3.0.10~rc10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-10 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-10 libicu44_4.4.2-2 libllvm2.9_2.9+dfsg-3 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libquadmath0_4.6.1-10 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-20 ncurses-base_5.9-1 ncurses-bin_5.9-1 nvi_1.81.6-8.2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 readline-common_6.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-disulfinder-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/var/lib/sbuild/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Thu Sep 1 14:45:13 2011 CEST 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 dpkg-buildpackage ───────────────── dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): dpkg-buildpackage: source package disulfinder dpkg-buildpackage: source version 1.2.11-2 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 `/build/disulfinder-tCZhDr/disulfinder-1.2.11' if [ -e "disulfind/src/Makefile" ]; then make -C disulfind/src clean; fi make[2]: Entering directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/disulfind/src' make -C NN clean make[3]: Entering directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/disulfind/src/NN' rm -f *~ *.o brnn-train brnn-test make[3]: Leaving directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/disulfind/src/NN' make -C Common clean make[3]: Entering directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/disulfind/src/Common' make -C eig clean make[4]: Entering directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/disulfind/src/Common/eig' rm *.o libeig.a *~ -f make[4]: Leaving directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/disulfind/src/Common/eig' rm *.o libCommon.a Eig Norm *~ -f make[3]: Leaving directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/disulfind/src/Common' make -C SVM clean make[3]: Entering directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/disulfind/src/SVM' rm *~ *.o *.a *.exe SVMClassifier -f make[3]: Leaving directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/disulfind/src/SVM' cd SVM && make clean make[3]: Entering directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/disulfind/src/SVM' rm *~ *.o *.a *.exe SVMClassifier -f make[3]: Leaving directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/disulfind/src/SVM' cd Input && make clean make[3]: Entering directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/disulfind/src/Input' rm *.o makeWindow makeSparseVector globalDescriptor createKernelDataset createBRNNDataset buildXfolds *~ -f make[3]: Leaving directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/disulfind/src/Input' cd Output && make clean make[3]: Entering directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/disulfind/src/Output' rm *.o makeASCIIOutput makeHTMLOutput *~ -f make[3]: Leaving directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/disulfind/src/Output' cd FSA-Alignment && make clean make[3]: Entering directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/disulfind/src/FSA-Alignment' rm *.o fold_automata viterbi_aligner timed_transitions *~ -f make[3]: Leaving directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/disulfind/src/FSA-Alignment' cd BRNN && make clean make[3]: Entering directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/disulfind/src/BRNN' rm -f *.o core rm -f ./RNNs/*.o ./RNNs/core disulfind-conn make[3]: Leaving directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/disulfind/src/BRNN' rm disulfinder disultrainer *.o *~ -f make[2]: Leaving directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/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 `/build/disulfinder-tCZhDr/disulfinder-1.2.11' 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 dpkg-source -b disulfinder-1.2.11 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: building disulfinder using existing ./disulfinder_1.2.11.orig.tar.gz dpkg-source: info: building disulfinder in disulfinder_1.2.11-2.debian.tar.gz dpkg-source: info: building disulfinder in disulfinder_1.2.11-2.dsc debian/rules build dh_testdir /usr/bin/make prefix=/usr make[1]: Entering directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11' /usr/bin/make -C disulfind/src disulfinder make[2]: Entering directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11/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 `/build/disulfinder-tCZhDr/disulfinder-1.2.11/disulfind/src' make[1]: *** [disulfinder] Error 2 make[1]: Leaving directory `/build/disulfinder-tCZhDr/disulfinder-1.2.11' make: *** [build-stamp] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20110911-1110 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64c-79563d06-236c-4172-a4f9-2ee4bf691563/build/disulfinder-tCZhDr Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 15728 Build-Time: 6 Distribution: lsid64c Fail-Stage: build Install-Time: 6 Job: disulfinder_1.2.11-2 Package: disulfinder Package-Time: 24 Source-Version: 1.2.11-2 Space: 15728 Status: attempted Version: 1.2.11-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20110911-1110 Build needed 00:00:24, 15728k disc space DC-Message: Failed, but took only 24.834845. Retrying, you never know. Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on talc-118.nancy.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ disulfinder 1.2.11-2 (amd64) 11 Sep 2011 11:38 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: disulfinder Version: 1.2.11-2 Source Version: 1.2.11-2 Distribution: lsid64c Architecture: amd64 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost sid InRelease Hit http://localhost sid Release.gpg Hit http://localhost sid Release Ign http://localhost sid/main Sources/DiffIndex Ign http://localhost sid/main amd64 Packages/DiffIndex Ign http://localhost sid/main TranslationIndex Hit http://localhost sid/main Sources Hit http://localhost sid/main amd64 Packages Ign http://localhost sid/main Translation-en Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: binutils cpp-4.6 g++-4.6 gcc-4.6 gcc-4.6-base libc-bin libc-dev-bin libc6 libc6-dev libgcc1 libgomp1 libquadmath0 libstdc++6 libstdc++6-4.6-dev multiarch-support 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 34.4 MB of archives. After this operation, 1073 kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libc6-dev libc-dev-bin libgomp1 gcc-4.6-base libgcc1 cpp-4.6 libquadmath0 libstdc++6-4.6-dev g++-4.6 gcc-4.6 libstdc++6 binutils libc-bin libc6 multiarch-support Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libc6-dev amd64 2.13-20 [2637 kB] Get:2 http://localhost/debian/ sid/main libc-dev-bin amd64 2.13-20 [217 kB] Get:3 http://localhost/debian/ sid/main libgomp1 amd64 4.6.1-10 [25.7 kB] Get:4 http://localhost/debian/ sid/main gcc-4.6-base amd64 4.6.1-10 [135 kB] Get:5 http://localhost/debian/ sid/main libgcc1 amd64 1:4.6.1-10 [42.9 kB] Get:6 http://localhost/debian/ sid/main cpp-4.6 amd64 4.6.1-10 [4816 kB] Get:7 http://localhost/debian/ sid/main libquadmath0 amd64 4.6.1-10 [126 kB] Get:8 http://localhost/debian/ sid/main libstdc++6-4.6-dev amd64 4.6.1-10 [1660 kB] Get:9 http://localhost/debian/ sid/main g++-4.6 amd64 4.6.1-10 [6952 kB] Get:10 http://localhost/debian/ sid/main gcc-4.6 amd64 4.6.1-10 [7303 kB] Get:11 http://localhost/debian/ sid/main libstdc++6 amd64 4.6.1-10 [337 kB] Get:12 http://localhost/debian/ sid/main binutils amd64 2.21.53.20110910-1 [4844 kB] Get:13 http://localhost/debian/ sid/main libc-bin amd64 2.13-20 [819 kB] Get:14 http://localhost/debian/ sid/main libc6 amd64 2.13-20 [4323 kB] Get:15 http://localhost/debian/ sid/main multiarch-support amd64 2.13-20 [141 kB] Preconfiguring packages ... Fetched 34.4 MB in 0s (64.0 MB/s) (Reading database ... 10788 files and directories currently installed.) Preparing to replace libc6-dev 2.13-18 (using .../libc6-dev_2.13-20_amd64.deb) ... Unpacking replacement libc6-dev ... Preparing to replace libc-dev-bin 2.13-18 (using .../libc-dev-bin_2.13-20_amd64.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libgomp1 4.6.1-9 (using .../libgomp1_4.6.1-10_amd64.deb) ... Unpacking replacement libgomp1 ... Preparing to replace gcc-4.6-base 4.6.1-9 (using .../gcc-4.6-base_4.6.1-10_amd64.deb) ... Unpacking replacement gcc-4.6-base ... Setting up gcc-4.6-base (4.6.1-10) ... (Reading database ... 10788 files and directories currently installed.) Preparing to replace libgcc1 1:4.6.1-9 (using .../libgcc1_1%3a4.6.1-10_amd64.deb) ... Unpacking replacement libgcc1 ... Setting up libgcc1 (1:4.6.1-10) ... (Reading database ... 10788 files and directories currently installed.) Preparing to replace cpp-4.6 4.6.1-9 (using .../cpp-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement cpp-4.6 ... Preparing to replace libquadmath0 4.6.1-9 (using .../libquadmath0_4.6.1-10_amd64.deb) ... Unpacking replacement libquadmath0 ... Preparing to replace libstdc++6-4.6-dev 4.6.1-9 (using .../libstdc++6-4.6-dev_4.6.1-10_amd64.deb) ... Unpacking replacement libstdc++6-4.6-dev ... Preparing to replace g++-4.6 4.6.1-9 (using .../g++-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement g++-4.6 ... Preparing to replace gcc-4.6 4.6.1-9 (using .../gcc-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement gcc-4.6 ... Preparing to replace libstdc++6 4.6.1-9 (using .../libstdc++6_4.6.1-10_amd64.deb) ... Unpacking replacement libstdc++6 ... Setting up libstdc++6 (4.6.1-10) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace binutils 2.21.53.20110823-3 (using .../binutils_2.21.53.20110910-1_amd64.deb) ... Unpacking replacement binutils ... Preparing to replace libc-bin 2.13-18 (using .../libc-bin_2.13-20_amd64.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.13-20) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace libc6 2.13-18 (using .../libc6_2.13-20_amd64.deb) ... Unpacking replacement libc6 ... Setting up libc6 (2.13-20) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace multiarch-support 2.13-18 (using .../multiarch-support_2.13-20_amd64.deb) ... Unpacking replacement multiarch-support ... Setting up multiarch-support (2.13-20) ... Setting up libc-dev-bin (2.13-20) ... Setting up libc6-dev (2.13-20) ... Setting up libgomp1 (4.6.1-10) ... Setting up cpp-4.6 (4.6.1-10) ... Setting up libquadmath0 (4.6.1-10) ... Setting up binutils (2.21.53.20110910-1) ... Setting up gcc-4.6 (4.6.1-10) ... Setting up libstdc++6-4.6-dev (4.6.1-10) ... Setting up g++-4.6 (4.6.1-10) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: '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/ sid/main disulfinder 1.2.11-2 (dsc) [1456 B] Get:2 http://localhost/debian/ sid/main disulfinder 1.2.11-2 (tar) [2481 kB] Get:3 http://localhost/debian/ sid/main disulfinder 1.2.11-2 (diff) [3527 B] Fetched 2486 kB in 0s (54.6 MB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/build/disulfinder-R4EcJR/resolver-g_mtLQ/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 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/700 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Selecting previously deselected package sbuild-build-depends-core-dummy. (Reading database ... 10801 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) ... Cannot open /var/lib/schroot/mount/lsid64c-e126c73f-4407-427b-aa37-ec99dc2cb05f/etc/lsb-release: No such file or directory 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 `/build/disulfinder-R4EcJR/resolver-XebD0_/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 libboost-dev libboost-graph-dev libboost-graph1.46-dev libboost-serialization1.46-dev libboost-serialization1.46.1 libboost-test1.46-dev libboost-test1.46.1 libboost1.46-dev libcroco3 libf2c2 libf2c2-dev libglib2.0-0 libicu44 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff libboost1.46-doc libboost-date-time1.46-dev libboost-filesystem1.46-dev libboost-graph-parallel1.46-dev libboost-iostreams1.46-dev libboost-math1.46-dev libboost-mpi1.46-dev libboost-program-options1.46-dev libboost-python1.46-dev libboost-random1.46-dev libboost-regex1.46-dev libboost-signals1.46-dev libboost-system1.46-dev libboost-thread1.46-dev libboost-wave1.46-dev xsltproc doxygen docbook-xml docbook-xsl default-jdk fop www-browser libmail-box-perl Recommended packages: curl wget lynx-cur autopoint libboost-graph1.46.1 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 libboost-dev libboost-graph-dev libboost-graph1.46-dev libboost-serialization1.46-dev libboost-serialization1.46.1 libboost-test1.46-dev libboost-test1.46.1 libboost1.46-dev libcroco3 libf2c2 libf2c2-dev libglib2.0-0 libicu44 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf sbuild-build-depends-disulfinder-dummy 0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 26.3 MB/26.3 MB of archives. After this operation, 134 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libpcre3 bsdmainutils groff-base man-db libmagic1 file gettext-base libxml2 html2text libglib2.0-0 libcroco3 libunistring0 gettext intltool-debian po-debconf debhelper libicu44 libboost1.46-dev libboost-dev libboost-serialization1.46.1 libboost-serialization1.46-dev libboost-test1.46.1 libboost-test1.46-dev libboost-graph1.46-dev libboost-graph-dev libf2c2 libf2c2-dev sbuild-build-depends-disulfinder-dummy Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libpipeline1 amd64 1.2.0-3 [37.9 kB] Get:2 http://localhost/debian/ sid/main libpcre3 amd64 8.12-4 [225 kB] Get:3 http://localhost/debian/ sid/main bsdmainutils amd64 8.2.3 [208 kB] Get:4 http://localhost/debian/ sid/main groff-base amd64 1.21-6 [1150 kB] Get:5 http://localhost/debian/ sid/main man-db amd64 2.6.0.2-2 [1023 kB] Get:6 http://localhost/debian/ sid/main libmagic1 amd64 5.08-1 [246 kB] Get:7 http://localhost/debian/ sid/main file amd64 5.08-1 [51.7 kB] Get:8 http://localhost/debian/ sid/main gettext-base amd64 0.18.1.1-4 [154 kB] Get:9 http://localhost/debian/ sid/main libxml2 amd64 2.7.8.dfsg-4 [892 kB] Get:10 http://localhost/debian/ sid/main html2text amd64 1.3.2a-15 [103 kB] Get:11 http://localhost/debian/ sid/main libglib2.0-0 amd64 2.28.6-1 [1648 kB] Get:12 http://localhost/debian/ sid/main libcroco3 amd64 0.6.2-1 [125 kB] Get:13 http://localhost/debian/ sid/main libunistring0 amd64 0.9.3-4 [437 kB] Get:14 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-4 [2079 kB] Get:15 http://localhost/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:16 http://localhost/debian/ sid/main po-debconf all 1.0.16+nmu1 [223 kB] Get:17 http://localhost/debian/ sid/main debhelper all 8.9.6 [562 kB] Get:18 http://localhost/debian/ sid/main libicu44 amd64 4.4.2-2 [7065 kB] Get:19 http://localhost/debian/ sid/main libboost1.46-dev amd64 1.46.1-7 [7832 kB] Get:20 http://localhost/debian/ sid/main libboost-dev amd64 1.46.1.1 [2610 B] Get:21 http://localhost/debian/ sid/main libboost-serialization1.46.1 amd64 1.46.1-7 [209 kB] Get:22 http://localhost/debian/ sid/main libboost-serialization1.46-dev amd64 1.46.1-7 [304 kB] Get:23 http://localhost/debian/ sid/main libboost-test1.46.1 amd64 1.46.1-7 [259 kB] Get:24 http://localhost/debian/ sid/main libboost-test1.46-dev amd64 1.46.1-7 [646 kB] Get:25 http://localhost/debian/ sid/main libboost-graph1.46-dev amd64 1.46.1-7 [165 kB] Get:26 http://localhost/debian/ sid/main libboost-graph-dev amd64 1.46.1.1 [2582 B] Get:27 http://localhost/debian/ sid/main libf2c2 amd64 20090411-2 [159 kB] Get:28 http://localhost/debian/ sid/main libf2c2-dev amd64 20090411-2 [478 kB] Preconfiguring packages ... Fetched 26.3 MB in 0s (63.3 MB/s) Selecting previously deselected package libpipeline1. (Reading database ... 10801 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_amd64.deb) ... Selecting previously deselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ... Selecting previously deselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_amd64.deb) ... Selecting previously deselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ... Selecting previously deselected package man-db. Unpacking man-db (from .../man-db_2.6.0.2-2_amd64.deb) ... Selecting previously deselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.08-1_amd64.deb) ... Selecting previously deselected package file. Unpacking file (from .../archives/file_5.08-1_amd64.deb) ... Selecting previously deselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_amd64.deb) ... Selecting previously deselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_amd64.deb) ... Selecting previously deselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously deselected package libglib2.0-0. Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_amd64.deb) ... Selecting previously deselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.2-1_amd64.deb) ... Selecting previously deselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-4_amd64.deb) ... Selecting previously deselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-4_amd64.deb) ... Selecting previously deselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously deselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ... Selecting previously deselected package debhelper. Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ... Selecting previously deselected package libicu44. Unpacking libicu44 (from .../libicu44_4.4.2-2_amd64.deb) ... Selecting previously deselected package libboost1.46-dev. Unpacking libboost1.46-dev (from .../libboost1.46-dev_1.46.1-7_amd64.deb) ... Selecting previously deselected package libboost-dev. Unpacking libboost-dev (from .../libboost-dev_1.46.1.1_amd64.deb) ... Selecting previously deselected package libboost-serialization1.46.1. Unpacking libboost-serialization1.46.1 (from .../libboost-serialization1.46.1_1.46.1-7_amd64.deb) ... Selecting previously deselected package libboost-serialization1.46-dev. Unpacking libboost-serialization1.46-dev (from .../libboost-serialization1.46-dev_1.46.1-7_amd64.deb) ... Selecting previously deselected package libboost-test1.46.1. Unpacking libboost-test1.46.1 (from .../libboost-test1.46.1_1.46.1-7_amd64.deb) ... Selecting previously deselected package libboost-test1.46-dev. Unpacking libboost-test1.46-dev (from .../libboost-test1.46-dev_1.46.1-7_amd64.deb) ... Selecting previously deselected package libboost-graph1.46-dev. Unpacking libboost-graph1.46-dev (from .../libboost-graph1.46-dev_1.46.1-7_amd64.deb) ... Selecting previously deselected package libboost-graph-dev. Unpacking libboost-graph-dev (from .../libboost-graph-dev_1.46.1.1_amd64.deb) ... Selecting previously deselected package libf2c2. Unpacking libf2c2 (from .../libf2c2_20090411-2_amd64.deb) ... Selecting previously deselected package libf2c2-dev. Unpacking libf2c2-dev (from .../libf2c2-dev_20090411-2_amd64.deb) ... Selecting previously deselected package sbuild-build-depends-disulfinder-dummy. Unpacking sbuild-build-depends-disulfinder-dummy (from .../sbuild-build-depends-disulfinder-dummy.deb) ... Processing triggers for install-info ... Setting up libpipeline1 (1.2.0-3) ... Setting up libpcre3 (8.12-4) ... Setting up bsdmainutils (8.2.3) ... 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 (1.21-6) ... Setting up man-db (2.6.0.2-2) ... Building database of manual pages ... Setting up libmagic1 (5.08-1) ... Setting up file (5.08-1) ... Setting up gettext-base (0.18.1.1-4) ... Setting up libxml2 (2.7.8.dfsg-4) ... Setting up html2text (1.3.2a-15) ... Setting up libglib2.0-0 (2.28.6-1) ... No schema files found: doing nothing. Setting up libcroco3 (0.6.2-1) ... Setting up libunistring0 (0.9.3-4) ... Setting up gettext (0.18.1.1-4) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu1) ... Setting up debhelper (8.9.6) ... Setting up libicu44 (4.4.2-2) ... Setting up libboost1.46-dev (1.46.1-7) ... Setting up libboost-dev (1.46.1.1) ... Setting up libboost-serialization1.46.1 (1.46.1-7) ... Setting up libboost-serialization1.46-dev (1.46.1-7) ... Setting up libboost-test1.46.1 (1.46.1-7) ... Setting up libboost-test1.46-dev (1.46.1-7) ... Setting up libboost-graph1.46-dev (1.46.1-7) ... Setting up libboost-graph-dev (1.46.1.1) ... 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-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-10 gcc-4.6_4.6.1-10 libc6-dev_2.13-20 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 linux-libc-dev_3.0.0-3 Package versions: apt_0.8.15.6 apt-utils_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 clang_2.9-11 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-10 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-10 gcc_4:4.6.1-2 gcc-4.6_4.6.1-10 gcc-4.6-base_4.6.1-10 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 less_444-1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libboost-dev_1.46.1.1 libboost-graph-dev_1.46.1.1 libboost-graph1.46-dev_1.46.1-7 libboost-serialization1.46-dev_1.46.1-7 libboost-serialization1.46.1_1.46.1-7 libboost-test1.46-dev_1.46.1-7 libboost-test1.46.1_1.46.1-7 libboost1.46-dev_1.46.1-7 libbz2-1.0_1.0.5-7 libc-bin_2.13-20 libc-dev-bin_2.13-20 libc6_2.13-20 libc6-dev_2.13-20 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libf2c2_20090411-2 libf2c2-dev_20090411-2 libffi5_3.0.10~rc10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-10 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-10 libicu44_4.4.2-2 libllvm2.9_2.9+dfsg-3 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libquadmath0_4.6.1-10 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-20 ncurses-base_5.9-1 ncurses-bin_5.9-1 nvi_1.81.6-8.2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 readline-common_6.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-disulfinder-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/var/lib/sbuild/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Thu Sep 1 14:45:13 2011 CEST 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 dpkg-buildpackage ───────────────── dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): dpkg-buildpackage: source package disulfinder dpkg-buildpackage: source version 1.2.11-2 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 `/build/disulfinder-R4EcJR/disulfinder-1.2.11' if [ -e "disulfind/src/Makefile" ]; then make -C disulfind/src clean; fi make[2]: Entering directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/disulfind/src' make -C NN clean make[3]: Entering directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/disulfind/src/NN' rm -f *~ *.o brnn-train brnn-test make[3]: Leaving directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/disulfind/src/NN' make -C Common clean make[3]: Entering directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/disulfind/src/Common' make -C eig clean make[4]: Entering directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/disulfind/src/Common/eig' rm *.o libeig.a *~ -f make[4]: Leaving directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/disulfind/src/Common/eig' rm *.o libCommon.a Eig Norm *~ -f make[3]: Leaving directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/disulfind/src/Common' make -C SVM clean make[3]: Entering directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/disulfind/src/SVM' rm *~ *.o *.a *.exe SVMClassifier -f make[3]: Leaving directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/disulfind/src/SVM' cd SVM && make clean make[3]: Entering directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/disulfind/src/SVM' rm *~ *.o *.a *.exe SVMClassifier -f make[3]: Leaving directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/disulfind/src/SVM' cd Input && make clean make[3]: Entering directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/disulfind/src/Input' rm *.o makeWindow makeSparseVector globalDescriptor createKernelDataset createBRNNDataset buildXfolds *~ -f make[3]: Leaving directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/disulfind/src/Input' cd Output && make clean make[3]: Entering directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/disulfind/src/Output' rm *.o makeASCIIOutput makeHTMLOutput *~ -f make[3]: Leaving directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/disulfind/src/Output' cd FSA-Alignment && make clean make[3]: Entering directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/disulfind/src/FSA-Alignment' rm *.o fold_automata viterbi_aligner timed_transitions *~ -f make[3]: Leaving directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/disulfind/src/FSA-Alignment' cd BRNN && make clean make[3]: Entering directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/disulfind/src/BRNN' rm -f *.o core rm -f ./RNNs/*.o ./RNNs/core disulfind-conn make[3]: Leaving directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/disulfind/src/BRNN' rm disulfinder disultrainer *.o *~ -f make[2]: Leaving directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/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 `/build/disulfinder-R4EcJR/disulfinder-1.2.11' 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 dpkg-source -b disulfinder-1.2.11 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: building disulfinder using existing ./disulfinder_1.2.11.orig.tar.gz dpkg-source: info: building disulfinder in disulfinder_1.2.11-2.debian.tar.gz dpkg-source: info: building disulfinder in disulfinder_1.2.11-2.dsc debian/rules build dh_testdir /usr/bin/make prefix=/usr make[1]: Entering directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11' /usr/bin/make -C disulfind/src disulfinder make[2]: Entering directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11/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 `/build/disulfinder-R4EcJR/disulfinder-1.2.11/disulfind/src' make[1]: *** [disulfinder] Error 2 make: *** [build-stamp] Error 2 make[1]: Leaving directory `/build/disulfinder-R4EcJR/disulfinder-1.2.11' dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20110911-1138 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64c-e126c73f-4407-427b-aa37-ec99dc2cb05f/build/disulfinder-R4EcJR Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 15728 Build-Time: 6 Distribution: lsid64c Fail-Stage: build Install-Time: 6 Job: disulfinder_1.2.11-2 Package: disulfinder Package-Time: 21 Source-Version: 1.2.11-2 Space: 15728 Status: attempted Version: 1.2.11-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20110911-1138 Build needed 00:00:21, 15728k disc space DC-Build-Status: Failed 1697.867927s ### Content of /var/log/daemon.log ### Sep 11 10:48:19 talc-118 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Sep 11 10:48:40 talc-118 approx: Concurrent download of debian/dists/sid/Release is taking too long Sep 11 10:48:49 talc-118 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Sep 11 10:48:57 talc-118 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:48:59 talc-118 approx: Concurrent download of debian/dists/sid/Release is taking too long Sep 11 10:49:18 talc-118 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Sep 11 10:49:18 talc-118 approx: Concurrent download of debian/dists/sid/Release is taking too long Sep 11 10:49:25 talc-118 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:49:29 talc-118 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Sep 11 10:49:45 talc-118 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Sep 11 10:49:54 talc-118 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en.bz2 is taking too long Sep 11 10:50:01 talc-118 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:50:12 talc-118 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:50:23 talc-118 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:50:43 talc-118 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Sep 11 10:50:55 talc-118 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Sep 11 10:51:16 talc-118 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Sep 11 10:51:22 talc-118 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en is taking too long ### End of content of /var/log/daemon.log ### DC-Time-Estimation: 1697.867927 versus expected 32000 (r/m: 17.847166785547 ; m: 1697.867927) DC-Build-Network: USED. See /tmp/rulesafter.xxg32R ! ************************************************************ # Generated by iptables-save v1.4.8 on Sun Sep 11 11:38:25 2011 *filter :INPUT ACCEPT [1941133:10453251471] :FORWARD ACCEPT [0:0] :OUTPUT DROP [0:0] :LD - [0:0] [712826:8956581568] -A OUTPUT -o lo -j ACCEPT [0:0] -A OUTPUT -d 129.88.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 10.0.0.0/8 -j ACCEPT [0:0] -A OUTPUT -d 192.168.133.0/24 -j ACCEPT [0:0] -A OUTPUT -d 192.168.159.0/24 -j ACCEPT [0:0] -A OUTPUT -d 192.168.160.0/24 -j ACCEPT [0:0] -A OUTPUT -d 10.69.0.0/17 -j ACCEPT [0:0] -A OUTPUT -d 172.28.52.0/22 -j ACCEPT [0:0] -A OUTPUT -d 172.24.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 131.254.202.0/23 -j ACCEPT [0:0] -A OUTPUT -d 138.96.20.0/22 -j ACCEPT [0:0] -A OUTPUT -d 192.168.22.0/24 -j ACCEPT [517404:40391481] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT [1931:187648] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT [5:280] -A OUTPUT -j LD [5:280] -A LD -j LOG [5:280] -A LD -j REJECT --reject-with icmp-port-unreachable COMMIT # Completed on Sun Sep 11 11:38:25 2011 ************************************************************ --- /tmp/rulesbefore.JmnChD 2011-09-11 11:10:07.927715316 +0200 +++ /tmp/rulesafter.xxg32R 2011-09-11 11:38:25.802709576 +0200 @@ -1,10 +1,10 @@ -# Generated by iptables-save v1.4.8 on Sun Sep 11 11:10:07 2011 +# Generated by iptables-save v1.4.8 on Sun Sep 11 11:38:25 2011 *filter -:INPUT ACCEPT [1438873:6706722238] +:INPUT ACCEPT [1941133:10453251471] :FORWARD ACCEPT [0:0] :OUTPUT DROP [0:0] :LD - [0:0] -[441946:5395944236] -A OUTPUT -o lo -j ACCEPT +[712826:8956581568] -A OUTPUT -o lo -j ACCEPT [0:0] -A OUTPUT -d 129.88.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 10.0.0.0/8 -j ACCEPT [0:0] -A OUTPUT -d 192.168.133.0/24 -j ACCEPT @@ -16,10 +16,10 @@ [0:0] -A OUTPUT -d 131.254.202.0/23 -j ACCEPT [0:0] -A OUTPUT -d 138.96.20.0/22 -j ACCEPT [0:0] -A OUTPUT -d 192.168.22.0/24 -j ACCEPT -[443429:30047386] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT -[993:99116] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT -[3:160] -A OUTPUT -j LD -[3:160] -A LD -j LOG -[3:160] -A LD -j REJECT --reject-with icmp-port-unreachable +[517404:40391481] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT +[1931:187648] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT +[5:280] -A OUTPUT -j LD +[5:280] -A LD -j LOG +[5:280] -A LD -j REJECT --reject-with icmp-port-unreachable COMMIT -# Completed on Sun Sep 11 11:10:07 2011 +# Completed on Sun Sep 11 11:38:25 2011 ************************************************************ [ 11.838519] ioatdma: Intel(R) QuickData Technology Driver 4.00 [ 11.838584] ioatdma 0000:00:0f.0: PCI INT A -> GSI 16 (level, low) -> IRQ 16 [ 11.918876] ioatdma 0000:00:0f.0: setting latency timer to 64 [ 11.918881] [ 11.927879] processor LNXCPU:07: registered as cooling_device7 [ 11.962860] alloc irq_desc for 56 on node -1 [ 11.962862] alloc kstat_irqs on node -1 [ 11.962870] ioatdma 0000:00:0f.0: irq 56 for MSI/MSI-X [ 11.962872] alloc irq_desc for 57 on node -1 [ 11.962874] alloc kstat_irqs on node -1 [ 11.962877] ioatdma 0000:00:0f.0: irq 57 for MSI/MSI-X [ 11.962879] alloc irq_desc for 58 on node -1 [ 11.962880] alloc kstat_irqs on node -1 [ 11.962882] ioatdma 0000:00:0f.0: irq 58 for MSI/MSI-X [ 11.962884] alloc irq_desc for 59 on node -1 [ 11.962885] alloc kstat_irqs on node -1 [ 11.962891] ioatdma 0000:00:0f.0: irq 59 for MSI/MSI-X [ 12.066607] EDAC MC: Ver: 2.1.0 Mar 7 2011 [ 12.092769] intel_rng: FWH not detected [ 12.199531] i801_smbus 0000:00:1f.3: PCI INT B -> GSI 23 (level, low) -> IRQ 23 [ 12.267794] EDAC MC0: Giving out device to 'i5400_edac.c' 'I5400': DEV 0000:00:10.0 [ 12.313744] EDAC PCI0: Giving out device to module 'i5400_edac' controller 'EDAC PCI controller': DEV '0000:00:10.0' (POLLED) [ 12.483998] Adding 3911788k swap on /dev/sda1. Priority:-1 extents:1 across:3911788k [ 12.534776] EXT3 FS on sda3, internal journal [ 12.761968] kjournald starting. Commit interval 5 seconds [ 12.761973] EXT3-fs warning: maximal mount count reached, running e2fsck is recommended [ 12.762615] EXT3 FS on sda5, internal journal [ 12.762616] EXT3-fs: recovery complete. [ 12.762769] EXT3-fs: mounted filesystem with ordered data mode. [ 13.266001] e1000e 0000:0f:00.0: irq 54 for MSI/MSI-X [ 13.320048] e1000e 0000:0f:00.0: irq 54 for MSI/MSI-X [ 13.322133] ADDRCONF(NETDEV_UP): eth0: link is not ready [ 16.347987] e1000e: eth0 NIC Link is Up 1000 Mbps Full Duplex, Flow Control: RX/TX [ 16.397692] ADDRCONF(NETDEV_CHANGE): eth0: link becomes ready [ 26.620006] eth0: no IPv6 routers present [ 157.186658] RPC: Registered udp transport module. [ 157.214904] RPC: Registered tcp transport module. [ 157.243113] RPC: Registered tcp NFSv4.1 backchannel transport module. [ 157.308024] Slow work thread pool: Starting up [ 157.334761] Slow work thread pool: Ready [ 157.358365] FS-Cache: Loaded [ 157.398508] FS-Cache: Netfs 'nfs' registered for caching [ 157.434924] svc: failed to register lockdv1 RPC service (errno 97). [ 185.809786] Adding 296929352k swap on /dev/sda5. Priority:-2 extents:1 across:296929352k [ 199.617791] ip_tables: (C) 2000-2006 Netfilter Core Team [ 202.964763] IN= OUT=eth0 SRC=172.16.66.118 DST=224.0.0.22 LEN=40 TOS=0x00 PREC=0xC0 TTL=1 ID=0 DF PROTO=2 [ 1518.393249] IN= OUT=eth0 SRC=172.16.66.118 DST=216.34.181.96 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=61350 DF PROTO=TCP SPT=48083 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 1521.484283] IN= OUT=eth0 SRC=172.16.66.118 DST=216.34.181.96 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=61351 DF PROTO=TCP SPT=48083 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 2535.782360] IN= OUT=eth0 SRC=172.16.66.118 DST=216.34.181.96 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=40002 DF PROTO=TCP SPT=39869 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 2538.868013] IN= OUT=eth0 SRC=172.16.66.118 DST=216.34.181.96 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=40003 DF PROTO=TCP SPT=39869 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 ************************************************************