DC-Build-Header: librg-blast-parser-perl 0.03-2 / 2014-06-17 15:17:06 +0000 DC-Task: source:librg-blast-parser-perl version:0.03-2 architecture:any chroot:unstable esttime:142 logfile:/tmp/librg-blast-parser-perl_0.03-2_unstable_clang.log modes:binary-only:parallel:clang DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/switch-to-clang --append-to-version "clang1" --maintainer "Lucas Nussbaum " --uploader "Lucas Nussbaum " librg-blast-parser-perl_0.03-2' sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on ip-172-31-15-35.us-west-2.compute.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ librg-blast-parser-perl 0.03-2clang1 (amd64) 17 Jun 2014 15:17 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: librg-blast-parser-perl Version: 0.03-2clang1 Source Version: 0.03-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/librg-blast-parser-perl-Shw2mE/librg-blast-parser-perl-0.03' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/librg-blast-parser-perl-Shw2mE' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-fe3a9a83-13f6-48ba-93d7-f72ed31de2d4' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Get:1 http://localhost:9999 unstable InRelease [206 kB] Get:2 http://localhost:9999 unstable/main Sources/DiffIndex [7876 B] Get:3 http://localhost:9999 unstable/main amd64 Packages/DiffIndex [7876 B] Get:4 http://localhost:9999 unstable/main Translation-en/DiffIndex [7876 B] Get:5 http://localhost:9999 unstable/main 2014-06-16-2054.31.pdiff [15.4 kB] Get:6 http://localhost:9999 unstable/main 2014-06-17-0253.05.pdiff [7983 B] Get:7 http://localhost:9999 unstable/main 2014-06-17-0856.27.pdiff [7757 B] Get:8 http://localhost:9999 unstable/main amd64 2014-06-16-2054.31.pdiff [20.7 kB] Get:9 http://localhost:9999 unstable/main 2014-06-17-0856.27.pdiff [7757 B] Get:10 http://localhost:9999 unstable/main amd64 2014-06-17-0253.05.pdiff [38.6 kB] Get:11 http://localhost:9999 unstable/main amd64 2014-06-17-0856.27.pdiff [9018 B] Get:12 http://localhost:9999 unstable/main 2014-06-16-2054.31.pdiff [699 B] Get:13 http://localhost:9999 unstable/main 2014-06-17-0856.27.pdiff [442 B] Get:14 http://localhost:9999 unstable/main amd64 2014-06-17-0856.27.pdiff [9018 B] Get:15 http://localhost:9999 unstable/main 2014-06-17-0856.27.pdiff [442 B] Fetched 330 kB in 4s (69.1 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: libc-bin libc-dev-bin libc6 libc6-dev linux-libc-dev multiarch-support 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 9447 kB of archives. After this operation, 10.2 kB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libc6-dev amd64 2.19-2 [2000 kB] Get:2 http://localhost:9999/debian/ unstable/main libc-dev-bin amd64 2.19-2 [235 kB] Get:3 http://localhost:9999/debian/ unstable/main linux-libc-dev amd64 3.14.7-1 [937 kB] Get:4 http://localhost:9999/debian/ unstable/main libc-bin amd64 2.19-2 [1288 kB] Get:5 http://localhost:9999/debian/ unstable/main libc6 amd64 2.19-2 [4816 kB] Get:6 http://localhost:9999/debian/ unstable/main multiarch-support amd64 2.19-2 [171 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 9447 kB in 0s (33.8 MB/s) (Reading database ... 14215 files and directories currently installed.) Preparing to unpack .../libc6-dev_2.19-2_amd64.deb ... Unpacking libc6-dev:amd64 (2.19-2) over (2.19-1) ... Preparing to unpack .../libc-dev-bin_2.19-2_amd64.deb ... Unpacking libc-dev-bin (2.19-2) over (2.19-1) ... Preparing to unpack .../linux-libc-dev_3.14.7-1_amd64.deb ... Unpacking linux-libc-dev:amd64 (3.14.7-1) over (3.14.5-1) ... Preparing to unpack .../libc-bin_2.19-2_amd64.deb ... Unpacking libc-bin (2.19-2) over (2.19-1) ... Preparing to unpack .../libc6_2.19-2_amd64.deb ... Unpacking libc6:amd64 (2.19-2) over (2.19-1) ... Setting up libc6:amd64 (2.19-2) ... Setting up libc-bin (2.19-2) ... (Reading database ... 14216 files and directories currently installed.) Preparing to unpack .../multiarch-support_2.19-2_amd64.deb ... Unpacking multiarch-support (2.19-2) over (2.19-1) ... Setting up multiarch-support (2.19-2) ... Setting up libc-dev-bin (2.19-2) ... Setting up linux-libc-dev:amd64 (3.14.7-1) ... Setting up libc6-dev:amd64 (2.19-2) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'librg-blast-parser-perl' packaging is maintained in the 'Svn' version control system at: svn://anonscm.debian.org/debian-med/trunk/packages/rostlab/librg-blast-parser-perl/trunk/ Need to get 18.7 kB of source archives. Get:1 http://localhost:9999/debian/ unstable/main librg-blast-parser-perl 0.03-2 (dsc) [2197 B] Get:2 http://localhost:9999/debian/ unstable/main librg-blast-parser-perl 0.03-2 (tar) [11.6 kB] Get:3 http://localhost:9999/debian/ unstable/main librg-blast-parser-perl 0.03-2 (diff) [4880 B] Fetched 18.7 kB in 0s (21.1 kB/s) Download complete and in download only mode Check arch ────────── ┌──────────────────────────────────────────────────────────────────────────────┐ │ Chroot Setup Commands │ └──────────────────────────────────────────────────────────────────────────────┘ /tmp/switch-to-clang ──────────────────── + echo 'Entering customization script...' Entering customization script... + echo 'Install of clang-3.4' Install of clang-3.4 + apt-get update Hit http://localhost:9999 unstable InRelease Hit http://localhost:9999 unstable/main Sources/DiffIndex Hit http://localhost:9999 unstable/main amd64 Packages/DiffIndex Hit http://localhost:9999 unstable/main Translation-en/DiffIndex Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-3.4 Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libclang-common-3.4-dev libclang1-3.4 libffi6 libllvm3.4 libobjc-4.9-dev libobjc4 Suggested packages: gnustep gnustep-devel Recommended packages: llvm-3.4-dev python The following NEW packages will be installed: clang-3.4 libclang-common-3.4-dev libclang1-3.4 libffi6 libllvm3.4 libobjc-4.9-dev libobjc4 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. Need to get 30.6 MB of archives. After this operation, 118 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libffi6 amd64 3.1-2 [19.8 kB] Get:2 http://localhost:9999/debian/ unstable/main libllvm3.4 amd64 1:3.4.2-2 [6721 kB] Get:3 http://localhost:9999/debian/ unstable/main libobjc4 amd64 4.9.0-6 [112 kB] Get:4 http://localhost:9999/debian/ unstable/main libobjc-4.9-dev amd64 4.9.0-6 [372 kB] Get:5 http://localhost:9999/debian/ unstable/main libclang1-3.4 amd64 1:3.4.2-2 [3619 kB] Get:6 http://localhost:9999/debian/ unstable/main libclang-common-3.4-dev amd64 1:3.4.2-2 [543 kB] Get:7 http://localhost:9999/debian/ unstable/main clang-3.4 amd64 1:3.4.2-2 [19.2 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 30.6 MB in 0s (35.6 MB/s) Selecting previously unselected package libffi6:amd64. (Reading database ... 14216 files and directories currently installed.) Preparing to unpack .../libffi6_3.1-2_amd64.deb ... Unpacking libffi6:amd64 (3.1-2) ... Selecting previously unselected package libllvm3.4:amd64. Preparing to unpack .../libllvm3.4_1%3a3.4.2-2_amd64.deb ... Unpacking libllvm3.4:amd64 (1:3.4.2-2) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../libobjc4_4.9.0-6_amd64.deb ... Unpacking libobjc4:amd64 (4.9.0-6) ... Selecting previously unselected package libobjc-4.9-dev:amd64. Preparing to unpack .../libobjc-4.9-dev_4.9.0-6_amd64.deb ... Unpacking libobjc-4.9-dev:amd64 (4.9.0-6) ... Selecting previously unselected package libclang1-3.4:amd64. Preparing to unpack .../libclang1-3.4_1%3a3.4.2-2_amd64.deb ... Unpacking libclang1-3.4:amd64 (1:3.4.2-2) ... Selecting previously unselected package libclang-common-3.4-dev. Preparing to unpack .../libclang-common-3.4-dev_1%3a3.4.2-2_amd64.deb ... Unpacking libclang-common-3.4-dev (1:3.4.2-2) ... Selecting previously unselected package clang-3.4. Preparing to unpack .../clang-3.4_1%3a3.4.2-2_amd64.deb ... Unpacking clang-3.4 (1:3.4.2-2) ... Setting up libffi6:amd64 (3.1-2) ... Setting up libllvm3.4:amd64 (1:3.4.2-2) ... Setting up libobjc4:amd64 (4.9.0-6) ... Setting up libobjc-4.9-dev:amd64 (4.9.0-6) ... Setting up libclang1-3.4:amd64 (1:3.4.2-2) ... Setting up libclang-common-3.4-dev (1:3.4.2-2) ... Setting up clang-3.4 (1:3.4.2-2) ... Processing triggers for libc-bin (2.19-2) ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9' + cd /usr/bin + for VERSION in '$VERSIONS' + rm -f g++-4.6 gcc-4.6 cpp-4.6 + ln -s clang++ g++-4.6 + ln -s clang gcc-4.6 + ln -s clang cpp-4.6 + echo 'gcc-4.6 hold' + dpkg --set-selections + echo 'g++-4.6 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f 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 + echo 'gcc-4.7 hold' + dpkg --set-selections + echo 'g++-4.7 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-4.8 gcc-4.8 cpp-4.8 + ln -s clang++ g++-4.8 + ln -s clang gcc-4.8 + ln -s clang cpp-4.8 + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.9 gcc-4.9 cpp-4.9 + ln -s clang++ g++-4.9 + ln -s clang gcc-4.9 + ln -s clang cpp-4.9 + echo 'gcc-4.9 hold' + dpkg --set-selections + echo 'g++-4.9 hold' + dpkg --set-selections + cd - /«BUILDDIR» + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang I: Finished running '/tmp/switch-to-clang'. Finished processing commands. ──────────────────────────────────────────────────────────────────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-yLGYwP/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/820 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 ... 14431 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), libextutils-xspp-perl, librostlab-blast0-dev, librostlab3-dev Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), libextutils-xspp-perl, librostlab-blast0-dev, librostlab3-dev dpkg-deb: building package `sbuild-build-depends-librg-blast-parser-perl-dummy' in `/«BUILDDIR»/resolver-iuYDbZ/apt_archive/sbuild-build-depends-librg-blast-parser-perl-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install librg-blast-parser-perl 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 intltool-debian libasprintf0c2 libcroco3 libextutils-xspp-perl libglib2.0-0 libmagic1 libpipeline1 librostlab-blast0 librostlab-blast0-dev librostlab3 librostlab3-dev libunistring0 libxml2 man-db po-debconf Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff librostlab-blast-doc librostlab-doc less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev 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 intltool-debian libasprintf0c2 libcroco3 libextutils-xspp-perl libglib2.0-0 libmagic1 libpipeline1 librostlab-blast0 librostlab-blast0-dev librostlab3 librostlab3-dev libunistring0 libxml2 man-db po-debconf sbuild-build-depends-librg-blast-parser-perl-dummy 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. Need to get 8995 kB/8996 kB of archives. After this operation, 29.4 MB of additional disk space will be used. 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(Reading database ... 14431 files and directories currently installed.) Preparing to unpack .../libpipeline1_1.3.0-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.3.0-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.2-5_amd64.deb ... Unpacking groff-base (1.22.2-5) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.5_amd64.deb ... Unpacking bsdmainutils (9.0.5) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.6.7.1-1_amd64.deb ... Unpacking man-db (2.6.7.1-1) ... Selecting previously unselected package libasprintf0c2:amd64. Preparing to unpack .../libasprintf0c2_0.18.3.2-2_amd64.deb ... Unpacking libasprintf0c2:amd64 (0.18.3.2-2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../libmagic1_1%3a5.19-1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.19-1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../libxml2_2.9.1+dfsg1-3_amd64.deb ... Unpacking libxml2:amd64 (2.9.1+dfsg1-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../libglib2.0-0_2.40.0-3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.40.0-3) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../libcroco3_0.6.8-2_amd64.deb ... Unpacking libcroco3:amd64 (0.6.8-2) ... Selecting previously unselected package libunistring0:amd64. Preparing to unpack .../libunistring0_0.9.3-5_amd64.deb ... Unpacking libunistring0:amd64 (0.9.3-5) ... Selecting previously unselected package file. Preparing to unpack .../file_1%3a5.19-1_amd64.deb ... Unpacking file (1:5.19-1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../gettext-base_0.18.3.2-2_amd64.deb ... Unpacking gettext-base (0.18.3.2-2) ... Selecting previously unselected package gettext. Preparing to unpack .../gettext_0.18.3.2-2_amd64.deb ... Unpacking gettext (0.18.3.2-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ... Unpacking intltool-debian (0.35.0+20060710.1) ... Selecting previously unselected package po-debconf. Preparing to unpack .../po-debconf_1.0.16+nmu2_all.deb ... Unpacking po-debconf (1.0.16+nmu2) ... Selecting previously unselected package debhelper. Preparing to unpack .../debhelper_9.20140613_all.deb ... Unpacking debhelper (9.20140613) ... Selecting previously unselected package libextutils-xspp-perl. Preparing to unpack .../libextutils-xspp-perl_0.1800-1_all.deb ... Unpacking libextutils-xspp-perl (0.1800-1) ... Selecting previously unselected package librostlab-blast0. Preparing to unpack .../librostlab-blast0_1.0.1-3_amd64.deb ... Unpacking librostlab-blast0 (1.0.1-3) ... Selecting previously unselected package librostlab-blast0-dev. Preparing to unpack .../librostlab-blast0-dev_1.0.1-3_amd64.deb ... Unpacking librostlab-blast0-dev (1.0.1-3) ... Selecting previously unselected package librostlab3. Preparing to unpack .../librostlab3_1.0.20-4_amd64.deb ... Unpacking librostlab3 (1.0.20-4) ... Selecting previously unselected package librostlab3-dev. Preparing to unpack .../librostlab3-dev_1.0.20-4_amd64.deb ... Unpacking librostlab3-dev (1.0.20-4) ... Selecting previously unselected package sbuild-build-depends-librg-blast-parser-perl-dummy. Preparing to unpack .../sbuild-build-depends-librg-blast-parser-perl-dummy.deb ... Unpacking sbuild-build-depends-librg-blast-parser-perl-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.3.0-1) ... Setting up groff-base (1.22.2-5) ... Setting up bsdmainutils (9.0.5) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up man-db (2.6.7.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libasprintf0c2:amd64 (0.18.3.2-2) ... Setting up libmagic1:amd64 (1:5.19-1) ... Setting up libxml2:amd64 (2.9.1+dfsg1-3) ... Setting up libglib2.0-0:amd64 (2.40.0-3) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.8-2) ... Setting up libunistring0:amd64 (0.9.3-5) ... Setting up file (1:5.19-1) ... Setting up gettext-base (0.18.3.2-2) ... Setting up gettext (0.18.3.2-2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20140613) ... Setting up libextutils-xspp-perl (0.1800-1) ... Setting up librostlab-blast0 (1.0.1-3) ... Setting up librostlab-blast0-dev (1.0.1-3) ... Setting up librostlab3 (1.0.20-4) ... Setting up librostlab3-dev (1.0.20-4) ... Setting up sbuild-build-depends-librg-blast-parser-perl-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.19-2) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-xen-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.24.51.20140604-3 dpkg-dev_1.17.10 g++-4.6_4.6.4-7 g++-4.9_4.9.0-6 gcc-4.6_4.6.4-7 gcc-4.7_4.7.4-1 gcc-4.9_4.9.0-6 libc6-dev_2.19-2 libstdc++-4.9-dev_4.9.0-6 libstdc++6_4.9.0-6 libstdc++6-4.6-dev_4.6.4-7 linux-libc-dev_3.14.7-1 Package versions: apt_1.0.4 base-files_7.3 base-passwd_3.5.33 bash_4.3-7 binutils_2.24.51.20140604-3 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.6 bzip2_1.0.6-5 clang-3.4_1:3.4.2-2 coreutils_8.21-1.2 cpp_4:4.9.0-3 cpp-4.6_4.6.4-7 cpp-4.7_4.7.4-1 cpp-4.9_4.9.0-6 dash_0.5.7-4 debconf_1.5.53 debconf-i18n_1.5.53 debfoster_2.7-1.2 debhelper_9.20140613 debian-archive-keyring_2012.4 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.10 dpkg-dev_1.17.10 e2fslibs_1.42.10-1 e2fsprogs_1.42.10-1 fakeroot_1.20-3 file_1:5.19-1 findutils_4.4.2-8 g++_4:4.9.0-3 g++-4.6_4.6.4-7 g++-4.9_4.9.0-6 gcc_4:4.9.0-3 gcc-4.4-base_4.4.7-8 gcc-4.5-base_4.5.4-1 gcc-4.6_4.6.4-7 gcc-4.6-base_4.6.4-7 gcc-4.7_4.7.4-1 gcc-4.7-base_4.7.4-1 gcc-4.8-base_4.8.3-3 gcc-4.9_4.9.0-6 gcc-4.9-base_4.9.0-6 gettext_0.18.3.2-2 gettext-base_0.18.3.2-2 gnupg_1.4.16-1.1 gpgv_1.4.16-1.1 grep_2.18-2 groff-base_1.22.2-5 gzip_1.6-3 hostname_3.15 initscripts_2.88dsf-53.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.52-1 libapt-pkg4.12_1.0.4 libarchive-extract-perl_0.72-1 libasan1_4.9.0-6 libasprintf0c2_0.18.3.2-2 libatomic1_4.9.0-6 libattr1_1:2.4.47-1 libaudit-common_1:2.3.7-1 libaudit1_1:2.3.7-1 libblkid1_2.20.1-5.8 libbz2-1.0_1.0.6-5 libc-bin_2.19-2 libc-dev-bin_2.19-2 libc6_2.19-2 libc6-dev_2.19-2 libcap2_1:2.22-1.2 libcilkrts5_4.9.0-6 libclang-common-3.4-dev_1:3.4.2-2 libclang1-3.4_1:3.4.2-2 libclass-isa-perl_0.36-5 libcloog-isl4_0.18.2-1 libcloog-ppl1_0.16.1-5 libcomerr2_1.42.10-1 libcroco3_0.6.8-2 libdb5.1_5.1.29-5 libdb5.3_5.3.28-3 libdebconfclient0_0.191 libdpkg-perl_1.17.10 libextutils-xspp-perl_0.1800-1 libfakeroot_1.20-3 libffi6_3.1-2 libfile-fcntllock-perl_0.20-1 libgc1c2_1:7.2d-6 libgcc-4.7-dev_4.7.4-1 libgcc-4.9-dev_4.9.0-6 libgcc1_1:4.9.0-6 libgdbm3_1.8.3-12 libglib2.0-0_2.40.0-3 libgmp10_2:6.0.0+dfsg-4 libgmpxx4ldbl_2:6.0.0+dfsg-4 libgomp1_4.9.0-6 libgpm2_1.20.4-6.1 libisl10_0.12.2-1 libitm1_4.9.0-6 libllvm3.4_1:3.4.2-2 liblocale-gettext-perl_1.05-8 liblog-message-simple-perl_0.10-1 liblsan0_4.9.0-6 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.19-1 libmodule-pluggable-perl_5.1-1 libmount1_2.20.1-5.8 libmpc2_0.9-4 libmpc3_1.0.1-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140118-1 libobjc-4.9-dev_4.9.0-6 libobjc4_4.9.0-6 libpam-modules_1.1.8-3 libpam-modules-bin_1.1.8-3 libpam-runtime_1.1.8-3 libpam0g_1.1.8-3 libpcre3_1:8.31-5 libpipeline1_1.3.0-1 libpod-latex-perl_0.61-1 libppl-c4_1:1.1-2+b1 libppl13_1:1.1-2+b1 libquadmath0_4.9.0-6 libreadline6_6.3-6 librostlab-blast0_1.0.1-3 librostlab-blast0-dev_1.0.1-3 librostlab3_1.0.20-4 librostlab3-dev_1.0.20-4 libselinux1_2.3-1 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-1 libslang2_2.2.4-16 libss2_1.42.10-1 libstdc++-4.9-dev_4.9.0-6 libstdc++6_4.9.0-6 libstdc++6-4.6-dev_4.6.4-7 libswitch-perl_2.17-1 libterm-ui-perl_0.42-1 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5+b1 libtext-soundex-perl_3.4-1+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140118-1 libtsan0_4.9.0-6 libubsan0_4.9.0-6 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.3 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.8 libvtv0_4.9.0-6 libxml2_2.9.1+dfsg1-3 linux-libc-dev_3.14.7-1 login_1:4.2-2 lsb-base_4.1+Debian13 make_4.0-8 man-db_2.6.7.1-1 mawk_1.3.3-17 mount_2.20.1-5.8 multiarch-support_2.19-2 ncurses-base_5.9+20140118-1 ncurses-bin_5.9+20140118-1 passwd_1:4.2-2 patch_2.7.1-5 perl_5.18.2-4 perl-base_5.18.2-4 perl-modules_5.18.2-4 po-debconf_1.0.16+nmu2 readline-common_6.3-6 rename_0.20-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-librg-blast-parser-perl-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 sudo_1.8.9p5-1 sysv-rc_2.88dsf-53.2 sysvinit_2.88dsf-53.2 sysvinit-core_2.88dsf-53.2 sysvinit-utils_2.88dsf-53.2 tar_1.27.1-2 tzdata_2014e-1 ucf_3.0030 util-linux_2.20.1-5.8 vim_2:7.4.273-2+b1 vim-common_2:7.4.273-2+b1 vim-runtime_2:7.4.273-2 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Sun Apr 27 15:43:13 2014 UTC using RSA key ID D1C646D1 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./librg-blast-parser-perl_0.03-2.dsc dpkg-source: info: extracting librg-blast-parser-perl in librg-blast-parser-perl-0.03 dpkg-source: info: unpacking librg-blast-parser-perl_0.03.orig.tar.gz dpkg-source: info: unpacking librg-blast-parser-perl_0.03-2.debian.tar.xz Check disc space ──────────────── Sufficient free space for build Hack binNMU version ─────────────────── Created changelog entry for binNMU version 0.03-2clang1 User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=10 HOME=/sbuild-nonexistent LOGNAME=user PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=user SCHROOT_SESSION_ID=unstable-amd64-sbuild-fe3a9a83-13f6-48ba-93d7-f72ed31de2d4 SCHROOT_UID=1000 SCHROOT_USER=user SHELL=/bin/sh USER=user dpkg-buildpackage ───────────────── dpkg-buildpackage: source package librg-blast-parser-perl dpkg-buildpackage: source version 0.03-2clang1 dpkg-buildpackage: source distribution unstable dpkg-source --before-build librg-blast-parser-perl-0.03 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --parallel dh_testdir -O--parallel dh_auto_clean -O--parallel dh_clean -O--parallel debian/rules build-arch dh build-arch --parallel dh_testdir -a -O--parallel debian/rules override_dh_auto_configure make[1]: Entering directory '/«PKGBUILDDIR»' dh_auto_configure -- OPTIMIZE="-D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" LD="'cc' -Wl,-z,relro" Checking if your kit is complete... Warning: the following files are missing in your kit: Parser.bs Parser.c Parser.o t/RG-Blast-Parser.t Please inform the author. Writing Makefile for RG::Blast::Parser Writing MYMETA.yml and MYMETA.json make[1]: Leaving directory '/«PKGBUILDDIR»' dh_auto_build -a -O--parallel make[1]: Entering directory '/«PKGBUILDDIR»' /usr/bin/perl /usr/share/perl/5.18/ExtUtils/xsubpp -C++ -hiertype -noprototypes -typemap /usr/share/perl/5.18/ExtUtils/typemap -typemap perlobject.map -typemap typemap Parser.xs > Parser.xsc && mv Parser.xsc Parser.c Running Mkbootstrap for RG::Blast::Parser () cp lib/RG/Blast/Parser.pm blib/lib/RG/Blast/Parser.pm AutoSplitting blib/lib/RG/Blast/Parser.pm (blib/lib/auto/RG/Blast/Parser) chmod 644 Parser.bs cp Parser.bs blib/arch/auto/RG/Blast/Parser/Parser.bs chmod 644 blib/arch/auto/RG/Blast/Parser/Parser.bs g++ -c -I. -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DVERSION=\"0.03\" -DXS_VERSION=\"0.03\" -fPIC "-I/usr/lib/perl/5.18/CORE" Parser.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated In file included from Parser.xs:15: /usr/include/rostlab/blast-parser-driver.h:61:12: error: expected a class or namespace friend YY_DECL_FRIEND; ^~~~~~~~~~~~~~ /usr/include/rostlab/blast-parser-driver.h:39:27: note: expanded from macro 'YY_DECL_FRIEND' rostlab::blast::parser::token_type \ ~~~~~~~~~~~~~~~~~~~~~~~~^ Parser.c:618:1: warning: duplicate 'extern' declaration specifier [-Wduplicate-decl-specifier] XS_EXTERNAL(boot_RG__Blast__Parser); /* prototype to pass -Wmissing-prototypes */ ^ /usr/lib/perl/5.18/CORE/XSUB.h:145:33: note: expanded from macro 'XS_EXTERNAL' # define XS_EXTERNAL(name) extern "C" XSPROTO(name) ^ In file included from Parser.xs:15: In file included from /usr/include/rostlab/blast-parser-driver.h:26: In file included from blast-parser-parser.ypp:26: In file included from /usr/include/rostlab/blast-result.h:25: /usr/include/rostlab/aux_functions.h:186:43: error: call to function 'operator<<' that is neither visible in the template definition nor found by argument-dependent lookup { if( v_i != v.begin() ) os << ", "; os << *v_i; } ^ /usr/include/rostlab/blast-result.h:237:90: note: in instantiation of function template specialization 'rostlab::operator<< >' requested here __os << "n = " << __r.name << " d = " << __r.desc << " Length = " << __r.length << " " << __r.hsps; ^ /usr/include/rostlab/blast-result.h:224:19: note: 'operator<<' should be declared prior to the call site or in namespace 'rostlab::blast' std::ostream& operator<<( std::ostream& __os, const rostlab::blast::hsp& __r ) ^ In file included from Parser.xs:15: In file included from /usr/include/rostlab/blast-parser-driver.h:26: In file included from blast-parser-parser.ypp:26: In file included from /usr/include/rostlab/blast-result.h:25: /usr/include/rostlab/aux_functions.h:186:43: error: call to function 'operator<<' that is neither visible in the template definition nor found by argument-dependent lookup { if( v_i != v.begin() ) os << ", "; os << *v_i; } ^ /usr/include/rostlab/blast-result.h:245:87: note: in instantiation of function template specialization 'rostlab::operator<< >' requested here __os << __r.blast_version << "\n\nreferences: " << __r.references << "\n\nrounds: " << __r.rounds << "\n\nn = " << __r.q_name << " d = " << __r.q_desc << " (" << __r.q_length << ^ /usr/include/rostlab/blast-result.h:208:19: note: 'operator<<' should be declared prior to the call site or in namespace 'rostlab::blast' std::ostream& operator<<( std::ostream& __os, const rostlab::blast::round& __r ) ^ In file included from Parser.xs:15: In file included from /usr/include/rostlab/blast-parser-driver.h:26: In file included from blast-parser-parser.ypp:26: In file included from /usr/include/rostlab/blast-result.h:25: /usr/include/rostlab/aux_functions.h:186:43: error: call to function 'operator<<' that is neither visible in the template definition nor found by argument-dependent lookup { if( v_i != v.begin() ) os << ", "; os << *v_i; } ^ /usr/include/rostlab/blast-result.h:246:143: note: in instantiation of function template specialization 'rostlab::operator<< >' requested here " letters)\n\nDatabase: " << __r.db_name << " " << __r.db_nseq << " sequences; " << __r.db_nletter << " total letters\n\none-line desc: " << __r.onelines << "\n\n" << ^ /usr/include/rostlab/blast-result.h:216:19: note: 'operator<<' should be declared prior to the call site or in namespace 'rostlab::blast' std::ostream& operator<<( std::ostream& __os, const rostlab::blast::oneline& __r ) ^ In file included from Parser.xs:15: In file included from /usr/include/rostlab/blast-parser-driver.h:26: In file included from blast-parser-parser.ypp:26: In file included from /usr/include/rostlab/blast-result.h:25: /usr/include/rostlab/aux_functions.h:186:43: error: call to function 'operator<<' that is neither visible in the template definition nor found by argument-dependent lookup { if( v_i != v.begin() ) os << ", "; os << *v_i; } ^ /usr/include/rostlab/blast-result.h:247:59: note: in instantiation of function template specialization 'rostlab::operator<< >' requested here ( __r.converged ? "CONVERGED!\n\n" : "" ) << "hits: " << __r.hits << "\n\n" << __r.tail; ^ /usr/include/rostlab/blast-result.h:235:19: note: 'operator<<' should be declared prior to the call site or in namespace 'rostlab::blast' std::ostream& operator<<( std::ostream& __os, const rostlab::blast::hit& __r ) ^ 1 warning and 5 errors generated. make[1]: *** [Parser.o] Error 1 Makefile:342: recipe for target 'Parser.o' failed make[1]: Leaving directory '/«PKGBUILDDIR»' dh_auto_build: make -j10 returned exit code 2 make: *** [build-arch] Error 2 debian/rules:16: recipe for target 'build-arch' failed dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20140617-1517 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 236 Build-Time: 5 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 10 Job: librg-blast-parser-perl_0.03-2 Machine Architecture: amd64 Package: librg-blast-parser-perl Package-Time: 44 Source-Version: 0.03-2 Space: 236 Status: attempted Version: 0.03-2clang1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20140617-1517 Build needed 00:00:44, 236k disc space DC-Status: Failed 45.252647334s DC-Time-Estimation: 45.252647334 versus expected 142 (r/m: 2.137937963097025 ; m: 45.252647334)