DC-Build-Header: biococoa 2.2.2-2 / 2014-09-04 19:20:43 +0000 DC-Task: source:biococoa version:2.2.2-2 architecture:any chroot:unstable esttime:212 logfile:/tmp/biococoa_2.2.2-2_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 " biococoa_2.2.2-2' sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on ip-172-31-5-36.us-west-2.compute.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ biococoa 2.2.2-2clang1 (amd64) 04 Sep 2014 19:20 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: biococoa Version: 2.2.2-2clang1 Source Version: 2.2.2-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/biococoa-qMUsM2/biococoa-2.2.2' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/biococoa-qMUsM2' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-e4c724c8-e10c-4046-bfd5-70e11e2c3585' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Get:1 http://localhost:9999 unstable InRelease [233 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 2014-09-03-1436.55.pdiff [24.7 kB] Get:6 http://localhost:9999 unstable/main 2014-09-03-2030.01.pdiff [10.5 kB] Get:7 http://localhost:9999 unstable/main 2014-09-04-0229.22.pdiff [7545 B] Get:8 http://localhost:9999 unstable/main 2014-09-04-0831.05.pdiff [14.0 kB] Get:9 http://localhost:9999 unstable/main amd64 2014-09-03-1436.55.pdiff [26.7 kB] Get:10 http://localhost:9999 unstable/main 2014-09-04-0831.05.pdiff [14.0 kB] Get:11 http://localhost:9999 unstable/main amd64 2014-09-03-2030.01.pdiff [12.4 kB] Get:12 http://localhost:9999 unstable/main amd64 2014-09-04-0229.22.pdiff [5892 B] Get:13 http://localhost:9999 unstable/main amd64 2014-09-04-0831.05.pdiff [18.1 kB] Get:14 http://localhost:9999 unstable/main 2014-09-03-1436.55.pdiff [3960 B] Get:15 http://localhost:9999 unstable/main 2014-09-03-2030.01.pdiff [1010 B] Get:16 http://localhost:9999 unstable/main 2014-09-04-0229.22.pdiff [648 B] Get:17 http://localhost:9999 unstable/main 2014-09-04-0831.05.pdiff [61 B] Get:18 http://localhost:9999 unstable/main amd64 2014-09-04-0831.05.pdiff [18.1 kB] Get:19 http://localhost:9999 unstable/main 2014-09-04-0831.05.pdiff [61 B] Fetched 382 kB in 5s (69.3 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: binutils 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3310 kB of archives. After this operation, 50.2 kB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main binutils amd64 2.24.51.20140903-1 [3310 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3310 kB in 0s (29.4 MB/s) (Reading database ... 15135 files and directories currently installed.) Preparing to unpack .../binutils_2.24.51.20140903-1_amd64.deb ... Unpacking binutils (2.24.51.20140903-1) over (2.24.51.20140818-1) ... Setting up binutils (2.24.51.20140903-1) ... Processing triggers for libc-bin (2.19-10) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'biococoa' packaging is maintained in the 'Svn' version control system at: svn://anonscm.debian.org/debian-med/trunk/packages/biococoa/trunk/ Need to get 370 kB of source archives. Get:1 http://localhost:9999/debian/ unstable/main biococoa 2.2.2-2 (dsc) [1491 B] Get:2 http://localhost:9999/debian/ unstable/main biococoa 2.2.2-2 (tar) [359 kB] Get:3 http://localhost:9999/debian/ unstable/main biococoa 2.2.2-2 (diff) [9346 B] Fetched 370 kB in 1s (243 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... + CLANG_VERSION=3.5 + echo 'Install of clang-3.5' Install of clang-3.5 + apt-get update Hit http://localhost:9999 unstable InRelease Get:1 http://localhost:9999 unstable/main Sources/DiffIndex [7876 B] Get:2 http://localhost:9999 unstable/main amd64 Packages/DiffIndex [7876 B] Get:3 http://localhost:9999 unstable/main Translation-en/DiffIndex [7876 B] Fetched 23.6 kB in 1s (12.0 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-3.5 Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libbsd0 libclang-common-3.5-dev libclang1-3.5 libedit2 libffi6 libllvm3.5 libobjc-4.9-dev libobjc4 Suggested packages: gnustep gnustep-devel clang-3.5-doc Recommended packages: llvm-3.5-dev python The following NEW packages will be installed: clang-3.5 libbsd0 libclang-common-3.5-dev libclang1-3.5 libedit2 libffi6 libllvm3.5 libobjc-4.9-dev libobjc4 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. Need to get 33.3 MB of archives. After this operation, 132 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libbsd0 amd64 0.7.0-2 [67.9 kB] Get:2 http://localhost:9999/debian/ unstable/main libedit2 amd64 3.1-20140620-2 [85.1 kB] Get:3 http://localhost:9999/debian/ unstable/main libffi6 amd64 3.1-2 [19.8 kB] Get:4 http://localhost:9999/debian/ unstable/main libllvm3.5 amd64 1:3.5-1 [7609 kB] Get:5 http://localhost:9999/debian/ unstable/main libobjc4 amd64 4.9.1-12 [112 kB] Get:6 http://localhost:9999/debian/ unstable/main libobjc-4.9-dev amd64 4.9.1-12 [372 kB] Get:7 http://localhost:9999/debian/ unstable/main libclang1-3.5 amd64 1:3.5-1 [3628 kB] Get:8 http://localhost:9999/debian/ unstable/main libclang-common-3.5-dev amd64 1:3.5-1 [677 kB] Get:9 http://localhost:9999/debian/ unstable/main clang-3.5 amd64 1:3.5-1 [20.7 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 33.3 MB in 1s (32.9 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 15135 files and directories currently installed.) Preparing to unpack .../libbsd0_0.7.0-2_amd64.deb ... Unpacking libbsd0:amd64 (0.7.0-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../libedit2_3.1-20140620-2_amd64.deb ... Unpacking libedit2:amd64 (3.1-20140620-2) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../libffi6_3.1-2_amd64.deb ... Unpacking libffi6:amd64 (3.1-2) ... Selecting previously unselected package libllvm3.5:amd64. Preparing to unpack .../libllvm3.5_1%3a3.5-1_amd64.deb ... Unpacking libllvm3.5:amd64 (1:3.5-1) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../libobjc4_4.9.1-12_amd64.deb ... Unpacking libobjc4:amd64 (4.9.1-12) ... Selecting previously unselected package libobjc-4.9-dev:amd64. Preparing to unpack .../libobjc-4.9-dev_4.9.1-12_amd64.deb ... Unpacking libobjc-4.9-dev:amd64 (4.9.1-12) ... Selecting previously unselected package libclang1-3.5:amd64. Preparing to unpack .../libclang1-3.5_1%3a3.5-1_amd64.deb ... Unpacking libclang1-3.5:amd64 (1:3.5-1) ... Selecting previously unselected package libclang-common-3.5-dev. Preparing to unpack .../libclang-common-3.5-dev_1%3a3.5-1_amd64.deb ... Unpacking libclang-common-3.5-dev (1:3.5-1) ... Selecting previously unselected package clang-3.5. Preparing to unpack .../clang-3.5_1%3a3.5-1_amd64.deb ... Unpacking clang-3.5 (1:3.5-1) ... Setting up libbsd0:amd64 (0.7.0-2) ... Setting up libedit2:amd64 (3.1-20140620-2) ... Setting up libffi6:amd64 (3.1-2) ... Setting up libllvm3.5:amd64 (1:3.5-1) ... Setting up libobjc4:amd64 (4.9.1-12) ... Setting up libobjc-4.9-dev:amd64 (4.9.1-12) ... Setting up libclang1-3.5:amd64 (1:3.5-1) ... Setting up libclang-common-3.5-dev (1:3.5-1) ... Setting up clang-3.5 (1:3.5-1) ... Processing triggers for libc-bin (2.19-10) ... + 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 '$VERSIONS' + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-3.5 g++-4.6 + ln -s clang-3.5 gcc-4.6 + ln -s clang-3.5 cpp-4.6 + ln -s clang-3.5 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections + echo 'g++-4.6 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-3.5 g++-4.7 + ln -s clang-3.5 gcc-4.7 + ln -s clang-3.5 cpp-4.7 + ln -s clang-3.5 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections + echo 'g++-4.7 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-3.5 g++-4.8 + ln -s clang-3.5 gcc-4.8 + ln -s clang-3.5 cpp-4.8 + ln -s clang-3.5 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-3.5 g++-4.9 + ln -s clang-3.5 gcc-4.9 + ln -s clang-3.5 cpp-4.9 + ln -s clang-3.5 gcc + 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-qsuyJ9/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/818 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 ... 15338 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, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), cdbs, gnustep-make, debhelper (>= 9), libgnustep-base-dev Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), cdbs, gnustep-make, debhelper (>= 9), libgnustep-base-dev dpkg-deb: building package `sbuild-build-depends-biococoa-dummy' in `/«BUILDDIR»/resolver-F2xN9B/apt_archive/sbuild-build-depends-biococoa-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install biococoa build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: autotools-dev bsdmainutils ca-certificates cdbs debhelper file gettext gettext-base gnustep-base-common gnustep-base-runtime gnustep-common gnustep-make gobjc gobjc-4.9 groff-base intltool-debian libasprintf0c2 libavahi-client3 libavahi-common-data libavahi-common3 libcroco3 libglib2.0-0 libgnustep-base-dev libgnustep-base1.24 libgnutls-deb0-28 libhogweed2 libicu52 libmagic1 libnettle4 libp11-kit0 libpipeline1 libssl1.0.0 libtasn1-6 libunistring0 libxml2 libxslt1.1 man-db openssl po-debconf Suggested packages: wamerican wordlist whois vacation devscripts dh-make gettext-doc gnustep-base-doc gnustep-make-doc gobjc-multilib gobjc-4.9-multilib gcc-4.9-doc libobjc4-dbg groff gnutls-bin 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: autotools-dev bsdmainutils ca-certificates cdbs debhelper file gettext gettext-base gnustep-base-common gnustep-base-runtime gnustep-common gnustep-make gobjc gobjc-4.9 groff-base intltool-debian libasprintf0c2 libavahi-client3 libavahi-common-data libavahi-common3 libcroco3 libglib2.0-0 libgnustep-base-dev libgnustep-base1.24 libgnutls-deb0-28 libhogweed2 libicu52 libmagic1 libnettle4 libp11-kit0 libpipeline1 libssl1.0.0 libtasn1-6 libunistring0 libxml2 libxslt1.1 man-db openssl po-debconf sbuild-build-depends-biococoa-dummy 0 upgraded, 40 newly installed, 0 to remove and 0 not upgraded. Need to get 27.8 MB/27.8 MB of archives. After this operation, 102 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libpipeline1 amd64 1.3.0-1 [25.8 kB] Get:2 http://localhost:9999/debian/ unstable/main libssl1.0.0 amd64 1.0.1i-2 [1026 kB] Get:3 http://localhost:9999/debian/ unstable/main groff-base amd64 1.22.2-7 [1142 kB] Get:4 http://localhost:9999/debian/ unstable/main bsdmainutils amd64 9.0.5 [211 kB] Get:5 http://localhost:9999/debian/ unstable/main man-db amd64 2.6.7.1-1 [990 kB] Get:6 http://localhost:9999/debian/ unstable/main libasprintf0c2 amd64 0.19.2-2 [30.8 kB] Get:7 http://localhost:9999/debian/ unstable/main libnettle4 amd64 2.7.1-3 [175 kB] Get:8 http://localhost:9999/debian/ unstable/main libhogweed2 amd64 2.7.1-3 [125 kB] Get:9 http://localhost:9999/debian/ unstable/main libp11-kit0 amd64 0.20.3-2 [153 kB] Get:10 http://localhost:9999/debian/ unstable/main libtasn1-6 amd64 4.1-1 [48.2 kB] Get:11 http://localhost:9999/debian/ unstable/main libgnutls-deb0-28 amd64 3.3.7-2 [685 kB] Get:12 http://localhost:9999/debian/ unstable/main libmagic1 amd64 1:5.19-1 [237 kB] Get:13 http://localhost:9999/debian/ unstable/main libxml2 amd64 2.9.1+dfsg1-4 [797 kB] Get:14 http://localhost:9999/debian/ unstable/main libavahi-common-data amd64 0.6.31-4 [98.3 kB] Get:15 http://localhost:9999/debian/ unstable/main libavahi-common3 amd64 0.6.31-4 [50.6 kB] Get:16 http://localhost:9999/debian/ unstable/main libavahi-client3 amd64 0.6.31-4 [53.8 kB] Get:17 http://localhost:9999/debian/ unstable/main libglib2.0-0 amd64 2.40.0-5 [2421 kB] Get:18 http://localhost:9999/debian/ unstable/main libcroco3 amd64 0.6.8-3 [135 kB] Get:19 http://localhost:9999/debian/ unstable/main libicu52 amd64 52.1-5 [6774 kB] Get:20 http://localhost:9999/debian/ unstable/main libunistring0 amd64 0.9.3-5.2 [283 kB] Get:21 http://localhost:9999/debian/ unstable/main libxslt1.1 amd64 1.1.28-2 [230 kB] Get:22 http://localhost:9999/debian/ unstable/main file amd64 1:5.19-1 [58.0 kB] Get:23 http://localhost:9999/debian/ unstable/main gettext-base amd64 0.19.2-2 [120 kB] Get:24 http://localhost:9999/debian/ unstable/main autotools-dev all 20140510.1 [70.3 kB] Get:25 http://localhost:9999/debian/ unstable/main openssl amd64 1.0.1i-2 [674 kB] Get:26 http://localhost:9999/debian/ unstable/main ca-certificates all 20140325 [193 kB] Get:27 http://localhost:9999/debian/ unstable/main cdbs all 0.4.126 [75.5 kB] Get:28 http://localhost:9999/debian/ unstable/main gettext amd64 0.19.2-2 [1237 kB] Get:29 http://localhost:9999/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:30 http://localhost:9999/debian/ unstable/main po-debconf all 1.0.16+nmu3 [220 kB] Get:31 http://localhost:9999/debian/ unstable/main debhelper all 9.20140817 [814 kB] Get:32 http://localhost:9999/debian/ unstable/main gnustep-common amd64 2.6.6-2 [119 kB] Get:33 http://localhost:9999/debian/ unstable/main gnustep-base-common all 1.24.6-2 [237 kB] Get:34 http://localhost:9999/debian/ unstable/main libgnustep-base1.24 amd64 1.24.6-2 [1240 kB] Get:35 http://localhost:9999/debian/ unstable/main gnustep-base-runtime amd64 1.24.6-2 [187 kB] Get:36 http://localhost:9999/debian/ unstable/main gobjc-4.9 amd64 4.9.1-12 [4972 kB] Get:37 http://localhost:9999/debian/ unstable/main gobjc amd64 4:4.9.1-3 [954 B] Get:38 http://localhost:9999/debian/ unstable/main gnustep-make all 2.6.6-2 [201 kB] Get:39 http://localhost:9999/debian/ unstable/main libgnustep-base-dev amd64 1.24.6-2 [1620 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 27.8 MB in 2s (12.4 MB/s) Selecting previously unselected package libpipeline1:amd64. (Reading database ... 15338 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 libssl1.0.0:amd64. Preparing to unpack .../libssl1.0.0_1.0.1i-2_amd64.deb ... Unpacking libssl1.0.0:amd64 (1.0.1i-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.2-7_amd64.deb ... Unpacking groff-base (1.22.2-7) ... 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_0.19.2-2_amd64.deb ... Unpacking libasprintf0c2:amd64 (0.19.2-2) ... Selecting previously unselected package libnettle4:amd64. Preparing to unpack .../libnettle4_2.7.1-3_amd64.deb ... Unpacking libnettle4:amd64 (2.7.1-3) ... Selecting previously unselected package libhogweed2:amd64. Preparing to unpack .../libhogweed2_2.7.1-3_amd64.deb ... Unpacking libhogweed2:amd64 (2.7.1-3) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../libp11-kit0_0.20.3-2_amd64.deb ... Unpacking libp11-kit0:amd64 (0.20.3-2) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../libtasn1-6_4.1-1_amd64.deb ... Unpacking libtasn1-6:amd64 (4.1-1) ... Selecting previously unselected package libgnutls-deb0-28:amd64. Preparing to unpack .../libgnutls-deb0-28_3.3.7-2_amd64.deb ... Unpacking libgnutls-deb0-28:amd64 (3.3.7-2) ... 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+dfsg1-4_amd64.deb ... Unpacking libxml2:amd64 (2.9.1+dfsg1-4) ... Selecting previously unselected package libavahi-common-data:amd64. Preparing to unpack .../libavahi-common-data_0.6.31-4_amd64.deb ... Unpacking libavahi-common-data:amd64 (0.6.31-4) ... Selecting previously unselected package libavahi-common3:amd64. Preparing to unpack .../libavahi-common3_0.6.31-4_amd64.deb ... Unpacking libavahi-common3:amd64 (0.6.31-4) ... Selecting previously unselected package libavahi-client3:amd64. Preparing to unpack .../libavahi-client3_0.6.31-4_amd64.deb ... Unpacking libavahi-client3:amd64 (0.6.31-4) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../libglib2.0-0_2.40.0-5_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.40.0-5) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../libcroco3_0.6.8-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.8-3) ... 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Selecting previously unselected package gnustep-make. Preparing to unpack .../gnustep-make_2.6.6-2_all.deb ... Unpacking gnustep-make (2.6.6-2) ... Selecting previously unselected package libgnustep-base-dev. Preparing to unpack .../libgnustep-base-dev_1.24.6-2_amd64.deb ... Unpacking libgnustep-base-dev (1.24.6-2) ... Selecting previously unselected package sbuild-build-depends-biococoa-dummy. Preparing to unpack .../sbuild-build-depends-biococoa-dummy.deb ... Unpacking sbuild-build-depends-biococoa-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.3.0-1) ... Setting up libssl1.0.0:amd64 (1.0.1i-2) ... Setting up groff-base (1.22.2-7) ... 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 (0.19.2-2) ... Setting up libnettle4:amd64 (2.7.1-3) ... Setting up libhogweed2:amd64 (2.7.1-3) ... Setting up libp11-kit0:amd64 (0.20.3-2) ... Setting up libtasn1-6:amd64 (4.1-1) ... Setting up libgnutls-deb0-28:amd64 (3.3.7-2) ... Setting up libmagic1:amd64 (1:5.19-1) ... Setting up libxml2:amd64 (2.9.1+dfsg1-4) ... Setting up libavahi-common-data:amd64 (0.6.31-4) ... Setting up libavahi-common3:amd64 (0.6.31-4) ... Setting up libavahi-client3:amd64 (0.6.31-4) ... Setting up libglib2.0-0:amd64 (2.40.0-5) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.8-3) ... Setting up libicu52:amd64 (52.1-5) ... Setting up libunistring0:amd64 (0.9.3-5.2) ... Setting up libxslt1.1:amd64 (1.1.28-2) ... Setting up file (1:5.19-1) ... Setting up gettext-base (0.19.2-2) ... Setting up autotools-dev (20140510.1) ... Setting up openssl (1.0.1i-2) ... Setting up ca-certificates (20140325) ... Setting up cdbs (0.4.126) ... Setting up gettext (0.19.2-2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu3) ... Setting up debhelper (9.20140817) ... Setting up gnustep-common (2.6.6-2) ... Setting up gnustep-base-common (1.24.6-2) ... Setting up libgnustep-base1.24 (1.24.6-2) ... Setting up gnustep-base-runtime (1.24.6-2) ... All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up gobjc-4.9 (4.9.1-12) ... Setting up gobjc (4:4.9.1-3) ... Setting up gnustep-make (2.6.6-2) ... Setting up libgnustep-base-dev (1.24.6-2) ... Setting up sbuild-build-depends-biococoa-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.19-10) ... Processing triggers for ca-certificates (20140325) ... Updating certificates in /etc/ssl/certs... 168 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d....done. ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-xen-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.24.51.20140903-1 dpkg-dev_1.17.13 g++-4.6_4.6.4-7 g++-4.9_4.9.1-12 gcc-4.6_4.6.4-7 gcc-4.7_4.7.4-3 gcc-4.9_4.9.1-12 libc6-dev_2.19-10 libstdc++-4.9-dev_4.9.1-12 libstdc++6_4.9.1-12 libstdc++6-4.6-dev_4.6.4-7 linux-libc-dev_3.14.15-2 Package versions: acl_2.2.52-1.1 adduser_3.113+nmu3 apt_1.0.7 autotools-dev_20140510.1 base-files_7.5 base-passwd_3.5.35 bash_4.3-9 binutils_2.24.51.20140903-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.7 bzip2_1.0.6-7 ca-certificates_20140325 cdbs_0.4.126 clang-3.5_1:3.5-1 coreutils_8.23-2 cpp_4:4.9.1-3 cpp-4.6_4.6.4-7 cpp-4.7_4.7.4-3 cpp-4.9_4.9.1-12 dash_0.5.7-4 dbus_1.8.6-2 debconf_1.5.53 debconf-i18n_1.5.53 debfoster_2.7-2 debhelper_9.20140817 debian-archive-keyring_2014.1 debianutils_4.4 diffutils_1:3.3-1 dmsetup_2:1.02.88-1 dpkg_1.17.13 dpkg-dev_1.17.13 e2fslibs_1.42.12-1 e2fsprogs_1.42.12-1 fakeroot_1.20.1-1.1 file_1:5.19-1 findutils_4.4.2-9 g++_4:4.9.1-3 g++-4.6_4.6.4-7 g++-4.9_4.9.1-12 gcc_4:4.9.1-3 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_4.7.4-3 gcc-4.7-base_4.7.4-3 gcc-4.8-base_4.8.3-10 gcc-4.9_4.9.1-12 gcc-4.9-base_4.9.1-12 gettext_0.19.2-2 gettext-base_0.19.2-2 gnupg_1.4.18-3 gnustep-base-common_1.24.6-2 gnustep-base-runtime_1.24.6-2 gnustep-common_2.6.6-2 gnustep-make_2.6.6-2 gobjc_4:4.9.1-3 gobjc-4.9_4.9.1-12 gpgv_1.4.18-3 grep_2.20-2 groff-base_1.22.2-7 gzip_1.6-3 hostname_3.15 init_1.21 initscripts_2.88dsf-53.4 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.52-1.1 libalgorithm-c3-perl_0.09-1 libapt-pkg4.12_1.0.7 libarchive-extract-perl_0.72-1 libasan1_4.9.1-12 libasprintf0c2_0.19.2-2 libatomic1_4.9.1-12 libattr1_1:2.4.47-1 libaudit-common_1:2.3.7-1 libaudit1_1:2.3.7-1 libavahi-client3_0.6.31-4 libavahi-common-data_0.6.31-4 libavahi-common3_0.6.31-4 libblkid1_2.20.1-5.8 libbsd0_0.7.0-2 libbz2-1.0_1.0.6-7 libc-bin_2.19-10 libc-dev-bin_2.19-10 libc6_2.19-10 libc6-dev_2.19-10 libcap-ng0_0.7.4-2 libcap2_1:2.24-4 libcap2-bin_1:2.24-4 libcgi-fast-perl_1:2.02-1 libcgi-pm-perl_4.03-1 libcilkrts5_4.9.1-12 libclang-common-3.5-dev_1:3.5-1 libclang1-3.5_1:3.5-1 libclass-c3-perl_0.26-1 libclass-c3-xs-perl_0.13-2+b1 libclass-isa-perl_0.36-5 libcloog-isl4_0.18.2-1 libcloog-ppl1_0.16.1-5 libcomerr2_1.42.12-1 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-1 libdata-optlist-perl_0.109-1 libdata-section-perl_0.200006-1 libdb5.1_5.1.29-5 libdb5.3_5.3.28-6 libdbus-1-3_1.8.6-2 libdebconfclient0_0.191 libdevmapper1.02.1_2:1.02.88-1 libdpkg-perl_1.17.13 libedit2_3.1-20140620-2 libexpat1_2.1.0-6 libfakeroot_1.20.1-1.1 libfcgi-perl_0.77-1+b1 libffi6_3.1-2 libfile-fcntllock-perl_0.22-1+b1 libgc1c2_1:7.2d-6.3 libgcc-4.7-dev_4.7.4-3 libgcc-4.9-dev_4.9.1-12 libgcc1_1:4.9.1-12 libgcrypt11_1.5.4-3 libgcrypt20_1.6.2-3 libgdbm3_1.8.3-13 libglib2.0-0_2.40.0-5 libgmp10_2:6.0.0+dfsg-6 libgmpxx4ldbl_2:6.0.0+dfsg-6 libgnustep-base-dev_1.24.6-2 libgnustep-base1.24_1.24.6-2 libgnutls-deb0-28_3.3.7-2 libgomp1_4.9.1-12 libgpg-error0_1.13-4 libgpm2_1.20.4-6.1 libhogweed2_2.7.1-3 libicu52_52.1-5 libisl10_0.12.2-2 libitm1_4.9.1-12 libkmod2_18-1 libllvm3.5_1:3.5-1 liblocale-gettext-perl_1.05-8+b1 liblog-message-perl_0.8-1 liblog-message-simple-perl_0.10-2 liblsan0_4.9.1-12 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.19-1 libmodule-build-perl_0.420800-1 libmodule-pluggable-perl_5.1-1 libmodule-signature-perl_0.73-1 libmount1_2.20.1-5.8 libmpc2_0.9-4 libmpc3_1.0.2-1 libmpfr4_3.1.2-1 libmro-compat-perl_0.12-1 libncurses5_5.9+20140712-2 libncursesw5_5.9+20140712-2 libnettle4_2.7.1-3 libobjc-4.9-dev_4.9.1-12 libobjc4_4.9.1-12 libp11-kit0_0.20.3-2 libpackage-constants-perl_0.04-1 libpam-cap_1:2.24-4 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam-systemd_208-8 libpam0g_1.1.8-3.1 libparams-util-perl_1.07-2+b1 libpcre3_1:8.35-3 libpipeline1_1.3.0-1 libpod-latex-perl_0.61-1 libpod-readme-perl_0.11-1 libppl-c4_1:1.1-3 libppl13_1:1.1-3 libprocps3_1:3.3.9-7 libquadmath0_4.9.1-12 libreadline6_6.3-8 libregexp-common-perl_2013031301-1 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.2.4-17 libsoftware-license-perl_0.103010-1 libss2_1.42.12-1 libssl1.0.0_1.0.1i-2 libstdc++-4.9-dev_4.9.1-12 libstdc++6_4.9.1-12 libstdc++6-4.6-dev_4.6.4-7 libsub-exporter-perl_0.986-1 libsub-install-perl_0.928-1 libswitch-perl_2.17-1 libsystemd-daemon0_208-8 libsystemd-journal0_208-8 libsystemd-login0_208-8 libtasn1-6_4.1-1 libterm-ui-perl_0.42-1 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b2 libtext-soundex-perl_3.4-1+b2 libtext-template-perl_1.46-1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140712-2 libtsan0_4.9.1-12 libubsan0_4.9.1-12 libudev1_208-8 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-24 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.8 libwrap0_7.6.q-25 libxml2_2.9.1+dfsg1-4 libxslt1.1_1.1.28-2 linux-libc-dev_3.14.15-2 login_1:4.2-2+b1 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_2.19-10 ncurses-base_5.9+20140712-2 ncurses-bin_5.9+20140712-2 openssl_1.0.1i-2 passwd_1:4.2-2+b1 patch_2.7.1-6 perl_5.20.0-6 perl-base_5.20.0-6 perl-modules_5.20.0-6 po-debconf_1.0.16+nmu3 procps_1:3.3.9-7 psmisc_22.21-2 readline-common_6.3-8 rename_0.20-3 sbuild-build-depends-biococoa-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 sudo_1.8.9p5-1 systemd_208-8 systemd-sysv_208-8 sysv-rc_2.88dsf-53.4 sysvinit_2.88dsf-53.4 sysvinit-utils_2.88dsf-53.4 tar_1.27.1-2 tcpd_7.6.q-25 tzdata_2014g-1 ucf_3.0030 udev_208-8 util-linux_2.20.1-5.8 vim_2:7.4.430-1 vim-common_2:7.4.430-1 vim-runtime_2:7.4.430-1 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-2 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Mon Nov 11 14:13:41 2013 UTC using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./biococoa_2.2.2-2.dsc dpkg-source: info: extracting biococoa in biococoa-2.2.2 dpkg-source: info: unpacking biococoa_2.2.2.orig.tar.gz dpkg-source: info: unpacking biococoa_2.2.2-2.debian.tar.gz dpkg-source: info: applying link-libs.patch Check disc space ──────────────── Sufficient free space for build Hack binNMU version ─────────────────── Created changelog entry for binNMU version 2.2.2-2clang1 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-e4c724c8-e10c-4046-bfd5-70e11e2c3585 SCHROOT_UID=1000 SCHROOT_USER=user SHELL=/bin/sh USER=user dpkg-buildpackage ───────────────── dpkg-buildpackage: source package biococoa dpkg-buildpackage: source version 2.2.2-2clang1 dpkg-buildpackage: source distribution unstable dpkg-source --before-build biococoa-2.2.2 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean test -x debian/rules rm -f debian/stamp-makefile-build debian/stamp-makefile-install GNUSTEP_MAKEFILES=/usr/share/GNUstep/Makefiles /usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro -Wl,-z,defs -Wl,--as-needed" OPTFLAG=-O2 -k clean make[1]: Entering directory '/«PKGBUILDDIR»' This is gnustep-make 2.6.6. Type 'make print-gnustep-make-help' for help. rm -rf ./*~ ./obj Making clean in subprojects of framework BioCocoa... make[2]: Entering directory '/«PKGBUILDDIR»/BCFoundation' rm -rf ./*~ ./obj Making clean in subprojects of subproject BCFoundation... make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCAlignment' rm -rf ./*~ ./obj make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCAlignment' make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCAnalysis' rm -rf ./*~ ./obj make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCAnalysis' make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCGeneExpression' rm -rf ./*~ ./obj make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCGeneExpression' make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCGeneticCode' rm -rf ./*~ ./obj make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCGeneticCode' make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCProteinStructure' rm -rf ./*~ ./obj make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCProteinStructure' make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCSequence' rm -rf ./*~ ./obj make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCSequence' make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCSequenceIO' rm -rf ./*~ ./obj make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCSequenceIO' make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCSymbol' rm -rf ./*~ ./obj make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCSymbol' make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCTools' rm -rf ./*~ ./obj make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCTools' make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCUtils' rm -rf ./*~ ./obj make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCUtils' make[2]: Leaving directory '/«PKGBUILDDIR»/BCFoundation' Making clean for framework BioCocoa... rm -rf \ \ ./BioCocoa.framework ./derived_src make[1]: Leaving directory '/«PKGBUILDDIR»' dh_clean rm -f debian/libbiococoa2.install rm -f debian/libbiococoa-dev.install debian/rules build-arch test -x debian/rules mkdir -p "." GNUSTEP_MAKEFILES=/usr/share/GNUstep/Makefiles /usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro -Wl,-z,defs -Wl,--as-needed" OPTFLAG=-O2 make[1]: Entering directory '/«PKGBUILDDIR»' This is gnustep-make 2.6.6. Type 'make print-gnustep-make-help' for help. Making build-headers in subprojects of framework BioCocoa... make[2]: Entering directory '/«PKGBUILDDIR»/BCFoundation' Making build-headers in subprojects of subproject BCFoundation... make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCAlignment' Making build-headers for subproject BCAlignment... /usr/share/GNUstep/Makefiles/mkinstalldirs ../../BioCocoa.framework/Versions/2/Headers /usr/bin/install -c -p -m 644 BCPairwiseAlignment.h ../../BioCocoa.framework/Versions/2/Headers/BCPairwiseAlignment.h /usr/bin/install -c -p -m 644 BCScoreMatrix.h ../../BioCocoa.framework/Versions/2/Headers/BCScoreMatrix.h /usr/bin/install -c -p -m 644 BCSequenceAlignment.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceAlignment.h make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCAlignment' make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCAnalysis' Making build-headers for subproject BCAnalysis... /usr/bin/install -c -p -m 644 BCMCP.h ../../BioCocoa.framework/Versions/2/Headers/BCMCP.h /usr/bin/install -c -p -m 644 BCSuffixArray.h ../../BioCocoa.framework/Versions/2/Headers/BCSuffixArray.h make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCAnalysis' make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCGeneExpression' Making build-headers for subproject BCGeneExpression... /usr/bin/install -c -p -m 644 BCSeries.h ../../BioCocoa.framework/Versions/2/Headers/BCSeries.h /usr/bin/install -c -p -m 644 BCSample.h ../../BioCocoa.framework/Versions/2/Headers/BCSample.h /usr/bin/install -c -p -m 644 BCPlatform.h ../../BioCocoa.framework/Versions/2/Headers/BCPlatform.h /usr/bin/install -c -p -m 644 BCParseSOFT.h ../../BioCocoa.framework/Versions/2/Headers/BCParseSOFT.h make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCGeneExpression' make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCGeneticCode' Making build-headers for subproject BCGeneticCode... /usr/bin/install -c -p -m 644 BCCodonDNA.h ../../BioCocoa.framework/Versions/2/Headers/BCCodonDNA.h /usr/bin/install -c -p -m 644 BCCodon.h ../../BioCocoa.framework/Versions/2/Headers/BCCodon.h /usr/bin/install -c -p -m 644 BCCodonRNA.h ../../BioCocoa.framework/Versions/2/Headers/BCCodonRNA.h /usr/bin/install -c -p -m 644 BCGeneticCode.h ../../BioCocoa.framework/Versions/2/Headers/BCGeneticCode.h make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCGeneticCode' make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCProteinStructure' Making build-headers for subproject BCProteinStructure... /usr/bin/install -c -p -m 644 BCAtom.h ../../BioCocoa.framework/Versions/2/Headers/BCAtom.h /usr/bin/install -c -p -m 644 BCProteinStructure.h ../../BioCocoa.framework/Versions/2/Headers/BCProteinStructure.h /usr/bin/install -c -p -m 644 BCSecondaryStructure.h ../../BioCocoa.framework/Versions/2/Headers/BCSecondaryStructure.h /usr/bin/install -c -p -m 644 BCChain.h ../../BioCocoa.framework/Versions/2/Headers/BCChain.h /usr/bin/install -c -p -m 644 BCResidue.h ../../BioCocoa.framework/Versions/2/Headers/BCResidue.h /usr/bin/install -c -p -m 644 BCSequenceStructure.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceStructure.h make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCProteinStructure' make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCSequence' Making build-headers for subproject BCSequence... /usr/bin/install -c -p -m 644 BCAnnotation.h ../../BioCocoa.framework/Versions/2/Headers/BCAnnotation.h /usr/bin/install -c -p -m 644 BCSequence.h ../../BioCocoa.framework/Versions/2/Headers/BCSequence.h /usr/bin/install -c -p -m 644 BCSequenceArray.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceArray.h /usr/bin/install -c -p -m 644 BCSequenceCodon.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceCodon.h make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCSequence' make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCSequenceIO' Making build-headers for subproject BCSequenceIO... /usr/bin/install -c -p -m 644 BCSequenceReader.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceReader.h /usr/bin/install -c -p -m 644 BCSequenceWriter.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceWriter.h /usr/bin/install -c -p -m 644 BCCachedSequenceFile.h ../../BioCocoa.framework/Versions/2/Headers/BCCachedSequenceFile.h /usr/bin/install -c -p -m 644 BCCachedFastaFile.h ../../BioCocoa.framework/Versions/2/Headers/BCCachedFastaFile.h make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCSequenceIO' make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCSymbol' Making build-headers for subproject BCSymbol... /usr/bin/install -c -p -m 644 BCAminoAcid.h ../../BioCocoa.framework/Versions/2/Headers/BCAminoAcid.h /usr/bin/install -c -p -m 644 BCNucleotide.h ../../BioCocoa.framework/Versions/2/Headers/BCNucleotide.h /usr/bin/install -c -p -m 644 BCSymbol.h ../../BioCocoa.framework/Versions/2/Headers/BCSymbol.h /usr/bin/install -c -p -m 644 BCNucleotideDNA.h ../../BioCocoa.framework/Versions/2/Headers/BCNucleotideDNA.h /usr/bin/install -c -p -m 644 BCNucleotideRNA.h ../../BioCocoa.framework/Versions/2/Headers/BCNucleotideRNA.h /usr/bin/install -c -p -m 644 BCSymbolSet.h ../../BioCocoa.framework/Versions/2/Headers/BCSymbolSet.h make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCSymbol' make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCTools' Making build-headers for subproject BCTools... /usr/bin/install -c -p -m 644 BCSequenceTool.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceTool.h /usr/bin/install -c -p -m 644 BCToolDigest.h ../../BioCocoa.framework/Versions/2/Headers/BCToolDigest.h /usr/bin/install -c -p -m 644 BCToolHydropathyCalculator.h ../../BioCocoa.framework/Versions/2/Headers/BCToolHydropathyCalculator.h /usr/bin/install -c -p -m 644 BCToolMassCalculator.h ../../BioCocoa.framework/Versions/2/Headers/BCToolMassCalculator.h /usr/bin/install -c -p -m 644 BCToolComplement.h ../../BioCocoa.framework/Versions/2/Headers/BCToolComplement.h /usr/bin/install -c -p -m 644 BCToolSequenceFinder.h ../../BioCocoa.framework/Versions/2/Headers/BCToolSequenceFinder.h /usr/bin/install -c -p -m 644 BCToolSymbolCounter.h ../../BioCocoa.framework/Versions/2/Headers/BCToolSymbolCounter.h /usr/bin/install -c -p -m 644 BCToolTranslator.h ../../BioCocoa.framework/Versions/2/Headers/BCToolTranslator.h /usr/bin/install -c -p -m 644 BCToolTranslatorDNA.h ../../BioCocoa.framework/Versions/2/Headers/BCToolTranslatorDNA.h make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCTools' make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCUtils' Making build-headers for subproject BCUtils... /usr/bin/install -c -p -m 644 BCDataMatrix.h ../../BioCocoa.framework/Versions/2/Headers/BCDataMatrix.h /usr/bin/install -c -p -m 644 BCUtilData.h ../../BioCocoa.framework/Versions/2/Headers/BCUtilData.h /usr/bin/install -c -p -m 644 BCUtilStrings.h ../../BioCocoa.framework/Versions/2/Headers/BCUtilStrings.h make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCUtils' Making build-headers for subproject BCFoundation... /usr/bin/install -c -p -m 644 BCFoundation.h ../BioCocoa.framework/Versions/2/Headers/BCFoundation.h /usr/bin/install -c -p -m 644 BCFoundationDefines.h ../BioCocoa.framework/Versions/2/Headers/BCFoundationDefines.h /usr/bin/install -c -p -m 644 BCStringDefinitions.h ../BioCocoa.framework/Versions/2/Headers/BCStringDefinitions.h /usr/bin/install -c -p -m 644 BCPreferences.h ../BioCocoa.framework/Versions/2/Headers/BCPreferences.h make[2]: Leaving directory '/«PKGBUILDDIR»/BCFoundation' Making build-headers for framework BioCocoa... /usr/share/GNUstep/Makefiles/mkinstalldirs ./derived_src; \ touch derived_src/.stamp /usr/share/GNUstep/Makefiles/mkinstalldirs BioCocoa.framework/Versions/2/Resources cd ./BioCocoa.framework/Versions; \ rm -f Current; \ ln -s 2 Current cd ./BioCocoa.framework; \ if [ ! -h "Resources" ]; then \ rm -f Resources; \ ln -s Versions/Current/Resources Resources; \ fi; \ if [ ! -h "Headers" ]; then \ rm -f Headers; \ ln -s Versions/Current/Headers Headers; \ fi cd ./derived_src; \ if [ ! -h "BioCocoa" ]; then \ rm -f ./BioCocoa; \ ln -s ../BioCocoa.framework/Headers \ ./BioCocoa; \ fi cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all in subprojects of framework BioCocoa... make[2]: Entering directory '/«PKGBUILDDIR»/BCFoundation' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all in subprojects of subproject BCFoundation... make[3]: Entering directory '/«PKGBUILDDIR»/BCFoundation/BCAlignment' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCAlignment... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCAlignment.obj/ gcc BCPairwiseAlignment.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fgnu-runtime -fconstant-string-class=NSConstantString -fexec-charset=UTF-8 -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCAlignment.obj/BCPairwiseAlignment.m.o gcc BCScoreMatrix.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fgnu-runtime -fconstant-string-class=NSConstantString -fexec-charset=UTF-8 -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCAlignment.obj/BCScoreMatrix.m.o gcc BCSequenceAlignment.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fgnu-runtime -fconstant-string-class=NSConstantString -fexec-charset=UTF-8 -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCAlignment.obj/BCSequenceAlignment.m.o gcc -nostdlib -r -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCAlignment.obj/BCPairwiseAlignment.m.o obj/BCAlignment.obj/BCScoreMatrix.m.o obj/BCAlignment.obj/BCSequenceAlignment.m.o ; clang: warning: argument unused during compilation: '-r' clang: warning: argument unused during compilation: '-pthread' /usr/bin/ld: warning: cannot find entry symbol _start; defaulting to 00000000004001c0 obj/BCAlignment.obj/BCPairwiseAlignment.m.o: In function `_c_BCSequenceAlignment_PairwiseAlignment_needlemanWunschAlignmentWithSequences_properties_': BCPairwiseAlignment.m:(.text+0x17): undefined reference to `BCSubstitutionMatrixProperty' BCPairwiseAlignment.m:(.text+0x2c): undefined reference to `objc_msg_lookup' BCPairwiseAlignment.m:(.text+0x4e): undefined reference to `objc_msg_lookup' BCPairwiseAlignment.m:(.text+0x66): undefined reference to `objc_msg_lookup' BCPairwiseAlignment.m:(.text+0x88): undefined reference to `objc_msg_lookup' BCPairwiseAlignment.m:(.text+0xa5): undefined reference to `objc_msg_lookup' obj/BCAlignment.obj/BCPairwiseAlignment.m.o:BCPairwiseAlignment.m:(.text+0xbd): more undefined references to `objc_msg_lookup' follow obj/BCAlignment.obj/BCPairwiseAlignment.m.o: In function `_c_BCSequenceAlignment_PairwiseAlignment_needlemanWunschAlignmentWithSequences_properties_': BCPairwiseAlignment.m:(.text+0xe7): undefined reference to `BCDefaultGapPenaltyProperty' BCPairwiseAlignment.m:(.text+0xfc): undefined reference to `objc_msg_lookup' BCPairwiseAlignment.m:(.text+0x11c): undefined reference to `objc_msg_lookup' BCPairwiseAlignment.m:(.text+0x13a): undefined reference to `objc_msg_lookup' BCPairwiseAlignment.m:(.text+0x155): undefined reference to `objc_msg_lookup' BCPairwiseAlignment.m:(.text+0x17c): undefined reference to `malloc' BCPairwiseAlignment.m:(.text+0x18c): undefined reference to `malloc' BCPairwiseAlignment.m:(.text+0x1bd): undefined reference to `objc_msg_lookup' BCPairwiseAlignment.m:(.text+0x2df): undefined reference to `objc_msg_lookup' BCPairwiseAlignment.m:(.text+0x3c5): undefined reference to `malloc' BCPairwiseAlignment.m:(.text+0x3d2): undefined reference to `malloc' BCPairwiseAlignment.m:(.text+0x4b2): undefined reference to `malloc' BCPairwiseAlignment.m:(.text+0x4bd): undefined reference to `malloc' BCPairwiseAlignment.m:(.text+0x930): undefined reference to `objc_lookup_class' BCPairwiseAlignment.m:(.text+0x944): undefined reference to `objc_lookup_class' BCPairwiseAlignment.m:(.text+0x959): undefined reference to `objc_msg_lookup' BCPairwiseAlignment.m:(.text+0x97f): undefined reference to `objc_msg_lookup' BCPairwiseAlignment.m:(.text+0x99d): undefined reference to `objc_lookup_class' BCPairwiseAlignment.m:(.text+0x9ae): undefined reference to `objc_lookup_class' BCPairwiseAlignment.m:(.text+0x9bc): undefined reference to `objc_msg_lookup' BCPairwiseAlignment.m:(.text+0x9d8): undefined reference to `objc_msg_lookup' BCPairwiseAlignment.m:(.text+0x9f4): undefined reference to `objc_lookup_class' BCPairwiseAlignment.m:(.text+0xa09): undefined reference to `objc_msg_lookup' BCPairwiseAlignment.m:(.text+0xa22): undefined reference to `objc_lookup_class' BCPairwiseAlignment.m:(.text+0xa37): undefined reference to `objc_msg_lookup' BCPairwiseAlignment.m:(.text+0xa64): undefined reference to `objc_msg_lookup' BCPairwiseAlignment.m:(.text+0xa84): undefined reference to `objc_msg_lookup' obj/BCAlignment.obj/BCPairwiseAlignment.m.o: In function `.objc_load_function': BCPairwiseAlignment.m:(.text+0xaca): undefined reference to `__objc_exec_class' obj/BCAlignment.obj/BCPairwiseAlignment.m.o:(.data.rel.ro.__objc_class_ref_BCSequence[__objc_class_ref_BCSequence]+0x0): undefined reference to `__objc_class_name_BCSequence' obj/BCAlignment.obj/BCPairwiseAlignment.m.o:(.data.rel.ro.__objc_class_ref_NSString[__objc_class_ref_NSString]+0x0): undefined reference to `__objc_class_name_NSString' obj/BCAlignment.obj/BCPairwiseAlignment.m.o:(.data.rel.ro.__objc_class_ref_NSArray[__objc_class_ref_NSArray]+0x0): undefined reference to `__objc_class_name_NSArray' obj/BCAlignment.obj/BCScoreMatrix.m.o: In function `_i_BCScoreMatrix__initWithSymbolSet_matrix_': BCScoreMatrix.m:(.text+0x39): undefined reference to `objc_msg_lookup_super' BCScoreMatrix.m:(.text+0x5b): undefined reference to `objc_msg_lookup' BCScoreMatrix.m:(.text+0x7c): undefined reference to `objc_msg_lookup' BCScoreMatrix.m:(.text+0x92): undefined reference to `malloc' BCScoreMatrix.m:(.text+0xa6): undefined reference to `memcpy' obj/BCAlignment.obj/BCScoreMatrix.m.o: In function `_i_BCScoreMatrix__containsSymbol_': BCScoreMatrix.m:(.text+0xda): undefined reference to `objc_msg_lookup' obj/BCAlignment.obj/BCScoreMatrix.m.o: In function `_i_BCScoreMatrix__substituteSymbol_forSymbol_': BCScoreMatrix.m:(.text+0x10c): undefined reference to `objc_msg_lookup' BCScoreMatrix.m:(.text+0x12d): undefined reference to `objc_msg_lookup' BCScoreMatrix.m:(.text+0x14a): undefined reference to `objc_msg_lookup' BCScoreMatrix.m:(.text+0x160): undefined reference to `objc_msg_lookup' obj/BCAlignment.obj/BCScoreMatrix.m.o:BCScoreMatrix.m:(.text+0x17d): more undefined references to `objc_msg_lookup' follow obj/BCAlignment.obj/BCScoreMatrix.m.o: In function `_i_BCScoreMatrix__dealloc': BCScoreMatrix.m:(.text+0x1fd): undefined reference to `objc_msg_lookup_super' obj/BCAlignment.obj/BCScoreMatrix.m.o: In function `.objc_load_function': BCScoreMatrix.m:(.text+0x22a): undefined reference to `__objc_exec_class' obj/BCAlignment.obj/BCScoreMatrix.m.o:(.data.rel.ro.__objc_class_ref_NSObject[__objc_class_ref_NSObject]+0x0): undefined reference to `__objc_class_name_NSObject' obj/BCAlignment.obj/BCSequenceAlignment.m.o: In function `_i_BCSequenceAlignment__initWithSequenceArray_': BCSequenceAlignment.m:(.text+0x32): undefined reference to `objc_msg_lookup_super' BCSequenceAlignment.m:(.text+0x54): undefined reference to `objc_msg_lookup' obj/BCAlignment.obj/BCSequenceAlignment.m.o: In function `_i_BCSequenceAlignment__dealloc': BCSequenceAlignment.m:(.text+0x9e): undefined reference to `objc_msg_lookup' BCSequenceAlignment.m:(.text+0xcd): undefined reference to `objc_msg_lookup_super' obj/BCAlignment.obj/BCSequenceAlignment.m.o: In function `_i_BCSequenceAlignment_AlignmentQuerying_sequenceAtIndex_': BCSequenceAlignment.m:(.text+0x10a): undefined reference to `objc_msg_lookup' obj/BCAlignment.obj/BCSequenceAlignment.m.o: In function `_i_BCSequenceAlignment_AlignmentQuerying_length': BCSequenceAlignment.m:(.text+0x152): undefined reference to `objc_msg_lookup' BCSequenceAlignment.m:(.text+0x171): undefined reference to `objc_msg_lookup' obj/BCAlignment.obj/BCSequenceAlignment.m.o: In function `_i_BCSequenceAlignment_AlignmentQuerying_sequenceCount': BCSequenceAlignment.m:(.text+0x1a6): undefined reference to `objc_msg_lookup' obj/BCAlignment.obj/BCSequenceAlignment.m.o: In function `.objc_load_function': BCSequenceAlignment.m:(.text+0x1da): undefined reference to `__objc_exec_class' clang: error: linker command failed with exit code 1 (use -v to see invocation) make[5]: *** [obj/subproject.o] Error 1 /usr/share/GNUstep/Makefiles/Instance/subproject.make:61: recipe for target 'obj/subproject.o' failed make[4]: *** [internal-subproject-all_] Error 2 /usr/share/GNUstep/Makefiles/Instance/subproject.make:45: recipe for target 'internal-subproject-all_' failed make[3]: *** [BCAlignment.all.subproject.variables] Error 2 /usr/share/GNUstep/Makefiles/Master/rules.make:298: recipe for target 'BCAlignment.all.subproject.variables' failed make[3]: Leaving directory '/«PKGBUILDDIR»/BCFoundation/BCAlignment' make[2]: *** [BCFoundation.all.subproject.variables] Error 2 /usr/share/GNUstep/Makefiles/Master/rules.make:298: recipe for target 'BCFoundation.all.subproject.variables' failed make[2]: Leaving directory '/«PKGBUILDDIR»/BCFoundation' make[1]: *** [BioCocoa.all.framework.variables] Error 2 make: *** [debian/stamp-makefile-build] Error 2 /usr/share/GNUstep/Makefiles/Master/rules.make:298: recipe for target 'BioCocoa.all.framework.variables' failed make[1]: Leaving directory '/«PKGBUILDDIR»' /usr/share/cdbs/1/class/makefile.mk:47: recipe for target 'debian/stamp-makefile-build' failed dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20140904-1921 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 2552 Build-Time: 6 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 21 Job: biococoa_2.2.2-2 Machine Architecture: amd64 Package: biococoa Package-Time: 57 Source-Version: 2.2.2-2 Space: 2552 Status: attempted Version: 2.2.2-2clang1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20140904-1921 Build needed 00:00:57, 2552k disc space DC-Status: Failed 58.453658399s DC-Time-Estimation: 58.453658399 versus expected 212 (r/m: 2.6268046484431298 ; m: 58.453658399)