RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux z13-025 4.3.0-0-generic #9 SMP Tue Dec 1 18:12:15 CET 2015 s390x Buildd toolchain package versions: launchpad-buildd_136 python-lpbuildd_136 sbuild_0.66.0-5ubuntu1 dpkg-dev_1.18.3ubuntu1 python-debian_0.1.27ubuntu1. Syncing the system clock with the buildd NTP service... 4 Dec 18:39:21 ntpdate[26920]: adjust time server 10.211.37.1 offset 0.000097 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-8372240', '/home/buildd/filecache-default/a064a0e569947625a7404b763659cb5b35808b40'] Unpacking chroot for build PACKAGEBUILD-8372240 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-8372240'] Mounting chroot for build PACKAGEBUILD-8372240 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-8372240', 'deb http://ftpmaster.internal/ubuntu xenial main universe'] Overriding sources.list in build-PACKAGEBUILD-8372240 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-8372240', 's390x'] Updating debian chroot for build PACKAGEBUILD-8372240 Get:1 http://ftpmaster.internal xenial InRelease [227 kB] Ign http://archive-team.internal xenial InRelease Ign http://archive-team.internal xenial Release.gpg Hit http://archive-team.internal xenial Release Ign http://archive-team.internal xenial/main s390x Packages/DiffIndex Hit http://archive-team.internal xenial/main Translation-en Hit http://archive-team.internal xenial/main s390x Packages Get:2 http://ftpmaster.internal xenial/main s390x Packages [1279 kB] Get:3 http://ftpmaster.internal xenial/universe s390x Packages [4438 kB] Get:4 http://ftpmaster.internal xenial/main Translation-en [848 kB] Get:5 http://ftpmaster.internal xenial/universe Translation-en [4728 kB] Fetched 11.5 MB in 5s (2045 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: libc6 linux-libc-dev 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5251 kB of archives. After this operation, 1024 B disk space will be freed. WARNING: The following packages cannot be authenticated! libc6 Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ xenial/main linux-libc-dev s390x 4.3.0-1.10 [805 kB] Get:2 http://archive-team.internal/bootstrap/s390x-stage2/ xenial/main libc6 s390x 2.21-0ubuntu4 [4446 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 5251 kB in 6s (865 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11407 files and directories currently installed.) Preparing to unpack .../libc6_2.21-0ubuntu4_s390x.deb ... Unpacking libc6:s390x (2.21-0ubuntu4) over (2.21-0ubuntu4) ... Setting up libc6:s390x (2.21-0ubuntu4) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11407 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_4.3.0-1.10_s390x.deb ... Unpacking linux-libc-dev:s390x (4.3.0-1.10) over (4.3.0-0.9) ... Setting up linux-libc-dev:s390x (4.3.0-1.10) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-8372240', 's390x', 'xenial', '-c', 'chroot:autobuild', '--arch=s390x', '--dist=xenial', '--purge=never', '--nolog', 'biococoa_2.2.2-2.dsc'] Initiating build PACKAGEBUILD-8372240 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.3.0-0-generic #9 SMP Tue Dec 1 18:12:15 CET 2015 s390x sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on z13-025.buildd +==============================================================================+ | biococoa 2.2.2-2 (s390x) 04 Dec 2015 18:39 | +==============================================================================+ Package: biococoa Version: 2.2.2-2 Source Version: 2.2.2-2 Distribution: xenial Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/biococoa-jcZHpT/biococoa-2.2.2' with '<>' I: NOTICE: Log filtering will replace 'build/biococoa-jcZHpT' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-8372240/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- biococoa_2.2.2-2.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-XSPBb_/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign file: ./ InRelease Ign file: ./ Release.gpg Get:1 file: ./ Release [2119 B] Ign file: ./ Translation-en Reading package lists... 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/776 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 debconf: delaying package configuration, since apt-utils is not installed Authentication warning overridden. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11407 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: cdbs, gnustep-make, debhelper (>= 9), libgnustep-base-dev Filtered Build-Depends: cdbs, gnustep-make, debhelper (>= 9), libgnustep-base-dev dpkg-deb: building package 'sbuild-build-depends-biococoa-dummy' in '/<>/resolver-Z7FGhA/apt_archive/sbuild-build-depends-biococoa-dummy.deb'. Ign file: ./ InRelease Ign file: ./ Release.gpg Get:1 file: ./ Release [2119 B] Ign file: ./ Translation-en Reading package lists... 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: autoconf automake autotools-dev bsdmainutils cdbs debhelper dh-strip-nondeterminism dh-translations file gettext gettext-base gnustep-base-common gnustep-base-runtime gnustep-common gnustep-make gobjc gobjc-5 groff-base intltool intltool-debian libarchive-zip-perl libasprintf0v5 libavahi-client3 libavahi-common-data libavahi-common3 libcroco3 libdbus-1-3 libencode-locale-perl libexpat1 libfile-listing-perl libfile-stripnondeterminism-perl libglib2.0-0 libgnustep-base-dev libgnustep-base1.24 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libicu55 libio-html-perl libio-socket-ssl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic1 libnet-http-perl libnet-ssleay-perl libobjc-5-dev libobjc4 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libtimedate-perl libunistring0 liburi-perl libwww-perl libwww-robotrules-perl libxml-parser-perl libxml2 libxslt1.1 m4 man-db mime-support netbase po-debconf python python-minimal python-scour python2.7 python2.7-minimal Suggested packages: autoconf-archive gnu-standards autoconf-doc libtool wamerican wordlist whois vacation devscripts dh-make gettext-doc gnustep-base-doc gnustep-make-doc gobjc-multilib gobjc-5-multilib gcc-5-doc libobjc4-dbg groff libdata-dump-perl libcrypt-ssleay-perl libauthen-ntlm-perl less www-browser libmail-box-perl python-doc python-tk python-rsvg python-cairo python2.7-doc binfmt-support Recommended packages: curl wget lynx-cur libasprintf-dev libgettextpo-dev dbus libglib2.0-data shared-mime-info xdg-user-dirs libhtml-format-perl libhtml-form-perl libhttp-daemon-perl libmailtools-perl xml-core ifupdown libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autotools-dev bsdmainutils cdbs debhelper dh-strip-nondeterminism dh-translations file gettext gettext-base gnustep-base-common gnustep-base-runtime gnustep-common gnustep-make gobjc gobjc-5 groff-base intltool intltool-debian libarchive-zip-perl libasprintf0v5 libavahi-client3 libavahi-common-data libavahi-common3 libcroco3 libdbus-1-3 libencode-locale-perl libexpat1 libfile-listing-perl libfile-stripnondeterminism-perl libglib2.0-0 libgnustep-base-dev libgnustep-base1.24 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libicu55 libio-html-perl libio-socket-ssl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic1 libnet-http-perl libnet-ssleay-perl libobjc-5-dev libobjc4 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libtimedate-perl libunistring0 liburi-perl libwww-perl libwww-robotrules-perl libxml-parser-perl libxml2 libxslt1.1 m4 man-db mime-support netbase po-debconf python python-minimal python-scour python2.7 python2.7-minimal sbuild-build-depends-biococoa-dummy 0 upgraded, 75 newly installed, 0 to remove and 0 not upgraded. Need to get 46.9 MB/46.9 MB of archives. After this operation, 222 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libasprintf0v5 groff-base libpython2.7-minimal python-minimal libpython2.7-stdlib python2.7 libpython-stdlib python file libdbus-1-3 libfile-stripnondeterminism-perl dh-strip-nondeterminism libhtml-parser-perl libnet-ssleay-perl libxml-parser-perl libobjc4 libobjc-5-dev gobjc-5 sbuild-build-depends-biococoa-dummy Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ xenial/main libasprintf0v5 s390x 0.19.4-1ubuntu3 [6638 B] Get:2 http://ftpmaster.internal/ubuntu/ xenial/main groff-base s390x 1.22.3-4 [1199 kB] Get:3 http://ftpmaster.internal/ubuntu/ xenial/main bsdmainutils s390x 9.0.6ubuntu1 [178 kB] Get:4 http://ftpmaster.internal/ubuntu/ xenial/main libpipeline1 s390x 1.4.1-1 [24.7 kB] Get:5 http://ftpmaster.internal/ubuntu/ xenial/main man-db s390x 2.7.5-1 [850 kB] Get:6 http://ftpmaster.internal/ubuntu/ xenial/main libpython2.7-minimal s390x 2.7.10-4ubuntu2 [337 kB] Get:7 http://ftpmaster.internal/ubuntu/ xenial/main python2.7-minimal s390x 2.7.10-4ubuntu2 [1048 kB] Get:8 http://ftpmaster.internal/ubuntu/ xenial/main python-minimal s390x 2.7.9-1 [28.2 kB] Get:9 http://ftpmaster.internal/ubuntu/ xenial/main mime-support all 3.59ubuntu1 [31.0 kB] Get:10 http://ftpmaster.internal/ubuntu/ xenial/main libexpat1 s390x 2.1.0-7 [65.4 kB] Get:11 http://ftpmaster.internal/ubuntu/ xenial/main libpython2.7-stdlib s390x 2.7.10-4ubuntu2 [1761 kB] Get:12 http://ftpmaster.internal/ubuntu/ xenial/main python2.7 s390x 2.7.10-4ubuntu2 [210 kB] Get:13 http://ftpmaster.internal/ubuntu/ xenial/main libpython-stdlib s390x 2.7.9-1 [7720 B] Get:14 http://ftpmaster.internal/ubuntu/ xenial/main python s390x 2.7.9-1 [137 kB] Get:15 http://ftpmaster.internal/ubuntu/ xenial/main libmagic1 s390x 1:5.25-2ubuntu1 [214 kB] Get:16 http://ftpmaster.internal/ubuntu/ xenial/main file s390x 1:5.25-2ubuntu1 [21.5 kB] Get:17 http://ftpmaster.internal/ubuntu/ xenial/main netbase all 5.3 [12.9 kB] Get:18 http://ftpmaster.internal/ubuntu/ xenial/main gettext-base s390x 0.19.4-1ubuntu3 [48.3 kB] Get:19 http://ftpmaster.internal/ubuntu/ xenial/main libdbus-1-3 s390x 1.10.4-1ubuntu2 [155 kB] Get:20 http://ftpmaster.internal/ubuntu/ xenial/main libglib2.0-0 s390x 2.47.3-3 [1041 kB] Get:21 http://ftpmaster.internal/ubuntu/ xenial/main libicu55 s390x 55.1-6ubuntu1 [7478 kB] Get:22 http://ftpmaster.internal/ubuntu/ xenial/main libxml2 s390x 2.9.2+zdfsg1-4ubuntu1 [640 kB] Get:23 http://ftpmaster.internal/ubuntu/ xenial/main libsigsegv2 s390x 2.10-4 [13.4 kB] Get:24 http://ftpmaster.internal/ubuntu/ xenial/main m4 s390x 1.4.17-4 [192 kB] Get:25 http://ftpmaster.internal/ubuntu/ xenial/main autoconf all 2.69-9 [321 kB] Get:26 http://ftpmaster.internal/ubuntu/ xenial/main autotools-dev all 20150820.1 [39.8 kB] Get:27 http://ftpmaster.internal/ubuntu/ xenial/main automake all 1:1.15-1ubuntu1 [511 kB] Get:28 http://ftpmaster.internal/ubuntu/ xenial/main libcroco3 s390x 0.6.9-1 [77.2 kB] Get:29 http://ftpmaster.internal/ubuntu/ xenial/main libunistring0 s390x 0.9.3-5.2ubuntu1 [262 kB] Get:30 http://ftpmaster.internal/ubuntu/ xenial/main gettext s390x 0.19.4-1ubuntu3 [838 kB] Get:31 http://ftpmaster.internal/ubuntu/ xenial/main intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:32 http://ftpmaster.internal/ubuntu/ xenial/main po-debconf all 1.0.18 [234 kB] Get:33 http://ftpmaster.internal/ubuntu/ xenial/main libarchive-zip-perl all 1.53-1 [87.0 kB] Get:34 http://ftpmaster.internal/ubuntu/ xenial/main libfile-stripnondeterminism-perl all 0.014-1 [10.1 kB] Get:35 http://ftpmaster.internal/ubuntu/ xenial/main libtimedate-perl all 2.3000-2 [37.5 kB] Get:36 http://ftpmaster.internal/ubuntu/ xenial/main dh-strip-nondeterminism all 0.014-1 [5596 B] Get:37 http://ftpmaster.internal/ubuntu/ xenial/main debhelper all 9.20151126ubuntu1 [741 kB] Get:38 http://ftpmaster.internal/ubuntu/ xenial/main liburi-perl all 1.69-1 [84.5 kB] Get:39 http://ftpmaster.internal/ubuntu/ xenial/main libencode-locale-perl all 1.05-1 [12.3 kB] Get:40 http://ftpmaster.internal/ubuntu/ xenial/main libhttp-date-perl all 6.02-1 [10.4 kB] Get:41 http://ftpmaster.internal/ubuntu/ xenial/main libfile-listing-perl all 6.04-1 [9774 B] Get:42 http://ftpmaster.internal/ubuntu/ xenial/main libhtml-tagset-perl all 3.20-2 [13.5 kB] Get:43 http://ftpmaster.internal/ubuntu/ xenial/main libhtml-parser-perl s390x 3.71-2 [89.8 kB] Get:44 http://ftpmaster.internal/ubuntu/ xenial/main libhtml-tree-perl all 5.03-2 [197 kB] Get:45 http://ftpmaster.internal/ubuntu/ xenial/main libio-html-perl all 1.001-1 [14.9 kB] Get:46 http://ftpmaster.internal/ubuntu/ xenial/main liblwp-mediatypes-perl all 6.02-1 [21.7 kB] Get:47 http://ftpmaster.internal/ubuntu/ xenial/main libhttp-message-perl all 6.11-1 [74.3 kB] Get:48 http://ftpmaster.internal/ubuntu/ xenial/main libhttp-cookies-perl all 6.01-1 [17.2 kB] Get:49 http://ftpmaster.internal/ubuntu/ xenial/main libhttp-negotiate-perl all 6.00-2 [13.4 kB] Get:50 http://ftpmaster.internal/ubuntu/ xenial/main libnet-ssleay-perl s390x 1.72-1 [253 kB] Get:51 http://ftpmaster.internal/ubuntu/ xenial/main libio-socket-ssl-perl all 2.021-1 [161 kB] Get:52 http://ftpmaster.internal/ubuntu/ xenial/main libnet-http-perl all 6.09-1 [24.0 kB] Get:53 http://ftpmaster.internal/ubuntu/ xenial/main liblwp-protocol-https-perl all 6.06-2 [8682 B] Get:54 http://ftpmaster.internal/ubuntu/ xenial/main libwww-robotrules-perl all 6.01-1 [14.1 kB] Get:55 http://ftpmaster.internal/ubuntu/ xenial/main libwww-perl all 6.13-1 [146 kB] Get:56 http://ftpmaster.internal/ubuntu/ xenial/main libxml-parser-perl s390x 2.44-1 [204 kB] Get:57 http://ftpmaster.internal/ubuntu/ xenial/main intltool all 0.51.0-1 [44.7 kB] Get:58 http://ftpmaster.internal/ubuntu/ xenial/main dh-translations all 123 [21.9 kB] Get:59 http://ftpmaster.internal/ubuntu/ xenial/main python-scour all 0.26-3ubuntu1 [40.4 kB] Get:60 http://ftpmaster.internal/ubuntu/ xenial/main cdbs all 0.4.130ubuntu2 [42.8 kB] Get:61 http://ftpmaster.internal/ubuntu/ xenial/universe gnustep-common s390x 2.6.6-3 [47.2 kB] Get:62 http://ftpmaster.internal/ubuntu/ xenial/universe gnustep-base-common all 1.24.7-1build1 [61.4 kB] Get:63 http://ftpmaster.internal/ubuntu/ xenial/main libavahi-common-data s390x 0.6.32~rc+dfsg-1ubuntu2 [21.9 kB] Get:64 http://ftpmaster.internal/ubuntu/ xenial/main libavahi-common3 s390x 0.6.32~rc+dfsg-1ubuntu2 [20.4 kB] Get:65 http://ftpmaster.internal/ubuntu/ xenial/main libavahi-client3 s390x 0.6.32~rc+dfsg-1ubuntu2 [22.8 kB] Get:66 http://ftpmaster.internal/ubuntu/ xenial/main libobjc4 s390x 5.2.1-27ubuntu1 [102 kB] Get:67 http://ftpmaster.internal/ubuntu/ xenial/main libxslt1.1 s390x 1.1.28-2.1 [139 kB] Get:68 http://ftpmaster.internal/ubuntu/ xenial/universe libgnustep-base1.24 s390x 1.24.7-1build1 [1123 kB] Get:69 http://ftpmaster.internal/ubuntu/ xenial/universe gnustep-base-runtime s390x 1.24.7-1build1 [190 kB] Get:70 http://ftpmaster.internal/ubuntu/ xenial/main libobjc-5-dev s390x 5.2.1-27ubuntu1 [365 kB] Get:71 http://ftpmaster.internal/ubuntu/ xenial/main gobjc-5 s390x 5.2.1-27ubuntu1 [22.8 MB] Get:72 http://ftpmaster.internal/ubuntu/ xenial/main gobjc s390x 4:5.2.1-16ubuntu2 [952 B] Get:73 http://ftpmaster.internal/ubuntu/ xenial/universe gnustep-make all 2.6.6-3 [118 kB] Get:74 http://ftpmaster.internal/ubuntu/ xenial/universe libgnustep-base-dev s390x 1.24.7-1build1 [1568 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 46.9 MB in 15s (3014 kB/s) Selecting previously unselected package libasprintf0v5:s390x. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11407 files and directories currently installed.) Preparing to unpack .../libasprintf0v5_0.19.4-1ubuntu3_s390x.deb ... Unpacking libasprintf0v5:s390x (0.19.4-1ubuntu3) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.3-4_s390x.deb ... Unpacking groff-base (1.22.3-4) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.6ubuntu1_s390x.deb ... Unpacking bsdmainutils (9.0.6ubuntu1) ... Selecting previously unselected package libpipeline1:s390x. Preparing to unpack .../libpipeline1_1.4.1-1_s390x.deb ... Unpacking libpipeline1:s390x (1.4.1-1) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.7.5-1_s390x.deb ... Unpacking man-db (2.7.5-1) ... Selecting previously unselected package libpython2.7-minimal:s390x. Preparing to unpack .../libpython2.7-minimal_2.7.10-4ubuntu2_s390x.deb ... Unpacking libpython2.7-minimal:s390x (2.7.10-4ubuntu2) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../python2.7-minimal_2.7.10-4ubuntu2_s390x.deb ... Unpacking python2.7-minimal (2.7.10-4ubuntu2) ... Selecting previously unselected package python-minimal. Preparing to unpack .../python-minimal_2.7.9-1_s390x.deb ... Unpacking python-minimal (2.7.9-1) ... Selecting previously unselected package mime-support. Preparing to unpack .../mime-support_3.59ubuntu1_all.deb ... Unpacking mime-support (3.59ubuntu1) ... Selecting previously unselected package libexpat1:s390x. Preparing to unpack .../libexpat1_2.1.0-7_s390x.deb ... Unpacking libexpat1:s390x (2.1.0-7) ... Selecting previously unselected package libpython2.7-stdlib:s390x. Preparing to unpack .../libpython2.7-stdlib_2.7.10-4ubuntu2_s390x.deb ... Unpacking libpython2.7-stdlib:s390x (2.7.10-4ubuntu2) ... Selecting previously unselected package python2.7. Preparing to unpack .../python2.7_2.7.10-4ubuntu2_s390x.deb ... Unpacking python2.7 (2.7.10-4ubuntu2) ... Selecting previously unselected package libpython-stdlib:s390x. Preparing to unpack .../libpython-stdlib_2.7.9-1_s390x.deb ... Unpacking libpython-stdlib:s390x (2.7.9-1) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Setting up libpython2.7-minimal:s390x (2.7.10-4ubuntu2) ... Setting up python2.7-minimal (2.7.10-4ubuntu2) ... Setting up python-minimal (2.7.9-1) ... Selecting previously unselected package python. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12680 files and directories currently installed.) Preparing to unpack .../python_2.7.9-1_s390x.deb ... Unpacking python (2.7.9-1) ... Selecting previously unselected package libmagic1:s390x. Preparing to unpack .../libmagic1_1%3a5.25-2ubuntu1_s390x.deb ... Unpacking libmagic1:s390x (1:5.25-2ubuntu1) ... Selecting previously unselected package file. Preparing to unpack .../file_1%3a5.25-2ubuntu1_s390x.deb ... Unpacking file (1:5.25-2ubuntu1) ... Selecting previously unselected package netbase. Preparing to unpack .../archives/netbase_5.3_all.deb ... Unpacking netbase (5.3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../gettext-base_0.19.4-1ubuntu3_s390x.deb ... Unpacking gettext-base (0.19.4-1ubuntu3) ... Selecting previously unselected package libdbus-1-3:s390x. Preparing to unpack .../libdbus-1-3_1.10.4-1ubuntu2_s390x.deb ... Unpacking libdbus-1-3:s390x (1.10.4-1ubuntu2) ... Selecting previously unselected package libglib2.0-0:s390x. Preparing to unpack .../libglib2.0-0_2.47.3-3_s390x.deb ... Unpacking libglib2.0-0:s390x (2.47.3-3) ... Selecting previously unselected package libicu55:s390x. Preparing to unpack .../libicu55_55.1-6ubuntu1_s390x.deb ... Unpacking libicu55:s390x (55.1-6ubuntu1) ... Selecting previously unselected package libxml2:s390x. Preparing to unpack .../libxml2_2.9.2+zdfsg1-4ubuntu1_s390x.deb ... Unpacking libxml2:s390x (2.9.2+zdfsg1-4ubuntu1) ... 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Unpacking sbuild-build-depends-biococoa-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Processing triggers for systemd (228-2ubuntu1) ... Setting up libasprintf0v5:s390x (0.19.4-1ubuntu3) ... Setting up groff-base (1.22.3-4) ... Setting up bsdmainutils (9.0.6ubuntu1) ... 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 libpipeline1:s390x (1.4.1-1) ... Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up mime-support (3.59ubuntu1) ... Setting up libexpat1:s390x (2.1.0-7) ... Setting up libpython2.7-stdlib:s390x (2.7.10-4ubuntu2) ... Setting up python2.7 (2.7.10-4ubuntu2) ... Setting up libpython-stdlib:s390x (2.7.9-1) ... Setting up python (2.7.9-1) ... Setting up libmagic1:s390x (1:5.25-2ubuntu1) ... Setting up file (1:5.25-2ubuntu1) ... Setting up netbase (5.3) ... Setting up gettext-base (0.19.4-1ubuntu3) ... Setting up libdbus-1-3:s390x (1.10.4-1ubuntu2) ... Setting up libglib2.0-0:s390x (2.47.3-3) ... No schema files found: doing nothing. Setting up libicu55:s390x (55.1-6ubuntu1) ... Setting up libxml2:s390x (2.9.2+zdfsg1-4ubuntu1) ... Setting up libsigsegv2:s390x (2.10-4) ... Setting up m4 (1.4.17-4) ... Setting up autoconf (2.69-9) ... Setting up autotools-dev (20150820.1) ... Setting up automake (1:1.15-1ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up libcroco3:s390x (0.6.9-1) ... Setting up libunistring0:s390x (0.9.3-5.2ubuntu1) ... Setting up gettext (0.19.4-1ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up po-debconf (1.0.18) ... Setting up libarchive-zip-perl (1.53-1) ... Setting up libfile-stripnondeterminism-perl (0.014-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up liburi-perl (1.69-1) ... Setting up libencode-locale-perl (1.05-1) ... Setting up libhttp-date-perl (6.02-1) ... Setting up libfile-listing-perl (6.04-1) ... Setting up libhtml-tagset-perl (3.20-2) ... Setting up libhtml-parser-perl (3.71-2) ... Setting up libhtml-tree-perl (5.03-2) ... Setting up libio-html-perl (1.001-1) ... Setting up liblwp-mediatypes-perl (6.02-1) ... Setting up libhttp-message-perl (6.11-1) ... Setting up libhttp-cookies-perl (6.01-1) ... Setting up libhttp-negotiate-perl (6.00-2) ... Setting up libnet-ssleay-perl (1.72-1) ... Setting up libio-socket-ssl-perl (2.021-1) ... Setting up libnet-http-perl (6.09-1) ... Setting up libwww-robotrules-perl (6.01-1) ... Setting up python-scour (0.26-3ubuntu1) ... Setting up gnustep-common (2.6.6-3) ... Setting up gnustep-base-common (1.24.7-1build1) ... Setting up libavahi-common-data:s390x (0.6.32~rc+dfsg-1ubuntu2) ... Setting up libavahi-common3:s390x (0.6.32~rc+dfsg-1ubuntu2) ... Setting up libavahi-client3:s390x (0.6.32~rc+dfsg-1ubuntu2) ... Setting up libobjc4:s390x (5.2.1-27ubuntu1) ... Setting up libxslt1.1:s390x (1.1.28-2.1) ... Setting up libgnustep-base1.24 (1.24.7-1build1) ... Setting up gnustep-base-runtime (1.24.7-1build1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libobjc-5-dev:s390x (5.2.1-27ubuntu1) ... Setting up gobjc-5 (5.2.1-27ubuntu1) ... Setting up gobjc (4:5.2.1-16ubuntu2) ... Setting up gnustep-make (2.6.6-3) ... Setting up libgnustep-base-dev (1.24.7-1build1) ... Setting up debhelper (9.20151126ubuntu1) ... Setting up libwww-perl (6.13-1) ... Setting up libxml-parser-perl (2.44-1) ... Setting up intltool (0.51.0-1) ... Setting up dh-translations (123) ... Setting up cdbs (0.4.130ubuntu2) ... Setting up sbuild-build-depends-biococoa-dummy (0.invalid.0) ... Setting up dh-strip-nondeterminism (0.014-1) ... Setting up liblwp-protocol-https-perl (6.06-2) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Processing triggers for systemd (228-2ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.3.0-0-generic s390x (s390x) Toolchain package versions: binutils_2.25.90.20151125-2ubuntu1 dpkg-dev_1.18.3ubuntu1 g++-5_5.2.1-27ubuntu1 gcc-5_5.2.1-27ubuntu1 libc6-dev_2.21-0ubuntu4 libstdc++-5-dev_5.2.1-27ubuntu1 libstdc++6_5.2.1-27ubuntu1 linux-libc-dev_4.3.0-1.10 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.0.10.2ubuntu1 apt-transport-https_1.0.10.2ubuntu1 autoconf_2.69-9 automake_1:1.15-1ubuntu1 autotools-dev_20150820.1 base-files_9.4ubuntu3 base-passwd_3.5.38 bash_4.3-14ubuntu1 binutils_2.25.90.20151125-2ubuntu1 bsdmainutils_9.0.6ubuntu1 bsdutils_1:2.27.1-1ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8 ca-certificates_20150426ubuntu1 cdbs_0.4.130ubuntu2 coreutils_8.23-4ubuntu2 cpp_4:5.2.1-16ubuntu2 cpp-5_5.2.1-27ubuntu1 dash_0.5.7-4ubuntu2 debconf_1.5.58ubuntu1 debhelper_9.20151126ubuntu1 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 dh-translations_123 diffutils_1:3.3-2 dmsetup_2:1.02.99-1ubuntu1 dpkg_1.18.3ubuntu1 dpkg-dev_1.18.3ubuntu1 e2fslibs_1.42.13-1ubuntu1 e2fsprogs_1.42.13-1ubuntu1 fakeroot_1.20.2-1ubuntu1 file_1:5.25-2ubuntu1 findutils_4.4.2-10 g++_4:5.2.1-16ubuntu2 g++-5_5.2.1-27ubuntu1 gcc_4:5.2.1-16ubuntu2 gcc-5_5.2.1-27ubuntu1 gcc-5-base_5.2.1-27ubuntu1 gettext_0.19.4-1ubuntu3 gettext-base_0.19.4-1ubuntu3 gnupg_1.4.19-6ubuntu1 gnustep-base-common_1.24.7-1build1 gnustep-base-runtime_1.24.7-1build1 gnustep-common_2.6.6-3 gnustep-make_2.6.6-3 gobjc_4:5.2.1-16ubuntu2 gobjc-5_5.2.1-27ubuntu1 gpgv_1.4.19-6ubuntu1 grep_2.21-2 groff-base_1.22.3-4 gzip_1.6-4ubuntu1 hostname_3.16ubuntu2 init_1.24ubuntu2 initscripts_2.88dsf-59.2ubuntu3 insserv_1.14.0-5ubuntu3 intltool_0.51.0-1 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-2 libapparmor1_2.10-0ubuntu8 libapt-pkg4.16_1.0.10.2ubuntu1 libarchive-zip-perl_1.53-1 libasn1-8-heimdal_1.6~rc2+dfsg-10ubuntu1 libasprintf0v5_0.19.4-1ubuntu3 libatomic1_5.2.1-27ubuntu1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-4ubuntu1 libaudit1_1:2.4.4-4ubuntu1 libavahi-client3_0.6.32~rc+dfsg-1ubuntu2 libavahi-common-data_0.6.32~rc+dfsg-1ubuntu2 libavahi-common3_0.6.32~rc+dfsg-1ubuntu2 libblkid1_2.27.1-1ubuntu3 libbz2-1.0_1.0.6-8 libc-bin_2.21-0ubuntu4 libc-dev-bin_2.21-0ubuntu4 libc6_2.21-0ubuntu4 libc6-dev_2.21-0ubuntu4 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.2.1-27ubuntu1 libcomerr2_1.42.13-1ubuntu1 libcroco3_0.6.9-1 libcryptsetup4_2:1.6.6-5ubuntu2 libcurl3-gnutls_7.45.0-1ubuntu1 libdb5.3_5.3.28-11 libdbus-1-3_1.10.4-1ubuntu2 libdebconfclient0_0.198ubuntu1 libdevmapper1.02.1_2:1.02.99-1ubuntu1 libdpkg-perl_1.18.3ubuntu1 libencode-locale-perl_1.05-1 libexpat1_2.1.0-7 libfakeroot_1.20.2-1ubuntu1 libfdisk1_2.27.1-1ubuntu3 libffi6_3.2.1-3 libfile-listing-perl_6.04-1 libfile-stripnondeterminism-perl_0.014-1 libgcc-5-dev_5.2.1-27ubuntu1 libgcc1_1:5.2.1-27ubuntu1 libgcrypt20_1.6.4-3 libgdbm3_1.8.3-13.1 libglib2.0-0_2.47.3-3 libgmp10_2:6.1.0+dfsg-2 libgnustep-base-dev_1.24.7-1build1 libgnustep-base1.24_1.24.7-1build1 libgnutls-deb0-28_3.3.18-1ubuntu1 libgomp1_5.2.1-27ubuntu1 libgpg-error0_1.20-1 libgssapi-krb5-2_1.13.2+dfsg-4 libgssapi3-heimdal_1.6~rc2+dfsg-10ubuntu1 libhcrypto4-heimdal_1.6~rc2+dfsg-10ubuntu1 libheimbase1-heimdal_1.6~rc2+dfsg-10ubuntu1 libheimntlm0-heimdal_1.6~rc2+dfsg-10ubuntu1 libhogweed4_3.1.1-4 libhtml-parser-perl_3.71-2 libhtml-tagset-perl_3.20-2 libhtml-tree-perl_5.03-2 libhttp-cookies-perl_6.01-1 libhttp-date-perl_6.02-1 libhttp-message-perl_6.11-1 libhttp-negotiate-perl_6.00-2 libhx509-5-heimdal_1.6~rc2+dfsg-10ubuntu1 libicu55_55.1-6ubuntu1 libidn11_1.32-3ubuntu1 libio-html-perl_1.001-1 libio-socket-ssl-perl_2.021-1 libisl15_0.15-3 libk5crypto3_1.13.2+dfsg-4 libkeyutils1_1.5.9-5ubuntu1 libkmod2_21-1ubuntu1 libkrb5-26-heimdal_1.6~rc2+dfsg-10ubuntu1 libkrb5-3_1.13.2+dfsg-4 libkrb5support0_1.13.2+dfsg-4 libldap-2.4-2_2.4.41+dfsg-1ubuntu2 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblwp-mediatypes-perl_6.02-1 liblwp-protocol-https-perl_6.06-2 liblzma5_5.1.1alpha+20120614-2ubuntu2 libmagic1_1:5.25-2ubuntu1 libmount1_2.27.1-1ubuntu3 libmpc3_1.0.3-1 libmpfr4_3.1.3-1 libncurses5_5.9+20150516-2ubuntu1 libncursesw5_5.9+20150516-2ubuntu1 libnet-http-perl_6.09-1 libnet-ssleay-perl_1.72-1 libnettle6_3.1.1-4 libobjc-5-dev_5.2.1-27ubuntu1 libobjc4_5.2.1-27ubuntu1 libp11-kit0_0.23.1-3 libpam-modules_1.1.8-3.1ubuntu3 libpam-modules-bin_1.1.8-3.1ubuntu3 libpam-runtime_1.1.8-3.1ubuntu3 libpam0g_1.1.8-3.1ubuntu3 libpcre3_2:8.35-7.1ubuntu1 libpipeline1_1.4.1-1 libpng12-0_1.2.54-1 libprocps3_1:3.3.9-1ubuntu8 libpython-stdlib_2.7.9-1 libpython2.7-minimal_2.7.10-4ubuntu2 libpython2.7-stdlib_2.7.10-4ubuntu2 libreadline6_6.3-8ubuntu1 libroken18-heimdal_1.6~rc2+dfsg-10ubuntu1 librtmp1_2.4+20150115.gita107cef-1build1 libsasl2-2_2.1.26.dfsg1-14 libsasl2-modules-db_2.1.26.dfsg1-14 libseccomp2_2.2.3-2ubuntu1 libselinux1_2.3-2build1 libsemanage-common_2.3-1build2 libsemanage1_2.3-1build2 libsepol1_2.4-2 libsigsegv2_2.10-4 libslang2_2.3.0-2ubuntu1 libsmartcols1_2.27.1-1ubuntu3 libsqlite3-0_3.9.2-1 libss2_1.42.13-1ubuntu1 libssl1.0.0_1.0.2d-0ubuntu2 libstdc++-5-dev_5.2.1-27ubuntu1 libstdc++6_5.2.1-27ubuntu1 libsystemd0_228-2ubuntu1 libtasn1-6_4.7-2 libtimedate-perl_2.3000-2 libtinfo5_5.9+20150516-2ubuntu1 libudev1_228-2ubuntu1 libunistring0_0.9.3-5.2ubuntu1 liburi-perl_1.69-1 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-1ubuntu3 libwind0-heimdal_1.6~rc2+dfsg-10ubuntu1 libwww-perl_6.13-1 libwww-robotrules-perl_6.01-1 libxml-parser-perl_2.44-1 libxml2_2.9.2+zdfsg1-4ubuntu1 libxslt1.1_1.1.28-2.1 linux-libc-dev_4.3.0-1.10 lockfile-progs_0.1.17 login_1:4.1.5.1-1.1ubuntu7 lsb-base_9.20150917ubuntu1 m4_1.4.17-4 make_4.0-8.2 man-db_2.7.5-1 mawk_1.3.3-17ubuntu2 mime-support_3.59ubuntu1 mount_2.27.1-1ubuntu3 multiarch-support_2.21-0ubuntu4 ncurses-base_5.9+20150516-2ubuntu1 ncurses-bin_5.9+20150516-2ubuntu1 netbase_5.3 openssl_1.0.2d-0ubuntu2 optipng_0.7.5-1 passwd_1:4.1.5.1-1.1ubuntu7 patch_2.7.5-1 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 pkg-create-dbgsym_0.70 pkgbinarymangler_123 po-debconf_1.0.18 policyrcd-script-zg2_0.1-2 procps_1:3.3.9-1ubuntu8 python_2.7.9-1 python-minimal_2.7.9-1 python-scour_0.26-3ubuntu1 python2.7_2.7.10-4ubuntu2 python2.7-minimal_2.7.10-4ubuntu2 readline-common_6.3-8ubuntu1 sbuild-build-depends-biococoa-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 systemd_228-2ubuntu1 systemd-sysv_228-2ubuntu1 sysv-rc_2.88dsf-59.2ubuntu3 sysvinit-utils_2.88dsf-59.2ubuntu3 tar_1.28-2.1 tzdata_2015g-1 ubuntu-keyring_2012.05.19 udev_228-2ubuntu1 util-linux_2.27.1-1ubuntu3 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-2ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- 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 User Environment ---------------- DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/<> SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: source package biococoa dpkg-buildpackage: source version 2.2.2-2 dpkg-buildpackage: source distribution unstable dpkg-source --before-build biococoa-2.2.2 dpkg-buildpackage: host architecture s390x 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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed" OPTFLAG=-O2 -k clean make[1]: Entering directory '/<>' 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 '/<>/BCFoundation' rm -rf ./*~ ./obj Making clean in subprojects of subproject BCFoundation... make[3]: Entering directory '/<>/BCFoundation/BCAlignment' rm -rf ./*~ ./obj make[3]: Leaving directory '/<>/BCFoundation/BCAlignment' make[3]: Entering directory '/<>/BCFoundation/BCAnalysis' rm -rf ./*~ ./obj make[3]: Leaving directory '/<>/BCFoundation/BCAnalysis' make[3]: Entering directory '/<>/BCFoundation/BCGeneExpression' rm -rf ./*~ ./obj make[3]: Leaving directory '/<>/BCFoundation/BCGeneExpression' make[3]: Entering directory '/<>/BCFoundation/BCGeneticCode' rm -rf ./*~ ./obj make[3]: Leaving directory '/<>/BCFoundation/BCGeneticCode' make[3]: Entering directory '/<>/BCFoundation/BCProteinStructure' rm -rf ./*~ ./obj make[3]: Leaving directory '/<>/BCFoundation/BCProteinStructure' make[3]: Entering directory '/<>/BCFoundation/BCSequence' rm -rf ./*~ ./obj make[3]: Leaving directory '/<>/BCFoundation/BCSequence' make[3]: Entering directory '/<>/BCFoundation/BCSequenceIO' rm -rf ./*~ ./obj make[3]: Leaving directory '/<>/BCFoundation/BCSequenceIO' make[3]: Entering directory '/<>/BCFoundation/BCSymbol' rm -rf ./*~ ./obj make[3]: Leaving directory '/<>/BCFoundation/BCSymbol' make[3]: Entering directory '/<>/BCFoundation/BCTools' rm -rf ./*~ ./obj make[3]: Leaving directory '/<>/BCFoundation/BCTools' make[3]: Entering directory '/<>/BCFoundation/BCUtils' rm -rf ./*~ ./obj make[3]: Leaving directory '/<>/BCFoundation/BCUtils' make[2]: Leaving directory '/<>/BCFoundation' Making clean for framework BioCocoa... rm -rf \ \ ./BioCocoa.framework ./derived_src make[1]: Leaving directory '/<>' 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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed" OPTFLAG=-O2 make[1]: Entering directory '/<>' 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 '/<>/BCFoundation' Making build-headers in subprojects of subproject BCFoundation... make[3]: Entering directory '/<>/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 '/<>/BCFoundation/BCAlignment' make[3]: Entering directory '/<>/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 '/<>/BCFoundation/BCAnalysis' make[3]: Entering directory '/<>/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 '/<>/BCFoundation/BCGeneExpression' make[3]: Entering directory '/<>/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 '/<>/BCFoundation/BCGeneticCode' make[3]: Entering directory '/<>/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 '/<>/BCFoundation/BCProteinStructure' make[3]: Entering directory '/<>/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 '/<>/BCFoundation/BCSequence' make[3]: Entering directory '/<>/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 '/<>/BCFoundation/BCSequenceIO' make[3]: Entering directory '/<>/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 '/<>/BCFoundation/BCSymbol' make[3]: Entering directory '/<>/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 '/<>/BCFoundation/BCTools' make[3]: Entering directory '/<>/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 '/<>/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 '/<>/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 "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 '/<>/BCFoundation' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all in subprojects of subproject BCFoundation... make[3]: Entering directory '/<>/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 -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 -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 -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,-Bsymbolic-functions -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 ; make[3]: Leaving directory '/<>/BCFoundation/BCAlignment' make[3]: Entering directory '/<>/BCFoundation/BCAnalysis' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCAnalysis... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCAnalysis.obj/ gcc BCMCP.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 -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/BCAnalysis.obj/BCMCP.m.o BCMCP.m: In function '+[BCMCP mcpToFile:suffixArray:withSuffixArray:lowerBound:]': BCMCP.m:160:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa1Offset, sizeof(int), 1, sa1); ^ BCMCP.m:161:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa1File, sizeof(int), 1, sa1); ^ BCMCP.m:163:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa2Offset, sizeof(int), 1, sa2); ^ BCMCP.m:164:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa2File, sizeof(int), 1, sa2); ^ BCMCP.m:334:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa2Offset, sizeof(int), 1, sa2); ^ BCMCP.m:335:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa2File, sizeof(int), 1, sa2); ^ BCMCP.m:352:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa1Offset, sizeof(int), 1, sa1); ^ BCMCP.m:353:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa1File, sizeof(int), 1, sa1); ^ BCMCP.m:358:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa2Offset, sizeof(int), 1, sa2); ^ BCMCP.m:359:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa2File, sizeof(int), 1, sa2); ^ BCMCP.m:366:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa2Offset, sizeof(int), 1, sa2); ^ BCMCP.m:367:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa2File, sizeof(int), 1, sa2); ^ BCMCP.m: In function '-[BCMCP intersectToFile:withMCP:]': BCMCP.m:486:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp1Length, sizeof(int), 1, mcp1); ^ BCMCP.m:487:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp1NumFiles, sizeof(int), 1, mcp1); ^ BCMCP.m:489:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp1Offset[i]), sizeof(int), 1, mcp1); ^ BCMCP.m:490:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp1File[i]), sizeof(int), 1, mcp1); ^ BCMCP.m:514:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp2Length, sizeof(int), 1, mcp2); ^ BCMCP.m:515:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp2NumFiles, sizeof(int), 1, mcp2); ^ BCMCP.m:517:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp2Offset[i]), sizeof(int), 1, mcp2); ^ BCMCP.m:518:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp2File[i]), sizeof(int), 1, mcp2); ^ BCMCP.m:735:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp1Length, sizeof(int), 1, mcp1); ^ BCMCP.m:736:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp1NumFiles, sizeof(int), 1, mcp1); ^ BCMCP.m:738:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp1Offset[i]), sizeof(int), 1, mcp1); ^ BCMCP.m:739:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp1File[i]), sizeof(int), 1, mcp1); ^ BCMCP.m:762:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp2Length, sizeof(int), 1, mcp2); ^ BCMCP.m:763:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp2NumFiles, sizeof(int), 1, mcp2); ^ BCMCP.m:765:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp2Offset[i]), sizeof(int), 1, mcp2); ^ BCMCP.m:766:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp2File[i]), sizeof(int), 1, mcp2); ^ BCMCP.m: In function '-[BCMCP unionToFile:withMCP:]': BCMCP.m:910:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp1Length, sizeof(int), 1, mcp1); ^ BCMCP.m:911:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp1NumFiles, sizeof(int), 1, mcp1); ^ BCMCP.m:913:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp1Offset[i]), sizeof(int), 1, mcp1); ^ BCMCP.m:914:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp1File[i]), sizeof(int), 1, mcp1); ^ BCMCP.m:936:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp2Length, sizeof(int), 1, mcp2); ^ BCMCP.m:937:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp2NumFiles, sizeof(int), 1, mcp2); ^ BCMCP.m:939:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp2Offset[i]), sizeof(int), 1, mcp2); ^ BCMCP.m:940:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp2File[i]), sizeof(int), 1, mcp2); ^ BCMCP.m:1093:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp1Length, sizeof(int), 1, mcp1); ^ BCMCP.m:1094:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp1NumFiles, sizeof(int), 1, mcp1); ^ BCMCP.m:1096:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp1Offset[i]), sizeof(int), 1, mcp1); ^ BCMCP.m:1097:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp1File[i]), sizeof(int), 1, mcp1); ^ BCMCP.m:1123:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp2Length, sizeof(int), 1, mcp2); ^ BCMCP.m:1124:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp2NumFiles, sizeof(int), 1, mcp2); ^ BCMCP.m:1126:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp2Offset[i]), sizeof(int), 1, mcp2); ^ BCMCP.m:1127:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp2File[i]), sizeof(int), 1, mcp2); ^ BCMCP.m:1167:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp1Length, sizeof(int), 1, mcp1); ^ BCMCP.m:1168:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp1NumFiles, sizeof(int), 1, mcp1); ^ BCMCP.m:1170:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp1Offset[i]), sizeof(int), 1, mcp1); ^ BCMCP.m:1171:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp1File[i]), sizeof(int), 1, mcp1); ^ BCMCP.m:1186:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp2Length, sizeof(int), 1, mcp2); ^ BCMCP.m:1187:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp2NumFiles, sizeof(int), 1, mcp2); ^ BCMCP.m:1189:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp2Offset[i]), sizeof(int), 1, mcp2); ^ BCMCP.m:1190:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp2File[i]), sizeof(int), 1, mcp2); ^ BCMCP.m:1222:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp2Length, sizeof(int), 1, mcp2); ^ BCMCP.m:1223:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp2NumFiles, sizeof(int), 1, mcp2); ^ BCMCP.m:1225:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp2Offset[i]), sizeof(int), 1, mcp2); ^ BCMCP.m:1226:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp2File[i]), sizeof(int), 1, mcp2); ^ BCMCP.m:1239:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp1Length, sizeof(int), 1, mcp1); ^ BCMCP.m:1240:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp1NumFiles, sizeof(int), 1, mcp1); ^ BCMCP.m:1242:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp1Offset[i]), sizeof(int), 1, mcp1); ^ BCMCP.m:1243:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcp1File[i]), sizeof(int), 1, mcp1); ^ BCMCP.m: In function '-[BCMCP trimToFile:]': BCMCP.m:1272:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcpLength, sizeof(int), 1, mcp); ^ BCMCP.m:1273:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcpNumFiles, sizeof(int), 1, mcp); ^ BCMCP.m:1275:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcpOffset[i]), sizeof(int), 1, mcp); ^ BCMCP.m:1276:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcpFile[i]), sizeof(int), 1, mcp); ^ BCMCP.m: In function '-[BCMCP outputFormat:withMinimumLength:]': BCMCP.m:1481:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcpLength, sizeof(int), 1, mcp); ^ BCMCP.m:1482:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcpNumFiles, sizeof(int), 1, mcp); ^ BCMCP.m:1485:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcpOffset[i]), sizeof(int), 1, mcp); ^ BCMCP.m:1486:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcpFile[i]), sizeof(int), 1, mcp); ^ BCMCP.m:1603:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcpLength, sizeof(int), 1, mcp); ^ BCMCP.m:1604:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcpNumFiles, sizeof(int), 1, mcp); ^ BCMCP.m:1606:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcpOffset[i]), sizeof(int), 1, mcp); ^ BCMCP.m:1607:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(mcpFile[i]), sizeof(int), 1, mcp); ^ gcc BCSuffixArray.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 -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/BCAnalysis.obj/BCSuffixArray.m.o BCSuffixArray.m: In function '-[BCSuffixArray dumpSuffixArray]': BCSuffixArray.m:896:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa1Offset, sizeof(int), 1, sa1); ^ BCSuffixArray.m:897:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa1File, sizeof(int), 1, sa1); ^ BCSuffixArray.m:932:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa1Offset, sizeof(int), 1, sa1); ^ BCSuffixArray.m:933:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa1File, sizeof(int), 1, sa1); ^ BCSuffixArray.m: In function '-[BCSuffixArrayUnionEnumerator nextSuffixPosition:sequence:suffixArray:]': BCSuffixArray.m:1464:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(suffixPositions[i]), sizeof(int), 1, arrayFiles[i]); ^ BCSuffixArray.m:1465:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(suffixSequences[i]), sizeof(int), 1, arrayFiles[i]); ^ BCSuffixArray.m:1598:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(suffixPositions[currentSuffix]), sizeof(int), 1, arrayFiles[currentSuffix]); ^ BCSuffixArray.m:1599:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(suffixSequences[currentSuffix]), sizeof(int), 1, arrayFiles[currentSuffix]); ^ gcc -nostdlib -r -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCAnalysis.obj/BCMCP.m.o obj/BCAnalysis.obj/BCSuffixArray.m.o ; make[3]: Leaving directory '/<>/BCFoundation/BCAnalysis' make[3]: Entering directory '/<>/BCFoundation/BCGeneExpression' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCGeneExpression... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCGeneExpression.obj/ gcc BCSeries.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 -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/BCGeneExpression.obj/BCSeries.m.o gcc BCSample.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 -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/BCGeneExpression.obj/BCSample.m.o gcc BCPlatform.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 -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/BCGeneExpression.obj/BCPlatform.m.o gcc BCParseSOFT.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 -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/BCGeneExpression.obj/BCParseSOFT.m.o gcc -nostdlib -r -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCGeneExpression.obj/BCSeries.m.o obj/BCGeneExpression.obj/BCSample.m.o obj/BCGeneExpression.obj/BCPlatform.m.o obj/BCGeneExpression.obj/BCParseSOFT.m.o ; make[3]: Leaving directory '/<>/BCFoundation/BCGeneExpression' make[3]: Entering directory '/<>/BCFoundation/BCGeneticCode' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCGeneticCode... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCGeneticCode.obj/ gcc BCCodonDNA.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 -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/BCGeneticCode.obj/BCCodonDNA.m.o gcc BCCodon.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 -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/BCGeneticCode.obj/BCCodon.m.o gcc BCCodonRNA.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 -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/BCGeneticCode.obj/BCCodonRNA.m.o gcc BCGeneticCode.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 -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/BCGeneticCode.obj/BCGeneticCode.m.o BCGeneticCode.m: In function '+[BCGeneticCode priv:createCodonArraysFromDictionary:]': BCGeneticCode.m:221:23: warning: variable 'RNACodon' set but not used [-Wunused-but-set-variable] BCCodon *aCodon, *RNACodon; ^ gcc -nostdlib -r -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCGeneticCode.obj/BCCodonDNA.m.o obj/BCGeneticCode.obj/BCCodon.m.o obj/BCGeneticCode.obj/BCCodonRNA.m.o obj/BCGeneticCode.obj/BCGeneticCode.m.o ; make[3]: Leaving directory '/<>/BCFoundation/BCGeneticCode' make[3]: Entering directory '/<>/BCFoundation/BCProteinStructure' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCProteinStructure... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCProteinStructure.obj/ gcc BCAtom.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 -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/BCProteinStructure.obj/BCAtom.m.o gcc BCProteinStructure.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 -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/BCProteinStructure.obj/BCProteinStructure.m.o gcc BCSecondaryStructure.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 -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/BCProteinStructure.obj/BCSecondaryStructure.m.o gcc BCChain.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 -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/BCProteinStructure.obj/BCChain.m.o gcc BCResidue.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 -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/BCProteinStructure.obj/BCResidue.m.o gcc BCSequenceStructure.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 -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/BCProteinStructure.obj/BCSequenceStructure.m.o gcc -nostdlib -r -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCProteinStructure.obj/BCAtom.m.o obj/BCProteinStructure.obj/BCProteinStructure.m.o obj/BCProteinStructure.obj/BCSecondaryStructure.m.o obj/BCProteinStructure.obj/BCChain.m.o obj/BCProteinStructure.obj/BCResidue.m.o obj/BCProteinStructure.obj/BCSequenceStructure.m.o ; make[3]: Leaving directory '/<>/BCFoundation/BCProteinStructure' make[3]: Entering directory '/<>/BCFoundation/BCSequence' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCSequence... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCSequence.obj/ gcc BCAnnotation.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 -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/BCSequence.obj/BCAnnotation.m.o gcc BCSequence.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 -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/BCSequence.obj/BCSequence.m.o gcc BCSequenceArray.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 -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/BCSequence.obj/BCSequenceArray.m.o gcc BCSequenceCodon.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 -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/BCSequence.obj/BCSequenceCodon.m.o BCSequenceCodon.m: In function '-[BCSequenceCodon openReadingFramesLongerThanCutoff:]': BCSequenceCodon.m:301:16: warning: 'inORF' may be used uninitialized in this function [-Wmaybe-uninitialized] if ( inORF ) ^ gcc -nostdlib -r -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCSequence.obj/BCAnnotation.m.o obj/BCSequence.obj/BCSequence.m.o obj/BCSequence.obj/BCSequenceArray.m.o obj/BCSequence.obj/BCSequenceCodon.m.o ; make[3]: Leaving directory '/<>/BCFoundation/BCSequence' make[3]: Entering directory '/<>/BCFoundation/BCSequenceIO' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCSequenceIO... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCSequenceIO.obj/ gcc BCSequenceReader.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 -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/BCSequenceIO.obj/BCSequenceReader.m.o BCSequenceReader.m: In function '-[BCSequenceReader readFileUsingText:]': BCSequenceReader.m:167:3: warning: no '-initWithRTF:documentAttributes:' method found NSAttributedString *rtfstring = [[NSAttributedString alloc] initWithRTF: [entryString dataUsingEncoding: NSUTF8StringEncoding] documentAttributes: nil]; ^ BCSequenceReader.m:167:3: warning: (Messages without a matching method signature BCSequenceReader.m:167:3: warning: will be assumed to return 'id' and accept BCSequenceReader.m:167:3: warning: '...' as arguments.) BCSequenceReader.m: In function '-[BCSequenceReader readMacVectorFile:]': BCSequenceReader.m:651:18: warning: variable 'annotationsArray' set but not used [-Wunused-but-set-variable] NSMutableArray *annotationsArray; ^ BCSequenceReader.m: In function '-[BCSequenceReader readClustalFile:]': BCSequenceReader.m:798:3: warning: passing argument 2 of 'scanUpToString:intoString:' from incompatible pointer type [-Wincompatible-pointer-types] [lineScanner scanUpToString:@" " intoString: nil]; ^ BCSequenceReader.m:798:3: note: expected 'struct NSString **' but argument is of type 'id' BCSequenceReader.m: In function '-[BCSequenceReader readPhylipFile:]': BCSequenceReader.m:1113:31: warning: variable 'annotationsArray' set but not used [-Wunused-but-set-variable] NSMutableArray *linesArray, *annotationsArray, *namesArray, *sequenceArray; ^ BCSequenceReader.m: In function '-[BCSequenceReader readSwissProtFile:]': BCSequenceReader.m:421:2: warning: 'sequenceString' may be used uninitialized in this function [-Wmaybe-uninitialized] if ( [sequenceString length]) ^ BCSequenceReader.m: In function '-[BCSequenceReader readClustalFile:]': BCSequenceReader.m:822:18: warning: 'sequenceRange.location' may be used uninitialized in this function [-Wmaybe-uninitialized] sequenceString = [line substringFromIndex: sequenceRange.location]; ^ BCSequenceReader.m: In function '-[BCSequenceReader readFASTQFile:]': BCSequenceReader.m:1310:18: warning: 'seqData' may be used uninitialized in this function [-Wmaybe-uninitialized] BCSequence *newSequence = [[BCSequence alloc] initWithData: seqData symbolSet: nil]; ^ gcc BCSequenceWriter.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 -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/BCSequenceIO.obj/BCSequenceWriter.m.o gcc BCCachedSequenceFile.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 -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/BCSequenceIO.obj/BCCachedSequenceFile.m.o gcc BCCachedFastaFile.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 -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/BCSequenceIO.obj/BCCachedFastaFile.m.o BCCachedFastaFile.m: In function '-[BCCachedFastaFile initWithContentsOfFile:]': BCCachedFastaFile.m:58:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&c, sizeof(char), 1, g1); ^ BCCachedFastaFile.m:73:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&c, sizeof(char), 1, g1); ^ BCCachedFastaFile.m:76:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&c, sizeof(char), 1, g1); ^ BCCachedFastaFile.m:97:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&c, sizeof(char), 1, g1); ^ BCCachedFastaFile.m: In function '-[BCCachedFastaFile symbols:ForCurrentSequenceAtPosition:ofLength:]': BCCachedFastaFile.m:149:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&c, sizeof(char), 1, fileHandle); ^ BCCachedFastaFile.m: In function '-[BCCachedFastaFile initWithContentsOfFile:]': BCCachedFastaFile.m:104:3: warning: 'filePos' may be used uninitialized in this function [-Wmaybe-uninitialized] [d setObject: [NSNumber numberWithUnsignedLongLong: (filePos - 1)] forKey: @"end"]; ^ gcc -nostdlib -r -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCSequenceIO.obj/BCSequenceReader.m.o obj/BCSequenceIO.obj/BCSequenceWriter.m.o obj/BCSequenceIO.obj/BCCachedSequenceFile.m.o obj/BCSequenceIO.obj/BCCachedFastaFile.m.o ; make[3]: Leaving directory '/<>/BCFoundation/BCSequenceIO' make[3]: Entering directory '/<>/BCFoundation/BCSymbol' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCSymbol... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCSymbol.obj/ gcc BCAminoAcid.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 -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/BCSymbol.obj/BCAminoAcid.m.o gcc BCNucleotide.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 -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/BCSymbol.obj/BCNucleotide.m.o gcc BCSymbol.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 -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/BCSymbol.obj/BCSymbol.m.o gcc BCNucleotideDNA.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 -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/BCSymbol.obj/BCNucleotideDNA.m.o gcc BCNucleotideRNA.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 -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/BCSymbol.obj/BCNucleotideRNA.m.o gcc BCSymbolSet.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 -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/BCSymbol.obj/BCSymbolSet.m.o gcc -nostdlib -r -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCSymbol.obj/BCAminoAcid.m.o obj/BCSymbol.obj/BCNucleotide.m.o obj/BCSymbol.obj/BCSymbol.m.o obj/BCSymbol.obj/BCNucleotideDNA.m.o obj/BCSymbol.obj/BCNucleotideRNA.m.o obj/BCSymbol.obj/BCSymbolSet.m.o ; make[3]: Leaving directory '/<>/BCFoundation/BCSymbol' make[3]: Entering directory '/<>/BCFoundation/BCTools' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCTools... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCTools.obj/ gcc BCSequenceTool.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 -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/BCTools.obj/BCSequenceTool.m.o gcc BCToolDigest.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 -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/BCTools.obj/BCToolDigest.m.o gcc BCToolHydropathyCalculator.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 -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/BCTools.obj/BCToolHydropathyCalculator.m.o gcc BCToolMassCalculator.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 -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/BCTools.obj/BCToolMassCalculator.m.o gcc BCToolComplement.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 -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/BCTools.obj/BCToolComplement.m.o gcc BCToolSequenceFinder.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 -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/BCTools.obj/BCToolSequenceFinder.m.o gcc BCToolSymbolCounter.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 -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/BCTools.obj/BCToolSymbolCounter.m.o gcc BCToolTranslator.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 -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/BCTools.obj/BCToolTranslator.m.o gcc BCToolTranslatorDNA.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 -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/BCTools.obj/BCToolTranslatorDNA.m.o gcc -nostdlib -r -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCTools.obj/BCSequenceTool.m.o obj/BCTools.obj/BCToolDigest.m.o obj/BCTools.obj/BCToolHydropathyCalculator.m.o obj/BCTools.obj/BCToolMassCalculator.m.o obj/BCTools.obj/BCToolComplement.m.o obj/BCTools.obj/BCToolSequenceFinder.m.o obj/BCTools.obj/BCToolSymbolCounter.m.o obj/BCTools.obj/BCToolTranslator.m.o obj/BCTools.obj/BCToolTranslatorDNA.m.o ; make[3]: Leaving directory '/<>/BCFoundation/BCTools' make[3]: Entering directory '/<>/BCFoundation/BCUtils' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCUtils... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCUtils.obj/ gcc BCDataMatrix.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 -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/BCUtils.obj/BCDataMatrix.m.o gcc BCUtilData.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 -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/BCUtils.obj/BCUtilData.m.o gcc BCUtilStrings.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 -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/BCUtils.obj/BCUtilStrings.m.o BCUtilStrings.m: In function '-[NSString(StringAdditions) stringBeginsWithTwoNumbers]': BCUtilStrings.m:98:2: warning: passing argument 1 of 'scanInt:' from incompatible pointer type [-Wincompatible-pointer-types] if ([scanner scanInt:nil]) ^ BCUtilStrings.m:98:2: note: expected 'int *' but argument is of type 'id' BCUtilStrings.m:100:3: warning: passing argument 1 of 'scanInt:' from incompatible pointer type [-Wincompatible-pointer-types] if ([scanner scanInt:nil]) ^ BCUtilStrings.m:100:3: note: expected 'int *' but argument is of type 'id' gcc -nostdlib -r -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCUtils.obj/BCDataMatrix.m.o obj/BCUtils.obj/BCUtilData.m.o obj/BCUtils.obj/BCUtilStrings.m.o ; make[3]: Leaving directory '/<>/BCFoundation/BCUtils' Making all for subproject BCFoundation... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCFoundation.obj/ gcc BCStringDefinitions.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 -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/BCFoundation.obj/BCStringDefinitions.m.o gcc BCPreferences.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 -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/BCFoundation.obj/BCPreferences.m.o gcc -nostdlib -r -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCFoundation.obj/BCStringDefinitions.m.o obj/BCFoundation.obj/BCPreferences.m.o BCAlignment/obj/subproject.o BCAnalysis/obj/subproject.o BCGeneExpression/obj/subproject.o BCGeneticCode/obj/subproject.o BCProteinStructure/obj/subproject.o BCSequence/obj/subproject.o BCSequenceIO/obj/subproject.o BCSymbol/obj/subproject.o BCTools/obj/subproject.o BCUtils/obj/subproject.o ; make[2]: Leaving directory '/<>/BCFoundation' Making all for framework BioCocoa... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BioCocoa.obj/ classes=""; \ for object_file in ./BCFoundation/obj/subproject.o __dummy__; do \ if [ "$object_file" != "__dummy__" ]; then \ sym=`nm -Pg $object_file | sed -n -e '/^__objc_class_name_[A-Za-z0-9_.]* [^U]/ {s/^__objc_class_name_\([A-Za-z0-9_.]*\) [^U].*/\1/p;}'`; \ classes="$classes $sym"; \ fi; \ done; \ classlist=""; \ classarray=""; \ for f in $classes __dummy__ ; do \ if [ "$f" != "__dummy__" ]; then \ if [ "$classlist" = "" ]; then \ classlist="@\"$f\""; \ classarray="(\"$f\""; \ else \ classlist="$classlist, @\"$f\""; \ classarray="$classarray, \"$f\""; \ fi; \ fi; \ done; \ if [ "$classlist" = "" ]; then \ classlist="NULL"; \ classarray="()"; \ else \ classlist="$classlist, NULL"; \ classarray="$classarray)"; \ fi; \ echo "$classarray" > ./derived_src/BioCocoa-class-list; \ echo "#include " > derived_src/NSFramework_BioCocoa.m; \ echo "#include " > derived_src/NSFramework_BioCocoa.m; \ echo "@interface NSFramework_BioCocoa : NSObject" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkEnv;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkPath;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkVersion;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *const*)frameworkClasses;" >> derived_src/NSFramework_BioCocoa.m; \ echo "@end" >> derived_src/NSFramework_BioCocoa.m; \ echo "@implementation NSFramework_BioCocoa" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkEnv { return nil; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkPath { return @\"/usr/lib/GNUstep/Frameworks\"; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkVersion { return @\"2\"; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "static NSString *allClasses[] = {$classlist};" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *const*)frameworkClasses { return allClasses; }" >> derived_src/NSFramework_BioCocoa.m;\ echo "@end" >> derived_src/NSFramework_BioCocoa.m gcc derived_src/NSFramework_BioCocoa.m -c -MMD -MP -D_FORTIFY_SOURCE=2 -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 -I./derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep -o obj/BioCocoa.obj/NSFramework_BioCocoa.o \ gcc -shared -Wl,-soname,libBioCocoa.so.2 -rdynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./BioCocoa.framework/Versions/2/./libBioCocoa.so.2.2.2 obj/BioCocoa.obj/NSFramework_BioCocoa.o BCFoundation/obj/subproject.o -L/usr/local/lib -L/usr/lib -lgnustep-base -lobjc && (cd ./BioCocoa.framework/Versions/2/.; rm -f libBioCocoa.so; if [ "libBioCocoa.so.2" != "libBioCocoa.so.2.2.2" ]; then rm -f libBioCocoa.so.2; ln -s libBioCocoa.so.2.2.2 libBioCocoa.so.2; fi; ln -s libBioCocoa.so.2 libBioCocoa.so; ) || rm -f ./BioCocoa.framework/Versions/2/./libBioCocoa.so.2.2.2 ; \ (cd ./BioCocoa.framework/Versions/2/.; \ rm -f BioCocoa; \ ln -s libBioCocoa.so BioCocoa) \ BCFoundation/obj/subproject.o: In function `_i_BCSuffixArray__constructFromSequenceArray_strand_': BCSuffixArray.m:(.text+0xdb8a): warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' for f in BCFoundation/BCSymbol/SymbolTemplates/nucleotides.plist BCFoundation/BCSymbol/SymbolTemplates/aminoacids.plist; do \ if [ -f $f -o -d $f ]; then \ cp -fr $f ./BioCocoa.framework/Versions/2/Resources/; \ else \ echo "Warning: $f not found - ignoring"; \ fi; \ done for subproject in BCFoundation; do \ if [ -d $subproject/Resources/Subproject ]; then \ for f in $subproject/Resources/Subproject/*; do \ if [ $f != $subproject'/Resources/Subproject/*' ]; then \ cp -fr $f ./BioCocoa.framework/Versions/2/Resources/; \ fi; \ done; \ fi; \ done (echo "{"; echo ' NOTE = "Automatically generated, do not edit!";'; \ echo " NSExecutable = \"BioCocoa\";"; \ echo " NSMainNibFile = \"\";"; \ echo " NSPrincipalClass = \"BioCocoa\";"; \ echo " Classes = "; \ cat ./derived_src/BioCocoa-class-list; \ echo " ;"; \ echo "}") >BioCocoa.framework/Versions/2/Resources/Info-gnustep.plist if [ -r "BioCocoaInfo.plist" ]; then \ plmerge BioCocoa.framework/Versions/2/Resources/Info-gnustep.plist BioCocoaInfo.plist; \ fi cd ./BioCocoa.framework/.; \ rm -f BioCocoa libBioCocoa.so; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh . \ Versions/Current/./BioCocoa short` \ BioCocoa; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh . \ Versions/Current/./libBioCocoa.so short` \ libBioCocoa.so make[1]: Leaving directory '/<>' touch debian/stamp-makefile-build DEB_MAKE_CHECK_TARGET unset, not running checks fakeroot debian/rules binary-arch test -x debian/rules dh_testroot dh_prep dh_installdirs -A sed -e "s:@GNUSTEP_SYSTEM_LIBRARIES@:/usr/lib:g" -e "s:@GNUSTEP_SYSTEM_LIBRARY@:/usr/lib/GNUstep:g" -e "s:@GNUSTEP_SYSTEM_HEADERS@:/usr/include/GNUstep:g" -e "s/@FRAMEWORK@/BioCocoa/g; s/@FRAMEWORKVER@/2/g" < /usr/share/GNUstep/debian/frameworklib.install.in > debian/libbiococoa2.install sed -e "s:@GNUSTEP_SYSTEM_LIBRARIES@:/usr/lib:g" -e "s:@GNUSTEP_SYSTEM_LIBRARY@:/usr/lib/GNUstep:g" -e "s:@GNUSTEP_SYSTEM_HEADERS@:/usr/include/GNUstep:g" -e "s/@FRAMEWORK@/BioCocoa/g; s/@FRAMEWORKVER@/2/g" < /usr/share/GNUstep/debian/frameworkdev.install.in > debian/libbiococoa-dev.install mkdir -p "." DEB_MAKE_CHECK_TARGET unset, not running checks 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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed" OPTFLAG=-O2 install DESTDIR=/<>/debian/tmp/ GNUSTEP_INSTALLATION_DOMAIN=SYSTEM make[1]: Entering directory '/<>' 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 '/<>/BCFoundation' Making build-headers in subprojects of subproject BCFoundation... make[3]: Entering directory '/<>/BCFoundation/BCAlignment' Making build-headers for subproject BCAlignment... make[4]: Nothing to be done for 'internal-subproject-build-headers'. make[3]: Leaving directory '/<>/BCFoundation/BCAlignment' make[3]: Entering directory '/<>/BCFoundation/BCAnalysis' Making build-headers for subproject BCAnalysis... make[4]: Nothing to be done for 'internal-subproject-build-headers'. make[3]: Leaving directory '/<>/BCFoundation/BCAnalysis' make[3]: Entering directory '/<>/BCFoundation/BCGeneExpression' Making build-headers for subproject BCGeneExpression... make[4]: Nothing to be done for 'internal-subproject-build-headers'. make[3]: Leaving directory '/<>/BCFoundation/BCGeneExpression' make[3]: Entering directory '/<>/BCFoundation/BCGeneticCode' Making build-headers for subproject BCGeneticCode... make[4]: Nothing to be done for 'internal-subproject-build-headers'. make[3]: Leaving directory '/<>/BCFoundation/BCGeneticCode' make[3]: Entering directory '/<>/BCFoundation/BCProteinStructure' Making build-headers for subproject BCProteinStructure... make[4]: Nothing to be done for 'internal-subproject-build-headers'. make[3]: Leaving directory '/<>/BCFoundation/BCProteinStructure' make[3]: Entering directory '/<>/BCFoundation/BCSequence' Making build-headers for subproject BCSequence... make[4]: Nothing to be done for 'internal-subproject-build-headers'. make[3]: Leaving directory '/<>/BCFoundation/BCSequence' make[3]: Entering directory '/<>/BCFoundation/BCSequenceIO' Making build-headers for subproject BCSequenceIO... make[4]: Nothing to be done for 'internal-subproject-build-headers'. make[3]: Leaving directory '/<>/BCFoundation/BCSequenceIO' make[3]: Entering directory '/<>/BCFoundation/BCSymbol' Making build-headers for subproject BCSymbol... make[4]: Nothing to be done for 'internal-subproject-build-headers'. make[3]: Leaving directory '/<>/BCFoundation/BCSymbol' make[3]: Entering directory '/<>/BCFoundation/BCTools' Making build-headers for subproject BCTools... make[4]: Nothing to be done for 'internal-subproject-build-headers'. make[3]: Leaving directory '/<>/BCFoundation/BCTools' make[3]: Entering directory '/<>/BCFoundation/BCUtils' Making build-headers for subproject BCUtils... make[4]: Nothing to be done for 'internal-subproject-build-headers'. make[3]: Leaving directory '/<>/BCFoundation/BCUtils' Making build-headers for subproject BCFoundation... make[3]: Nothing to be done for 'internal-subproject-build-headers'. make[2]: Leaving directory '/<>/BCFoundation' Making build-headers for framework BioCocoa... cd ./BioCocoa.framework; \ 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 Making all in subprojects of framework BioCocoa... make[2]: Entering directory '/<>/BCFoundation' Making all in subprojects of subproject BCFoundation... make[3]: Entering directory '/<>/BCFoundation/BCAlignment' Making all for subproject BCAlignment... make[5]: Nothing to be done for 'internal-subproject-compile'. make[3]: Leaving directory '/<>/BCFoundation/BCAlignment' make[3]: Entering directory '/<>/BCFoundation/BCAnalysis' Making all for subproject BCAnalysis... make[5]: Nothing to be done for 'internal-subproject-compile'. make[3]: Leaving directory '/<>/BCFoundation/BCAnalysis' make[3]: Entering directory '/<>/BCFoundation/BCGeneExpression' Making all for subproject BCGeneExpression... make[5]: Nothing to be done for 'internal-subproject-compile'. make[3]: Leaving directory '/<>/BCFoundation/BCGeneExpression' make[3]: Entering directory '/<>/BCFoundation/BCGeneticCode' Making all for subproject BCGeneticCode... make[5]: Nothing to be done for 'internal-subproject-compile'. make[3]: Leaving directory '/<>/BCFoundation/BCGeneticCode' make[3]: Entering directory '/<>/BCFoundation/BCProteinStructure' Making all for subproject BCProteinStructure... make[5]: Nothing to be done for 'internal-subproject-compile'. make[3]: Leaving directory '/<>/BCFoundation/BCProteinStructure' make[3]: Entering directory '/<>/BCFoundation/BCSequence' Making all for subproject BCSequence... make[5]: Nothing to be done for 'internal-subproject-compile'. make[3]: Leaving directory '/<>/BCFoundation/BCSequence' make[3]: Entering directory '/<>/BCFoundation/BCSequenceIO' Making all for subproject BCSequenceIO... make[5]: Nothing to be done for 'internal-subproject-compile'. make[3]: Leaving directory '/<>/BCFoundation/BCSequenceIO' make[3]: Entering directory '/<>/BCFoundation/BCSymbol' Making all for subproject BCSymbol... make[5]: Nothing to be done for 'internal-subproject-compile'. make[3]: Leaving directory '/<>/BCFoundation/BCSymbol' make[3]: Entering directory '/<>/BCFoundation/BCTools' Making all for subproject BCTools... make[5]: Nothing to be done for 'internal-subproject-compile'. make[3]: Leaving directory '/<>/BCFoundation/BCTools' make[3]: Entering directory '/<>/BCFoundation/BCUtils' Making all for subproject BCUtils... make[5]: Nothing to be done for 'internal-subproject-compile'. make[3]: Leaving directory '/<>/BCFoundation/BCUtils' Making all for subproject BCFoundation... make[4]: Nothing to be done for 'internal-subproject-compile'. make[2]: Leaving directory '/<>/BCFoundation' Making all for framework BioCocoa... make[3]: Nothing to be done for 'internal-framework-compile'. for f in BCFoundation/BCSymbol/SymbolTemplates/nucleotides.plist BCFoundation/BCSymbol/SymbolTemplates/aminoacids.plist; do \ if [ -f $f -o -d $f ]; then \ cp -fr $f ./BioCocoa.framework/Versions/2/Resources/; \ else \ echo "Warning: $f not found - ignoring"; \ fi; \ done for subproject in BCFoundation; do \ if [ -d $subproject/Resources/Subproject ]; then \ for f in $subproject/Resources/Subproject/*; do \ if [ $f != $subproject'/Resources/Subproject/*' ]; then \ cp -fr $f ./BioCocoa.framework/Versions/2/Resources/; \ fi; \ done; \ fi; \ done cd ./BioCocoa.framework/.; \ rm -f BioCocoa libBioCocoa.so; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh . \ Versions/Current/./BioCocoa short` \ BioCocoa; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh . \ Versions/Current/./libBioCocoa.so short` \ libBioCocoa.so Making install in subprojects of framework BioCocoa... make[2]: Entering directory '/<>/BCFoundation' Making install in subprojects of subproject BCFoundation... make[3]: Entering directory '/<>/BCFoundation/BCAlignment' Making install for subproject BCAlignment... make[4]: Nothing to be done for 'internal-subproject-install'. make[3]: Leaving directory '/<>/BCFoundation/BCAlignment' make[3]: Entering directory '/<>/BCFoundation/BCAnalysis' Making install for subproject BCAnalysis... make[4]: Nothing to be done for 'internal-subproject-install'. make[3]: Leaving directory '/<>/BCFoundation/BCAnalysis' make[3]: Entering directory '/<>/BCFoundation/BCGeneExpression' Making install for subproject BCGeneExpression... make[4]: Nothing to be done for 'internal-subproject-install'. make[3]: Leaving directory '/<>/BCFoundation/BCGeneExpression' make[3]: Entering directory '/<>/BCFoundation/BCGeneticCode' Making install for subproject BCGeneticCode... make[4]: Nothing to be done for 'internal-subproject-install'. make[3]: Leaving directory '/<>/BCFoundation/BCGeneticCode' make[3]: Entering directory '/<>/BCFoundation/BCProteinStructure' Making install for subproject BCProteinStructure... make[4]: Nothing to be done for 'internal-subproject-install'. make[3]: Leaving directory '/<>/BCFoundation/BCProteinStructure' make[3]: Entering directory '/<>/BCFoundation/BCSequence' Making install for subproject BCSequence... make[4]: Nothing to be done for 'internal-subproject-install'. make[3]: Leaving directory '/<>/BCFoundation/BCSequence' make[3]: Entering directory '/<>/BCFoundation/BCSequenceIO' Making install for subproject BCSequenceIO... make[4]: Nothing to be done for 'internal-subproject-install'. make[3]: Leaving directory '/<>/BCFoundation/BCSequenceIO' make[3]: Entering directory '/<>/BCFoundation/BCSymbol' Making install for subproject BCSymbol... make[4]: Nothing to be done for 'internal-subproject-install'. make[3]: Leaving directory '/<>/BCFoundation/BCSymbol' make[3]: Entering directory '/<>/BCFoundation/BCTools' Making install for subproject BCTools... make[4]: Nothing to be done for 'internal-subproject-install'. make[3]: Leaving directory '/<>/BCFoundation/BCTools' make[3]: Entering directory '/<>/BCFoundation/BCUtils' Making install for subproject BCUtils... make[4]: Nothing to be done for 'internal-subproject-install'. make[3]: Leaving directory '/<>/BCFoundation/BCUtils' Making install for subproject BCFoundation... make[3]: Nothing to be done for 'internal-subproject-install'. make[2]: Leaving directory '/<>/BCFoundation' Making install for framework BioCocoa... /usr/share/GNUstep/Makefiles/mkinstalldirs /<>/debian/tmp///usr/lib/GNUstep/Frameworks /usr/share/GNUstep/Makefiles/mkinstalldirs /<>/debian/tmp///usr/include/GNUstep (cd .; \ tar cfX - /usr/share/GNUstep/Makefiles/tar-exclude-list \ BioCocoa.framework) \ | (cd /<>/debian/tmp///usr/lib/GNUstep/Frameworks; tar xf -) cd /<>/debian/tmp///usr/include/GNUstep; \ rm -f BioCocoa; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /<>/debian/tmp///usr/include/GNUstep /<>/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Headers short` BioCocoa; \ cd /<>/debian/tmp///usr/lib/.; \ rm -f libBioCocoa.so; \ rm -f libBioCocoa.so.2; \ rm -f libBioCocoa.so.2.2.2; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /<>/debian/tmp///usr/lib/. /<>/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so short` libBioCocoa.so; \ if test -r "/<>/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/./libBioCocoa.so.2"; then \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /<>/debian/tmp///usr/lib/. /<>/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/./libBioCocoa.so.2 short` libBioCocoa.so.2; \ fi; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /<>/debian/tmp///usr/lib/. /<>/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/./libBioCocoa.so.2.2.2 short` libBioCocoa.so.2.2.2 make[1]: Leaving directory '/<>' touch debian/stamp-makefile-install Adding cdbs dependencies to debian/libbiococoa-dev.substvars dh_installdirs -plibbiococoa-dev Adding cdbs dependencies to debian/libbiococoa2.substvars dh_installdirs -plibbiococoa2 dh_installdocs -plibbiococoa-dev dh_installexamples -plibbiococoa-dev dh_installman -plibbiococoa-dev dh_installinfo -plibbiococoa-dev dh_installmenu -plibbiococoa-dev dh_installcron -plibbiococoa-dev dh_installinit -plibbiococoa-dev dh_installdebconf -plibbiococoa-dev dh_installemacsen -plibbiococoa-dev dh_installcatalogs -plibbiococoa-dev dh_installpam -plibbiococoa-dev dh_installlogrotate -plibbiococoa-dev dh_installlogcheck -plibbiococoa-dev dh_installchangelogs -plibbiococoa-dev ./ChangeLog dh_installudev -plibbiococoa-dev dh_lintian -plibbiococoa-dev dh_bugfiles -plibbiococoa-dev dh_install -plibbiococoa-dev --sourcedir=/<>/debian/tmp/ dh_link -plibbiococoa-dev dh_installmime -plibbiococoa-dev dh_installgsettings -plibbiococoa-dev gsdh_gnustep -plibbiococoa-dev dh_link -plibbiococoa-dev dh_installdocs -plibbiococoa2 dh_installexamples -plibbiococoa2 dh_installman -plibbiococoa2 dh_installinfo -plibbiococoa2 dh_installmenu -plibbiococoa2 dh_installcron -plibbiococoa2 dh_installinit -plibbiococoa2 dh_installdebconf -plibbiococoa2 dh_installemacsen -plibbiococoa2 dh_installcatalogs -plibbiococoa2 dh_installpam -plibbiococoa2 dh_installlogrotate -plibbiococoa2 dh_installlogcheck -plibbiococoa2 dh_installchangelogs -plibbiococoa2 ./ChangeLog dh_installudev -plibbiococoa2 dh_lintian -plibbiococoa2 dh_bugfiles -plibbiococoa2 dh_install -plibbiococoa2 --sourcedir=/<>/debian/tmp/ dh_link -plibbiococoa2 dh_installmime -plibbiococoa2 dh_installgsettings -plibbiococoa2 gsdh_gnustep -plibbiococoa2 dh_link -plibbiococoa2 dh_strip -plibbiococoa-dev dh_strip debug symbol extraction: enabling -a due to Build-Debug-Symbols: yes in /CurrentlyBuilding dh_strip debug symbol extraction: all non-arch-all packages for this build platform s390x: libbiococoa-dev libbiococoa2 dh_strip debug symbol extraction: packages to act on: libbiococoa-dev dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 libbiococoa-dev has no unstripped objects, ignoring find: `/<>/debian/libbiococoa-dev-dbgsym': No such file or directory /usr/bin/pkg_create_dbgsym: nothing in /<>/debian/libbiococoa-dev-dbgsym and no dbgdepends, ignoring dh_compress -plibbiococoa-dev dh_fixperms -plibbiococoa-dev dh_makeshlibs -plibbiococoa-dev dh_strip -plibbiococoa2 dh_strip debug symbol extraction: enabling -a due to Build-Debug-Symbols: yes in /CurrentlyBuilding dh_strip debug symbol extraction: all non-arch-all packages for this build platform s390x: libbiococoa-dev libbiococoa2 dh_strip debug symbol extraction: packages to act on: libbiococoa2 dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 libbiococoa2 has no unstripped objects, ignoring find: `/<>/debian/libbiococoa2-dbgsym': No such file or directory /usr/bin/pkg_create_dbgsym: nothing in /<>/debian/libbiococoa2-dbgsym and no dbgdepends, ignoring dh_compress -plibbiococoa2 dh_fixperms -plibbiococoa2 dh_makeshlibs -plibbiococoa2 --noscripts dh_installdeb -plibbiococoa-dev dh_perl -plibbiococoa-dev dh_shlibdeps -plibbiococoa-dev dh_installdeb -plibbiococoa2 dh_perl -plibbiococoa2 dh_shlibdeps -plibbiococoa2 dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libbiococoa2/usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/libBioCocoa.so.2.2.2 was not linked against libpthread.so.0 (it uses none of the library's symbols) dh_gencontrol -plibbiococoa-dev dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform s390x: libbiococoa-dev libbiococoa2 dh_gencontrol debug symbol wrapper: packages to act on: libbiococoa-dev dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: no debian/libbiococoa-dev-dbgsym, skipping package libbiococoa-dev # only call dh_scour for packages in main if grep -q '^Component:[[:space:]]*main' /CurrentlyBuilding 2>/dev/null; then dh_scour -plibbiococoa-dev ; fi dh_md5sums -plibbiococoa-dev dh_builddeb -plibbiococoa-dev INFO: pkgstriptranslations version 123 pkgstriptranslations: processing libbiococoa-dev (in debian/libbiococoa-dev); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libbiococoa-dev/DEBIAN/control, package libbiococoa-dev, directory debian/libbiococoa-dev .. removing usr/share/doc/libbiococoa-dev/changelog.gz grep: ../libbiococoa2/DEBIAN/control: No such file or directory Searching for duplicated docs in dependency libbiococoa2... symlinking changelog.Debian.gz in libbiococoa-dev to file in libbiococoa2 /usr/bin/pkgstripfiles: line 177: [: /<>/debian/libbiococoa-dev/../libbiococoa2/usr/share/doc/libbiococoa2/Tests/Test-BCFoundation/DataFiles/hB26H-N,S: binary operator expected pkgstripfiles: Running PNG optimization (using 4 cpus) for package libbiococoa-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libbiococoa-dev' in '../libbiococoa-dev_2.2.2-2_s390x.deb'. dh_gencontrol -plibbiococoa2 dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform s390x: libbiococoa-dev libbiococoa2 dh_gencontrol debug symbol wrapper: packages to act on: libbiococoa2 dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: no debian/libbiococoa2-dbgsym, skipping package libbiococoa2 # only call dh_scour for packages in main if grep -q '^Component:[[:space:]]*main' /CurrentlyBuilding 2>/dev/null; then dh_scour -plibbiococoa2 ; fi dh_md5sums -plibbiococoa2 dh_builddeb -plibbiococoa2 INFO: pkgstriptranslations version 123 pkgstriptranslations: processing libbiococoa2 (in debian/libbiococoa2); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libbiococoa2/DEBIAN/control, package libbiococoa2, directory debian/libbiococoa2 .. removing usr/share/doc/libbiococoa2/changelog.gz pkgstripfiles: Truncating usr/share/doc/libbiococoa2/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package libbiococoa2 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libbiococoa2' in '../libbiococoa2_2.2.2-2_s390x.deb'. dpkg-genchanges -B -mLaunchpad Build Daemon >../biococoa_2.2.2-2_s390x.changes dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build biococoa-2.2.2 dpkg-buildpackage: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20151204-1840 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ biococoa_2.2.2-2_s390x.changes: ------------------------------- Format: 1.8 Date: Mon, 11 Nov 2013 15:12:00 +0100 Source: biococoa Binary: libbiococoa-dev libbiococoa2 Architecture: s390x Version: 2.2.2-2 Distribution: xenial Urgency: low Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: libbiococoa-dev - Bioinformatics framework for GNUstep and Cocoa (development files libbiococoa2 - Bioinformatics framework for GNUstep and Cocoa (library files) Changes: biococoa (2.2.2-2) unstable; urgency=low . [ Andreas Tille ] * Fixed watch file to not report demos. * debian/control: - cme fix dpkg-control - Debhelper 9 - canonical Vcs fields - add missing Build-Depends: gnustep-make . [ Thorsten Alteholz ] * debian/rules: target get-orig-source added Checksums-Sha1: 99ca6444fc0a98bef6390675dfa4d6e56f39ec5b 114834 libbiococoa-dev_2.2.2-2_s390x.deb 0446d10bd4b1116750168ef6ed0f6ef5418cc02f 110796 libbiococoa2_2.2.2-2_s390x.deb Checksums-Sha256: 5d87e20df49376cff79a9715658c67a8f1366207faa09110243d724521a438ca 114834 libbiococoa-dev_2.2.2-2_s390x.deb 47215b87689ae0e777faed8cd5e6afef0d2f1d8e9e904d36f7dc1fdaa74d71b2 110796 libbiococoa2_2.2.2-2_s390x.deb Files: 65876826519b51a6c8fcb53d41debd09 114834 libdevel optional libbiococoa-dev_2.2.2-2_s390x.deb 018dab57745a4b0e5efc94e843f16e0b 110796 libs optional libbiococoa2_2.2.2-2_s390x.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libbiococoa-dev_2.2.2-2_s390x.deb --------------------------------- new debian package, version 2.0. size 114834 bytes: control archive=3673 bytes. 1368 bytes, 25 lines control 9990 bytes, 92 lines md5sums Package: libbiococoa-dev Source: biococoa Version: 2.2.2-2 Architecture: s390x Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 417 Depends: libbiococoa2 (= 2.2.2-2), libgnustep-base-dev, gnustep-fslayout-fhs Section: libdevel Priority: optional Homepage: http://bioinformatics.org/biococoa/ Description: Bioinformatics framework for GNUstep and Cocoa (development files) BioCocoa is an open source Cocoa framework for bioinformatics. It intends to provide Cocoa programmers with a full suite of tools for handling and manipulating biological sequences. Cocoa is a great framework for rapid application development and it is therefore often used to create innovative bioscientific apps. To speed up development even more, BioCocoa wants to offer reusable Cocoa classes that are specific for molecular biology and biofinformatics. At this time, BioCocoa offers model classes for biological sequences, controller classes for alignment, sequence manipulation and I/O, interfacing with ENTREZ and view classes that let you easily display and work with sequences in your own applications. . This package contains the development files, documentation and examples for developing GNUstep applications using the BioCocoa framework. drwxr-xr-x root/root 0 2015-12-04 18:40 ./ drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/ drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/include/ drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/include/GNUstep/ lrwxrwxrwx root/root 0 2015-12-04 18:40 ./usr/include/GNUstep/BioCocoa -> ../../lib/GNUstep/Frameworks/BioCocoa.framework/Headers drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/include/GNUstep/Frameworks/ drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/include/GNUstep/Frameworks/BioCocoa.framework/ lrwxrwxrwx root/root 0 2015-12-04 18:40 ./usr/include/GNUstep/Frameworks/BioCocoa.framework/Headers -> Versions/2 drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/include/GNUstep/Frameworks/BioCocoa.framework/Versions/ drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/include/GNUstep/Frameworks/BioCocoa.framework/Versions/2/ -rw-r--r-- root/root 6582 2009-07-02 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./usr/share/doc/libbiococoa-dev/Tests/Test-BCFoundation/TestBCSuffixArray.m.gz lrwxrwxrwx root/root 0 2015-12-04 18:40 ./usr/share/doc/libbiococoa-dev/changelog.Debian.gz -> ../libbiococoa2/changelog.Debian.gz -rw-r--r-- root/root 13904 2010-09-14 20:17 ./usr/share/doc/libbiococoa-dev/copyright drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/share/man/ drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/share/man/man3/ -rw-r--r-- root/root 605 2015-12-04 18:40 ./usr/share/man/man3/BioCocoa.3.gz libbiococoa2_2.2.2-2_s390x.deb ------------------------------ new debian package, version 2.0. size 110796 bytes: control archive=1156 bytes. 1320 bytes, 24 lines control 597 bytes, 6 lines md5sums 27 bytes, 1 lines shlibs Package: libbiococoa2 Source: biococoa Version: 2.2.2-2 Architecture: s390x Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 555 Depends: gnustep-base-runtime (>= 1.24.7), libc6 (>= 2.4), libgnustep-base1.24 (>= 1.24.7), libobjc4 (>= 4.2.1), gnustep-fslayout-fhs Section: libs Priority: optional Homepage: http://bioinformatics.org/biococoa/ Description: Bioinformatics framework for GNUstep and Cocoa (library files) BioCocoa is an open source Cocoa framework for bioinformatics. It intends to provide Cocoa programmers with a full suite of tools for handling and manipulating biological sequences. Cocoa is a great framework for rapid application development and it is therefore often used to create innovative bioscientific apps. To speed up development even more, BioCocoa wants to offer reusable Cocoa classes that are specific for molecular biology and biofinformatics. At this time, BioCocoa offers model classes for biological sequences, controller classes for alignment, sequence manipulation and I/O, interfacing with ENTREZ and view classes that let you easily display and work with sequences in your own applications. . This package contains the runtime libraries. drwxr-xr-x root/root 0 2015-12-04 18:40 ./ drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/ drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/lib/ drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/lib/GNUstep/ drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/lib/GNUstep/Frameworks/ drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/lib/GNUstep/Frameworks/BioCocoa.framework/ drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/ drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/ lrwxrwxrwx root/root 0 2015-12-04 18:40 ./usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/Resources -> ../../../../../../share/GNUstep/Frameworks/BioCocoa.framework/Versions/2 lrwxrwxrwx root/root 0 2015-12-04 18:40 ./usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/libBioCocoa.so.2 -> libBioCocoa.so.2.2.2 -rw-r--r-- root/root 498624 2015-12-04 18:40 ./usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/libBioCocoa.so.2.2.2 lrwxrwxrwx root/root 0 2015-12-04 18:40 ./usr/lib/libBioCocoa.so.2 -> GNUstep/Frameworks/BioCocoa.framework/Versions/2/libBioCocoa.so.2 lrwxrwxrwx root/root 0 2015-12-04 18:40 ./usr/lib/libBioCocoa.so.2.2.2 -> GNUstep/Frameworks/BioCocoa.framework/Versions/2/libBioCocoa.so.2.2.2 drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/share/ drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/share/GNUstep/ drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/share/GNUstep/Frameworks/ drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/share/GNUstep/Frameworks/BioCocoa.framework/ drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/share/GNUstep/Frameworks/BioCocoa.framework/Versions/ drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/share/GNUstep/Frameworks/BioCocoa.framework/Versions/2/ -rw-r--r-- root/root 957 2015-12-04 18:40 ./usr/share/GNUstep/Frameworks/BioCocoa.framework/Versions/2/Info-gnustep.plist -rw-r--r-- root/root 13143 2015-12-04 18:40 ./usr/share/GNUstep/Frameworks/BioCocoa.framework/Versions/2/aminoacids.plist -rw-r--r-- root/root 15033 2015-12-04 18:40 ./usr/share/GNUstep/Frameworks/BioCocoa.framework/Versions/2/nucleotides.plist drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/share/doc/ drwxr-xr-x root/root 0 2015-12-04 18:40 ./usr/share/doc/libbiococoa2/ -rw-r--r-- root/root 1642 2015-12-04 18:40 ./usr/share/doc/libbiococoa2/changelog.Debian.gz -rw-r--r-- root/root 13904 2010-09-14 20:17 ./usr/share/doc/libbiococoa2/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 9820 Build-Time: 14 Distribution: xenial Host Architecture: s390x Install-Time: 27 Job: biococoa_2.2.2-2.dsc Machine Architecture: s390x Package: biococoa Package-Time: 41 Source-Version: 2.2.2-2 Space: 9820 Status: successful Version: 2.2.2-2 -------------------------------------------------------------------------------- Finished at 20151204-1840 Build needed 00:00:41, 9820k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-8372240'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-8372240/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-8372240'] Unmounting chroot for build PACKAGEBUILD-8372240... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-8372240'] Removing build PACKAGEBUILD-8372240