RUN: /bin/echo ['echo', 'Forking build subprocess...'] Forking build subprocess... RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'e0e6c5ab29c07ba7130c0fba08f37c0b274aba27', '/home/buildd/filecache-default/54f0a0022ad47cbc59d2c6b625e2bfb99be21df0'] Synching the system clock with the buildd NTP service... 14 Aug 18:15:30 ntpdate[11450]: adjust time server 10.211.37.1 offset 0.000575 sec Unpacking chroot for build e0e6c5ab29c07ba7130c0fba08f37c0b274aba27 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'e0e6c5ab29c07ba7130c0fba08f37c0b274aba27'] Mounting chroot for build e0e6c5ab29c07ba7130c0fba08f37c0b274aba27 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'e0e6c5ab29c07ba7130c0fba08f37c0b274aba27', 'deb http://ftpmaster.internal/ubuntu oneiric main universe'] Overriding sources.list in build-e0e6c5ab29c07ba7130c0fba08f37c0b274aba27 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'e0e6c5ab29c07ba7130c0fba08f37c0b274aba27', 'armel'] Updating debian chroot for build e0e6c5ab29c07ba7130c0fba08f37c0b274aba27 Ign http://ftpmaster.internal oneiric InRelease Get:1 http://ftpmaster.internal oneiric Release.gpg [198 B] Get:2 http://ftpmaster.internal oneiric Release [39.8 kB] Get:3 http://ftpmaster.internal oneiric/main armel Packages [1635 kB] Get:4 http://ftpmaster.internal oneiric/universe armel Packages [6233 kB] Ign http://ftpmaster.internal oneiric/main TranslationIndex Ign http://ftpmaster.internal oneiric/universe TranslationIndex Ign http://ftpmaster.internal oneiric/main Translation-en Ign http://ftpmaster.internal oneiric/universe Translation-en Fetched 7907 kB in 21s (365 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: iproute libapt-pkg4.11 The following packages will be upgraded: apt apt-transport-https base-files base-passwd binutils bsdutils cpp cpp-4.6 g++ g++-4.6 gcc gcc-4.6 gcc-4.6-base grep ifupdown libacl1 libattr1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libgcc1 libglib2.0-0 libgomp1 libidn11 libkeyutils1 libmount1 libmpfr4 libplymouth2 libpng12-0 libsasl2-2 libstdc++6 libstdc++6-4.6-dev libudev0 libusb-0.1-4 libuuid1 linux-libc-dev mount multiarch-support perl perl-base perl-modules plymouth python-minimal python2.7-minimal udev upstart util-linux 49 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 41.7 MB of archives. After this operation, 311 kB disk space will be freed. WARNING: The following packages cannot be authenticated! base-files grep mount perl perl-base perl-modules iproute ifupdown upstart libc-dev-bin libc6-dev libc-bin libc6 libgomp1 gcc-4.6-base libgcc1 cpp-4.6 libstdc++6-4.6-dev g++-4.6 gcc-4.6 libstdc++6 libmpfr4 linux-libc-dev binutils libudev0 util-linux base-passwd bsdutils python2.7-minimal python-minimal libattr1 libacl1 libuuid1 libblkid1 libmount1 libglib2.0-0 libpng12-0 libidn11 libkeyutils1 libapt-pkg4.11 apt-transport-https apt libusb-0.1-4 multiarch-support udev plymouth libplymouth2 libsasl2-2 cpp gcc g++ Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ oneiric/main base-files armel 6.4ubuntu4 [64.6 kB] Get:2 http://ftpmaster.internal/ubuntu/ oneiric/main grep armel 2.9-1 [218 kB] Get:3 http://ftpmaster.internal/ubuntu/ oneiric/main mount armel 2.19.1-2ubuntu3 [152 kB] Get:4 http://ftpmaster.internal/ubuntu/ oneiric/main perl armel 5.12.4-2 [3480 kB] Get:5 http://ftpmaster.internal/ubuntu/ oneiric/main perl-base armel 5.12.4-2 [1311 kB] Get:6 http://ftpmaster.internal/ubuntu/ oneiric/main perl-modules all 5.12.4-2 [4713 kB] Get:7 http://ftpmaster.internal/ubuntu/ oneiric/main iproute armel 20110315-1build1 [379 kB] Get:8 http://ftpmaster.internal/ubuntu/ oneiric/main ifupdown armel 0.7~alpha5.1ubuntu2 [43.0 kB] Get:9 http://ftpmaster.internal/ubuntu/ oneiric/main upstart armel 1.3-0ubuntu6 [284 kB] Get:10 http://ftpmaster.internal/ubuntu/ oneiric/main libc-dev-bin armel 2.13-16ubuntu3 [73.7 kB] Get:11 http://ftpmaster.internal/ubuntu/ oneiric/main libc6-dev armel 2.13-16ubuntu3 [2215 kB] Get:12 http://ftpmaster.internal/ubuntu/ oneiric/main libc-bin armel 2.13-16ubuntu3 [845 kB] Get:13 http://ftpmaster.internal/ubuntu/ oneiric/main libc6 armel 2.13-16ubuntu3 [3840 kB] Get:14 http://ftpmaster.internal/ubuntu/ oneiric/main libgomp1 armel 4.6.1-6ubuntu6 [23.6 kB] Get:15 http://ftpmaster.internal/ubuntu/ oneiric/main gcc-4.6-base armel 4.6.1-6ubuntu6 [15.4 kB] Get:16 http://ftpmaster.internal/ubuntu/ oneiric/main libgcc1 armel 1:4.6.1-6ubuntu6 [22.2 kB] Get:17 http://ftpmaster.internal/ubuntu/ oneiric/main cpp-4.6 armel 4.6.1-6ubuntu6 [4034 kB] Get:18 http://ftpmaster.internal/ubuntu/ oneiric/main libstdc++6-4.6-dev armel 4.6.1-6ubuntu6 [1675 kB] Get:19 http://ftpmaster.internal/ubuntu/ oneiric/main g++-4.6 armel 4.6.1-6ubuntu6 [4366 kB] Get:20 http://ftpmaster.internal/ubuntu/ oneiric/main gcc-4.6 armel 4.6.1-6ubuntu6 [4492 kB] Get:21 http://ftpmaster.internal/ubuntu/ oneiric/main libstdc++6 armel 4.6.1-6ubuntu6 [275 kB] Get:22 http://ftpmaster.internal/ubuntu/ oneiric/main libmpfr4 armel 3.0.1-5 [169 kB] Get:23 http://ftpmaster.internal/ubuntu/ oneiric/main linux-libc-dev armel 3.0.0-8.11 [799 kB] Get:24 http://ftpmaster.internal/ubuntu/ oneiric/main binutils armel 2.21.53.20110810-0ubuntu1 [2611 kB] Get:25 http://ftpmaster.internal/ubuntu/ oneiric/main libudev0 armel 172-0ubuntu5 [26.6 kB] Get:26 http://ftpmaster.internal/ubuntu/ oneiric/main util-linux armel 2.19.1-2ubuntu3 [534 kB] Get:27 http://ftpmaster.internal/ubuntu/ oneiric/main base-passwd armel 3.5.23 [37.0 kB] Get:28 http://ftpmaster.internal/ubuntu/ oneiric/main bsdutils armel 1:2.19.1-2ubuntu3 [32.6 kB] Get:29 http://ftpmaster.internal/ubuntu/ oneiric/main python2.7-minimal armel 2.7.2-4 [1490 kB] Get:30 http://ftpmaster.internal/ubuntu/ oneiric/main python-minimal all 2.7.2-5ubuntu1 [30.5 kB] Get:31 http://ftpmaster.internal/ubuntu/ oneiric/main libattr1 armel 1:2.4.46-3 [9608 B] Get:32 http://ftpmaster.internal/ubuntu/ oneiric/main libacl1 armel 2.2.51-3 [14.8 kB] Get:33 http://ftpmaster.internal/ubuntu/ oneiric/main libuuid1 armel 2.19.1-2ubuntu3 [13.6 kB] Get:34 http://ftpmaster.internal/ubuntu/ oneiric/main libblkid1 armel 2.19.1-2ubuntu3 [69.2 kB] Get:35 http://ftpmaster.internal/ubuntu/ oneiric/main libmount1 armel 2.19.1-2ubuntu3 [51.2 kB] Get:36 http://ftpmaster.internal/ubuntu/ oneiric/main libglib2.0-0 armel 2.29.14-0ubuntu1 [996 kB] Get:37 http://ftpmaster.internal/ubuntu/ oneiric/main libpng12-0 armel 1.2.46-3ubuntu1 [118 kB] Get:38 http://ftpmaster.internal/ubuntu/ oneiric/main libidn11 armel 1.22-2 [107 kB] Get:39 http://ftpmaster.internal/ubuntu/ oneiric/main libkeyutils1 armel 1.4-6 [6048 B] Get:40 http://ftpmaster.internal/ubuntu/ oneiric/main libapt-pkg4.11 armel 0.8.16~exp5ubuntu5 [451 kB] Get:41 http://ftpmaster.internal/ubuntu/ oneiric/main apt-transport-https armel 0.8.16~exp5ubuntu5 [14.9 kB] Get:42 http://ftpmaster.internal/ubuntu/ oneiric/main apt armel 0.8.16~exp5ubuntu5 [1026 kB] Get:43 http://ftpmaster.internal/ubuntu/ oneiric/main libusb-0.1-4 armel 2:0.1.12-18 [14.9 kB] Get:44 http://ftpmaster.internal/ubuntu/ oneiric/main multiarch-support armel 2.13-16ubuntu3 [4476 B] Get:45 http://ftpmaster.internal/ubuntu/ oneiric/main udev armel 172-0ubuntu5 [300 kB] Get:46 http://ftpmaster.internal/ubuntu/ oneiric/main plymouth armel 0.8.2-2ubuntu25 [101 kB] Get:47 http://ftpmaster.internal/ubuntu/ oneiric/main libplymouth2 armel 0.8.2-2ubuntu25 [72.2 kB] Get:48 http://ftpmaster.internal/ubuntu/ oneiric/main libsasl2-2 armel 2.1.24~rc1.dfsg1+cvs2011-05-23-4ubuntu1 [57.2 kB] Get:49 http://ftpmaster.internal/ubuntu/ oneiric/main cpp armel 4:4.6.1-2ubuntu5 [27.8 kB] Get:50 http://ftpmaster.internal/ubuntu/ oneiric/main gcc armel 4:4.6.1-2ubuntu5 [5120 B] Get:51 http://ftpmaster.internal/ubuntu/ oneiric/main g++ armel 4:4.6.1-2ubuntu5 [1458 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 41.7 MB in 5s (8102 kB/s) (Reading database ... 14011 files and directories currently installed.) Preparing to replace base-files 6.4ubuntu2 (using .../base-files_6.4ubuntu4_armel.deb) ... Unpacking replacement base-files ... Setting up base-files (6.4ubuntu4) ... (Reading database ... 14011 files and directories currently installed.) Preparing to replace grep 2.8-2 (using .../archives/grep_2.9-1_armel.deb) ... Unpacking replacement grep ... Setting up grep (2.9-1) ... (Reading database ... 14011 files and directories currently installed.) Preparing to replace mount 2.19.1-2ubuntu2 (using .../mount_2.19.1-2ubuntu3_armel.deb) ... Unpacking replacement mount ... Setting up mount (2.19.1-2ubuntu3) ... (Reading database ... 14011 files and directories currently installed.) Preparing to replace perl 5.12.4-1ubuntu2 (using .../perl_5.12.4-2_armel.deb) ... Unpacking replacement perl ... Preparing to replace perl-base 5.12.4-1ubuntu2 (using .../perl-base_5.12.4-2_armel.deb) ... Unpacking replacement perl-base ... Setting up perl-base (5.12.4-2) ... (Reading database ... 14011 files and directories currently installed.) Preparing to replace perl-modules 5.12.4-1ubuntu2 (using .../perl-modules_5.12.4-2_all.deb) ... Unpacking replacement perl-modules ... Selecting previously deselected package iproute. Unpacking iproute (from .../iproute_20110315-1build1_armel.deb) ... Preparing to replace ifupdown 0.6.10ubuntu4 (using .../ifupdown_0.7~alpha5.1ubuntu2_armel.deb) ... Unpacking replacement ifupdown ... Preparing to replace upstart 1.3-0ubuntu3 (using .../upstart_1.3-0ubuntu6_armel.deb) ... Unpacking replacement upstart ... Preparing to replace libc-dev-bin 2.13-9ubuntu2 (using .../libc-dev-bin_2.13-16ubuntu3_armel.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libc6-dev 2.13-9ubuntu2 (using .../libc6-dev_2.13-16ubuntu3_armel.deb) ... Unpacking replacement libc6-dev ... Preparing to replace libc-bin 2.13-9ubuntu2 (using .../libc-bin_2.13-16ubuntu3_armel.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.13-16ubuntu3) ... (Reading database ... 14067 files and directories currently installed.) Preparing to replace libc6 2.13-9ubuntu2 (using .../libc6_2.13-16ubuntu3_armel.deb) ... Unpacking replacement libc6 ... Setting up libc6 (2.13-16ubuntu3) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 14067 files and directories currently installed.) Preparing to replace libgomp1 4.6.1-4ubuntu1 (using .../libgomp1_4.6.1-6ubuntu6_armel.deb) ... Unpacking replacement libgomp1 ... Preparing to replace gcc-4.6-base 4.6.1-4ubuntu1 (using .../gcc-4.6-base_4.6.1-6ubuntu6_armel.deb) ... Unpacking replacement gcc-4.6-base ... Setting up gcc-4.6-base (4.6.1-6ubuntu6) ... (Reading database ... 14067 files and directories currently installed.) Preparing to replace libgcc1 1:4.6.1-4ubuntu1 (using .../libgcc1_1%3a4.6.1-6ubuntu6_armel.deb) ... Unpacking replacement libgcc1 ... Setting up libgcc1 (1:4.6.1-6ubuntu6) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 14067 files and directories currently installed.) Preparing to replace cpp-4.6 4.6.1-4ubuntu1 (using .../cpp-4.6_4.6.1-6ubuntu6_armel.deb) ... Unpacking replacement cpp-4.6 ... Preparing to replace libstdc++6-4.6-dev 4.6.1-4ubuntu1 (using .../libstdc++6-4.6-dev_4.6.1-6ubuntu6_armel.deb) ... Unpacking replacement libstdc++6-4.6-dev ... Preparing to replace g++-4.6 4.6.1-4ubuntu1 (using .../g++-4.6_4.6.1-6ubuntu6_armel.deb) ... Unpacking replacement g++-4.6 ... Preparing to replace gcc-4.6 4.6.1-4ubuntu1 (using .../gcc-4.6_4.6.1-6ubuntu6_armel.deb) ... Unpacking replacement gcc-4.6 ... Preparing to replace libstdc++6 4.6.1-4ubuntu1 (using .../libstdc++6_4.6.1-6ubuntu6_armel.deb) ... Unpacking replacement libstdc++6 ... Setting up libstdc++6 (4.6.1-6ubuntu6) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 14083 files and directories currently installed.) Preparing to replace libmpfr4 3.0.1-4 (using .../libmpfr4_3.0.1-5_armel.deb) ... Unpacking replacement libmpfr4 ... Preparing to replace linux-libc-dev 3.0.0-5.6 (using .../linux-libc-dev_3.0.0-8.11_armel.deb) ... Unpacking replacement linux-libc-dev ... Preparing to replace binutils 2.21.52.20110707-1ubuntu1 (using .../binutils_2.21.53.20110810-0ubuntu1_armel.deb) ... Unpacking replacement binutils ... Preparing to replace libudev0 172-0ubuntu3 (using .../libudev0_172-0ubuntu5_armel.deb) ... Unpacking replacement libudev0 ... Preparing to replace util-linux 2.19.1-2ubuntu2 (using .../util-linux_2.19.1-2ubuntu3_armel.deb) ... Unpacking replacement util-linux ... Setting up libudev0 (172-0ubuntu5) ... Setting up iproute (20110315-1build1) ... Setting up ifupdown (0.7~alpha5.1ubuntu2) ... Installing new version of config file /etc/network/if-up.d/upstart ... Setting up upstart (1.3-0ubuntu6) ... Installing new version of config file /etc/init/rc.conf ... Installing new version of config file /etc/init/upstart-udev-bridge.conf ... Installing new version of config file /etc/init/rc-sysinit.conf ... Setting up util-linux (2.19.1-2ubuntu3) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 14084 files and directories currently installed.) Preparing to replace base-passwd 3.5.22 (using .../base-passwd_3.5.23_armel.deb) ... Unpacking replacement base-passwd ... Setting up base-passwd (3.5.23) ... (Reading database ... 14086 files and directories currently installed.) Preparing to replace bsdutils 1:2.19.1-2ubuntu2 (using .../bsdutils_1%3a2.19.1-2ubuntu3_armel.deb) ... Unpacking replacement bsdutils ... Setting up bsdutils (1:2.19.1-2ubuntu3) ... (Reading database ... 14086 files and directories currently installed.) Preparing to replace python2.7-minimal 2.7.2-3 (using .../python2.7-minimal_2.7.2-4_armel.deb) ... Unpacking replacement python2.7-minimal ... Setting up python2.7-minimal (2.7.2-4) ... (Reading database ... 14086 files and directories currently installed.) Preparing to replace python-minimal 2.7.2-1ubuntu2 (using .../python-minimal_2.7.2-5ubuntu1_all.deb) ... Unpacking replacement python-minimal ... Setting up python-minimal (2.7.2-5ubuntu1) ... (Reading database ... 14086 files and directories currently installed.) Preparing to replace libattr1 1:2.4.46-1 (using .../libattr1_1%3a2.4.46-3_armel.deb) ... Unpacking replacement libattr1 ... Setting up libattr1 (1:2.4.46-3) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 14086 files and directories currently installed.) Preparing to replace libacl1 2.2.51-1 (using .../libacl1_2.2.51-3_armel.deb) ... Unpacking replacement libacl1 ... Setting up libacl1 (2.2.51-3) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 14086 files and directories currently installed.) Preparing to replace libuuid1 2.19.1-2ubuntu2 (using .../libuuid1_2.19.1-2ubuntu3_armel.deb) ... Unpacking replacement libuuid1 ... Setting up libuuid1 (2.19.1-2ubuntu3) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 14086 files and directories currently installed.) Preparing to replace libblkid1 2.19.1-2ubuntu2 (using .../libblkid1_2.19.1-2ubuntu3_armel.deb) ... Unpacking replacement libblkid1 ... Setting up libblkid1 (2.19.1-2ubuntu3) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 14086 files and directories currently installed.) Preparing to replace libmount1 2.19.1-2ubuntu2 (using .../libmount1_2.19.1-2ubuntu3_armel.deb) ... Unpacking replacement libmount1 ... Setting up libmount1 (2.19.1-2ubuntu3) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 14086 files and directories currently installed.) Preparing to replace libglib2.0-0 2.29.10-0ubuntu2 (using .../libglib2.0-0_2.29.14-0ubuntu1_armel.deb) ... Unpacking replacement libglib2.0-0 ... Preparing to replace libpng12-0 1.2.44-2ubuntu1 (using .../libpng12-0_1.2.46-3ubuntu1_armel.deb) ... Unpacking replacement libpng12-0 ... Preparing to replace libidn11 1.22-1ubuntu1 (using .../libidn11_1.22-2_armel.deb) ... Unpacking replacement libidn11 ... Preparing to replace libkeyutils1 1.4-5 (using .../libkeyutils1_1.4-6_armel.deb) ... Unpacking replacement libkeyutils1 ... Selecting previously deselected package libapt-pkg4.11. Unpacking libapt-pkg4.11 (from .../libapt-pkg4.11_0.8.16~exp5ubuntu5_armel.deb) ... Setting up libapt-pkg4.11 (0.8.16~exp5ubuntu5) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 14091 files and directories currently installed.) Preparing to replace apt-transport-https 0.8.15.2ubuntu1 (using .../apt-transport-https_0.8.16~exp5ubuntu5_armel.deb) ... Unpacking replacement apt-transport-https ... Preparing to replace apt 0.8.15.2ubuntu1 (using .../apt_0.8.16~exp5ubuntu5_armel.deb) ... Unpacking replacement apt ... Setting up apt (0.8.16~exp5ubuntu5) ... gpg: key 437D05B5: "Ubuntu Archive Automatic Signing Key " not changed gpg: key FBB75451: "Ubuntu CD Image Automatic Signing Key " not changed gpg: Total number processed: 2 gpg: unchanged: 2 (Reading database ... 14006 files and directories currently installed.) Preparing to replace libusb-0.1-4 2:0.1.12-17 (using .../libusb-0.1-4_2%3a0.1.12-18_armel.deb) ... Unpacking replacement libusb-0.1-4 ... Setting up libusb-0.1-4 (2:0.1.12-18) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 14006 files and directories currently installed.) Preparing to replace multiarch-support 2.13-9ubuntu2 (using .../multiarch-support_2.13-16ubuntu3_armel.deb) ... Unpacking replacement multiarch-support ... Setting up multiarch-support (2.13-16ubuntu3) ... (Reading database ... 14006 files and directories currently installed.) Preparing to replace udev 172-0ubuntu3 (using .../udev_172-0ubuntu5_armel.deb) ... Adding 'diversion of /sbin/udevadm to /sbin/udevadm.upgrade by fake-udev' Unpacking replacement udev ... Preparing to replace plymouth 0.8.2-2ubuntu24 (using .../plymouth_0.8.2-2ubuntu25_armel.deb) ... Unpacking replacement plymouth ... Preparing to replace libplymouth2 0.8.2-2ubuntu24 (using .../libplymouth2_0.8.2-2ubuntu25_armel.deb) ... Unpacking replacement libplymouth2 ... Preparing to replace libsasl2-2 2.1.23.dfsg1-5ubuntu3 (using .../libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-4ubuntu1_armel.deb) ... Unpacking replacement libsasl2-2 ... Preparing to replace cpp 4:4.6.1-2ubuntu2 (using .../cpp_4%3a4.6.1-2ubuntu5_armel.deb) ... Unpacking replacement cpp ... Preparing to replace gcc 4:4.6.1-2ubuntu2 (using .../gcc_4%3a4.6.1-2ubuntu5_armel.deb) ... Removing old gcc doc directory. Unpacking replacement gcc ... Preparing to replace g++ 4:4.6.1-2ubuntu2 (using .../g++_4%3a4.6.1-2ubuntu5_armel.deb) ... Unpacking replacement g++ ... Setting up libc-dev-bin (2.13-16ubuntu3) ... Setting up linux-libc-dev (3.0.0-8.11) ... Setting up libc6-dev (2.13-16ubuntu3) ... Setting up libgomp1 (4.6.1-6ubuntu6) ... Setting up libmpfr4 (3.0.1-5) ... Setting up cpp-4.6 (4.6.1-6ubuntu6) ... Setting up binutils (2.21.53.20110810-0ubuntu1) ... Setting up gcc-4.6 (4.6.1-6ubuntu6) ... Setting up libglib2.0-0 (2.29.14-0ubuntu1) ... Setting up libpng12-0 (1.2.46-3ubuntu1) ... Setting up libidn11 (1.22-2) ... Setting up libkeyutils1 (1.4-6) ... Setting up apt-transport-https (0.8.16~exp5ubuntu5) ... Setting up udev (172-0ubuntu5) ... Removing 'diversion of /sbin/udevadm to /sbin/udevadm.upgrade by fake-udev' update-initramfs: deferring update (trigger activated) Setting up libplymouth2 (0.8.2-2ubuntu25) ... Setting up plymouth (0.8.2-2ubuntu25) ... update-initramfs: deferring update (trigger activated) Setting up libsasl2-2 (2.1.24~rc1.dfsg1+cvs2011-05-23-4ubuntu1) ... Setting up cpp (4:4.6.1-2ubuntu5) ... Setting up gcc (4:4.6.1-2ubuntu5) ... Setting up libstdc++6-4.6-dev (4.6.1-6ubuntu6) ... Setting up perl-modules (5.12.4-2) ... Setting up perl (5.12.4-2) ... Setting up g++-4.6 (4.6.1-6ubuntu6) ... Setting up g++ (4:4.6.1-2ubuntu5) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Processing triggers for initramfs-tools ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'e0e6c5ab29c07ba7130c0fba08f37c0b274aba27', 'armel', 'oneiric', '--nolog', '--batch', '--archive=ubuntu', '--dist=oneiric', '--purpose=PRIMARY', '--architecture=armel', '--comp=universe', 'biococoa_2.2.2-1build1.dsc'] Initiating build e0e6c5ab29c07ba7130c0fba08f37c0b274aba27 with 0 processor cores. Automatic build of biococoa_2.2.2-1build1 on hubbard by sbuild/armel 1.170.5 Build started at 20110814-1819 ****************************************************************************** biococoa_2.2.2-1build1.dsc exists in cwd sh: gcc: not found dpkg-architecture: warning: Couldn't determine gcc system type, falling back to default (native compilation) ** Using build dependencies supplied by package: Build-Depends: cdbs, debhelper, libgnustep-base-dev (>= 1.16.1), quilt sh: gcc: not found dpkg-architecture: warning: Couldn't determine gcc system type, falling back to default (native compilation) sh: gcc: not found dpkg-architecture: warning: Couldn't determine gcc system type, falling back to default (native compilation) sh: gcc: not found dpkg-architecture: warning: Couldn't determine gcc system type, falling back to default (native compilation) sh: gcc: not found dpkg-architecture: warning: Couldn't determine gcc system type, falling back to default (native compilation) sh: gcc: not found dpkg-architecture: warning: Couldn't determine gcc system type, falling back to default (native compilation) sh: gcc: not found dpkg-architecture: warning: Couldn't determine gcc system type, falling back to default (native compilation) sh: gcc: not found dpkg-architecture: warning: Couldn't determine gcc system type, falling back to default (native compilation) sh: gcc: not found dpkg-architecture: warning: Couldn't determine gcc system type, falling back to default (native compilation) Checking for already installed source dependencies... cdbs: missing debhelper: missing libgnustep-base-dev: missing quilt: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install cdbs debhelper libgnustep-base-dev quilt Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: autoconf automake autotools-dev bsdmainutils dh-translations diffstat file gettext gettext-base gnustep-base-common gnustep-base-runtime gnustep-common gnustep-make gobjc gobjc-4.6 groff-base html2text intltool intltool-debian libavahi-client3 libavahi-common-data libavahi-common3 libcroco3 libencode-locale-perl libexpat1 libfile-listing-perl libgnustep-base1.22 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libicu44 libio-socket-ssl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic1 libnet-http-perl libnet-ssleay-perl libobjc3 libpipeline1 libsqlite3-0 libunistring0 liburi-perl libwww-perl libwww-robotrules-perl libxml-parser-perl libxml2 libxslt1.1 m4 man-db mime-support po-debconf python python-scour python2.7 sgml-base xml-core Suggested packages: autoconf2.13 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-4.6-multilib gcc-4.6-doc libobjc3-dbg groff libffi-dev libxml2-dev zlib1g-dev libxslt1-dev libgnutls-dev libdata-dump-perl libio-socket-inet6-perl libcrypt-ssleay-perl libauthen-ntlm-perl less www-browser libmail-box-perl python-doc python-tk python-rsvg python-cairo python2.7-doc procmail graphviz sgml-base-doc Recommended packages: curl wget lynx-cur libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libmailtools-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autotools-dev bsdmainutils cdbs debhelper dh-translations diffstat file gettext gettext-base gnustep-base-common gnustep-base-runtime gnustep-common gnustep-make gobjc gobjc-4.6 groff-base html2text intltool intltool-debian libavahi-client3 libavahi-common-data libavahi-common3 libcroco3 libencode-locale-perl libexpat1 libfile-listing-perl libgnustep-base-dev libgnustep-base1.22 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libicu44 libio-socket-ssl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic1 libnet-http-perl libnet-ssleay-perl libobjc3 libpipeline1 libsqlite3-0 libunistring0 liburi-perl libwww-perl libwww-robotrules-perl libxml-parser-perl libxml2 libxslt1.1 m4 man-db mime-support po-debconf python python-scour python2.7 quilt sgml-base xml-core 0 upgraded, 64 newly installed, 0 to remove and 0 not upgraded. Need to get 26.6 MB of archives. After this operation, 81.5 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libexpat1 libsqlite3-0 libpipeline1 libavahi-common-data libavahi-common3 libavahi-client3 libobjc3 libmagic1 file mime-support python2.7 python bsdmainutils gettext-base groff-base libxml2 man-db sgml-base xml-core m4 autoconf autotools-dev automake html2text libcroco3 libunistring0 gettext intltool-debian po-debconf debhelper liburi-perl libencode-locale-perl libhttp-date-perl libfile-listing-perl libhtml-tagset-perl libhtml-parser-perl libhtml-tree-perl liblwp-mediatypes-perl libhttp-message-perl libhttp-cookies-perl libhttp-negotiate-perl libnet-http-perl libnet-ssleay-perl libio-socket-ssl-perl liblwp-protocol-https-perl libwww-robotrules-perl libwww-perl libxml-parser-perl intltool dh-translations python-scour cdbs diffstat gnustep-common gnustep-base-common libicu44 libxslt1.1 libgnustep-base1.22 gnustep-base-runtime gnustep-make gobjc-4.6 gobjc libgnustep-base-dev quilt Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ oneiric/main libexpat1 armel 2.0.1-7ubuntu3 [103 kB] Get:2 http://ftpmaster.internal/ubuntu/ oneiric/main libsqlite3-0 armel 3.7.7-2ubuntu1 [280 kB] Get:3 http://ftpmaster.internal/ubuntu/ oneiric/main libpipeline1 armel 1.2.0-3 [20.6 kB] Get:4 http://ftpmaster.internal/ubuntu/ oneiric/main libavahi-common-data armel 0.6.30-4ubuntu1 [22.4 kB] Get:5 http://ftpmaster.internal/ubuntu/ oneiric/main libavahi-common3 armel 0.6.30-4ubuntu1 [24.1 kB] Get:6 http://ftpmaster.internal/ubuntu/ oneiric/main libavahi-client3 armel 0.6.30-4ubuntu1 [41.2 kB] Get:7 http://ftpmaster.internal/ubuntu/ oneiric/main libobjc3 armel 4.6.1-6ubuntu6 [141 kB] Get:8 http://ftpmaster.internal/ubuntu/ oneiric/main libmagic1 armel 5.04-5ubuntu3 [199 kB] Get:9 http://ftpmaster.internal/ubuntu/ oneiric/main file armel 5.04-5ubuntu3 [19.5 kB] Get:10 http://ftpmaster.internal/ubuntu/ oneiric/main mime-support all 3.51-1ubuntu1 [30.7 kB] Get:11 http://ftpmaster.internal/ubuntu/ oneiric/main python2.7 armel 2.7.2-4 [2514 kB] Get:12 http://ftpmaster.internal/ubuntu/ oneiric/main python all 2.7.2-5ubuntu1 [165 kB] Get:13 http://ftpmaster.internal/ubuntu/ oneiric/main bsdmainutils armel 8.2.3 [194 kB] Get:14 http://ftpmaster.internal/ubuntu/ oneiric/main gettext-base armel 0.18.1.1-3ubuntu1 [56.1 kB] Get:15 http://ftpmaster.internal/ubuntu/ oneiric/main groff-base armel 1.21-6 [934 kB] Get:16 http://ftpmaster.internal/ubuntu/ oneiric/main libxml2 armel 2.7.8.dfsg-4 [559 kB] Get:17 http://ftpmaster.internal/ubuntu/ oneiric/main man-db armel 2.6.0.2-2 [675 kB] Get:18 http://ftpmaster.internal/ubuntu/ oneiric/main sgml-base all 1.26+nmu1ubuntu1 [8360 B] Get:19 http://ftpmaster.internal/ubuntu/ oneiric/main xml-core all 0.13 [23.4 kB] Get:20 http://ftpmaster.internal/ubuntu/ oneiric/main m4 armel 1.4.16-1 [182 kB] Get:21 http://ftpmaster.internal/ubuntu/ oneiric/main autoconf all 2.68-1ubuntu1 [560 kB] Get:22 http://ftpmaster.internal/ubuntu/ oneiric/main autotools-dev all 20110511.1 [44.7 kB] Get:23 http://ftpmaster.internal/ubuntu/ oneiric/main automake all 1:1.11.1-1ubuntu1 [544 kB] Get:24 http://ftpmaster.internal/ubuntu/ oneiric/main html2text armel 1.3.2a-15 [94.3 kB] Get:25 http://ftpmaster.internal/ubuntu/ oneiric/main libcroco3 armel 0.6.2-1 [89.5 kB] Get:26 http://ftpmaster.internal/ubuntu/ oneiric/main libunistring0 armel 0.9.3-4 [394 kB] Get:27 http://ftpmaster.internal/ubuntu/ oneiric/main gettext armel 0.18.1.1-3ubuntu1 [1156 kB] Get:28 http://ftpmaster.internal/ubuntu/ oneiric/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:29 http://ftpmaster.internal/ubuntu/ oneiric/main po-debconf all 1.0.16+nmu1 [212 kB] Get:30 http://ftpmaster.internal/ubuntu/ oneiric/main debhelper all 8.9.0ubuntu1 [487 kB] Get:31 http://ftpmaster.internal/ubuntu/ oneiric/main liburi-perl all 1.58-1 [89.8 kB] Get:32 http://ftpmaster.internal/ubuntu/ oneiric/main libencode-locale-perl all 1.02-1 [11.8 kB] Get:33 http://ftpmaster.internal/ubuntu/ oneiric/main libhttp-date-perl all 6.00-1 [10.1 kB] Get:34 http://ftpmaster.internal/ubuntu/ oneiric/main libfile-listing-perl all 6.01-1 [8988 B] Get:35 http://ftpmaster.internal/ubuntu/ oneiric/main libhtml-tagset-perl all 3.20-2 [13.5 kB] Get:36 http://ftpmaster.internal/ubuntu/ oneiric/main libhtml-parser-perl armel 3.68-1build1 [95.5 kB] Get:37 http://ftpmaster.internal/ubuntu/ oneiric/main libhtml-tree-perl all 4.2-1 [205 kB] Get:38 http://ftpmaster.internal/ubuntu/ oneiric/main liblwp-mediatypes-perl all 6.01-1 [17.5 kB] Get:39 http://ftpmaster.internal/ubuntu/ oneiric/main libhttp-message-perl all 6.01-1 [77.6 kB] Get:40 http://ftpmaster.internal/ubuntu/ oneiric/main libhttp-cookies-perl all 6.00-2 [23.3 kB] Get:41 http://ftpmaster.internal/ubuntu/ oneiric/main libhttp-negotiate-perl all 6.00-2 [13.4 kB] Get:42 http://ftpmaster.internal/ubuntu/ oneiric/main libnet-http-perl all 6.01-1 [20.5 kB] Get:43 http://ftpmaster.internal/ubuntu/ oneiric/main libnet-ssleay-perl armel 1.36-3 [195 kB] Get:44 http://ftpmaster.internal/ubuntu/ oneiric/main libio-socket-ssl-perl all 1.43-1 [47.2 kB] Get:45 http://ftpmaster.internal/ubuntu/ oneiric/main liblwp-protocol-https-perl all 6.02-1 [6746 B] Get:46 http://ftpmaster.internal/ubuntu/ oneiric/main libwww-robotrules-perl all 6.01-1 [14.1 kB] Get:47 http://ftpmaster.internal/ubuntu/ oneiric/main libwww-perl all 6.02-1ubuntu1 [155 kB] Get:48 http://ftpmaster.internal/ubuntu/ oneiric/main libxml-parser-perl armel 2.41-1 [282 kB] Get:49 http://ftpmaster.internal/ubuntu/ oneiric/main intltool all 0.41.1-1 [103 kB] Get:50 http://ftpmaster.internal/ubuntu/ oneiric/main dh-translations all 101 [19.3 kB] Get:51 http://ftpmaster.internal/ubuntu/ oneiric/main python-scour all 0.26-1 [46.2 kB] Get:52 http://ftpmaster.internal/ubuntu/ oneiric/main cdbs all 0.4.94ubuntu1 [48.5 kB] Get:53 http://ftpmaster.internal/ubuntu/ oneiric/main diffstat armel 1.54-1 [20.5 kB] Get:54 http://ftpmaster.internal/ubuntu/ oneiric/universe gnustep-common armel 2.6.0-1 [49.9 kB] Get:55 http://ftpmaster.internal/ubuntu/ oneiric/universe gnustep-base-common all 1.22.0-1ubuntu1 [66.6 kB] Get:56 http://ftpmaster.internal/ubuntu/ oneiric/main libicu44 armel 4.4.2-2 [6733 kB] Get:57 http://ftpmaster.internal/ubuntu/ oneiric/main libxslt1.1 armel 1.1.26-7 [143 kB] Get:58 http://ftpmaster.internal/ubuntu/ oneiric/universe libgnustep-base1.22 armel 1.22.0-1ubuntu1 [1221 kB] Get:59 http://ftpmaster.internal/ubuntu/ oneiric/universe gnustep-base-runtime armel 1.22.0-1ubuntu1 [218 kB] Get:60 http://ftpmaster.internal/ubuntu/ oneiric/universe gnustep-make all 2.6.0-1 [148 kB] Get:61 http://ftpmaster.internal/ubuntu/ oneiric/main gobjc-4.6 armel 4.6.1-6ubuntu6 [4199 kB] Get:62 http://ftpmaster.internal/ubuntu/ oneiric/main gobjc armel 4:4.6.1-2ubuntu5 [890 B] Get:63 http://ftpmaster.internal/ubuntu/ oneiric/universe libgnustep-base-dev armel 1.22.0-1ubuntu1 [2147 kB] Get:64 http://ftpmaster.internal/ubuntu/ oneiric/main quilt all 0.48-7 [319 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 26.6 MB in 9s (2805 kB/s) Selecting previously deselected package libexpat1. (Reading database ... 14005 files and directories currently installed.) Unpacking libexpat1 (from .../libexpat1_2.0.1-7ubuntu3_armel.deb) ... Selecting previously deselected package libsqlite3-0. Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.7-2ubuntu1_armel.deb) ... Selecting previously deselected package libpipeline1. Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_armel.deb) ... Selecting previously deselected package libavahi-common-data. Unpacking libavahi-common-data (from .../libavahi-common-data_0.6.30-4ubuntu1_armel.deb) ... Selecting previously deselected package libavahi-common3. Unpacking libavahi-common3 (from .../libavahi-common3_0.6.30-4ubuntu1_armel.deb) ... Selecting previously deselected package libavahi-client3. Unpacking libavahi-client3 (from .../libavahi-client3_0.6.30-4ubuntu1_armel.deb) ... Selecting previously deselected package libobjc3. Unpacking libobjc3 (from .../libobjc3_4.6.1-6ubuntu6_armel.deb) ... 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Setting up python2.7 (2.7.2-4) ... Setting up python (2.7.2-5ubuntu1) ... Setting up bsdmainutils (8.2.3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode. Setting up gettext-base (0.18.1.1-3ubuntu1) ... Setting up groff-base (1.21-6) ... Setting up libxml2 (2.7.8.dfsg-4) ... Setting up man-db (2.6.0.2-2) ... Building database of manual pages ... Setting up sgml-base (1.26+nmu1ubuntu1) ... Setting up xml-core (0.13) ... Setting up m4 (1.4.16-1) ... Setting up autoconf (2.68-1ubuntu1) ... Setting up autotools-dev (20110511.1) ... Setting up automake (1:1.11.1-1ubuntu1) ... update-alternatives: using /usr/bin/automake-1.11 to provide /usr/bin/automake (automake) in auto mode. Setting up html2text (1.3.2a-15) ... Setting up libcroco3 (0.6.2-1) ... Setting up libunistring0 (0.9.3-4) ... Setting up gettext (0.18.1.1-3ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu1) ... Setting up debhelper (8.9.0ubuntu1) ... Setting up liburi-perl (1.58-1) ... Setting up libencode-locale-perl (1.02-1) ... Setting up libhttp-date-perl (6.00-1) ... Setting up libfile-listing-perl (6.01-1) ... Setting up libhtml-tagset-perl (3.20-2) ... Setting up libhtml-parser-perl (3.68-1build1) ... Setting up libhtml-tree-perl (4.2-1) ... Setting up liblwp-mediatypes-perl (6.01-1) ... Setting up libhttp-message-perl (6.01-1) ... Setting up libhttp-cookies-perl (6.00-2) ... Setting up libhttp-negotiate-perl (6.00-2) ... Setting up libnet-http-perl (6.01-1) ... Setting up libnet-ssleay-perl (1.36-3) ... Setting up libio-socket-ssl-perl (1.43-1) ... Setting up libwww-robotrules-perl (6.01-1) ... Setting up python-scour (0.26-1) ... Setting up diffstat (1.54-1) ... Setting up gnustep-common (2.6.0-1) ... Setting up gnustep-base-common (1.22.0-1ubuntu1) ... Setting up libicu44 (4.4.2-2) ... Setting up libxslt1.1 (1.1.26-7) ... Setting up libgnustep-base1.22 (1.22.0-1ubuntu1) ... Setting up gnustep-base-runtime (1.22.0-1ubuntu1) ... invoke-rc.d: policy-rc.d denied execution of start. Setting up gnustep-make (2.6.0-1) ... Setting up gobjc-4.6 (4.6.1-6ubuntu6) ... Setting up gobjc (4:4.6.1-2ubuntu5) ... Setting up libgnustep-base-dev (1.22.0-1ubuntu1) ... Setting up quilt (0.48-7) ... Setting up liblwp-protocol-https-perl (6.02-1) ... Setting up libwww-perl (6.02-1ubuntu1) ... Setting up libxml-parser-perl (2.41-1) ... Setting up intltool (0.41.1-1) ... Setting up dh-translations (101) ... Setting up cdbs (0.4.94ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.13-16ubuntu3 make_3.81-8.1ubuntu1 dpkg-dev_1.16.0.3ubuntu3 gcc-4.6_4.6.1-6ubuntu6 g++-4.6_4.6.1-6ubuntu6 binutils_2.21.53.20110810-0ubuntu1 libstdc++6_4.6.1-6ubuntu6 libstdc++6-4.6-dev_4.6.1-6ubuntu6 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt gpgv: Signature made Sun Aug 14 18:12:38 2011 UTC using DSA key ID 0F932C9C gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./biococoa_2.2.2-1build1.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_2.2.2-1build1.debian.tar.gz dpkg-source: info: applying link-libs.patch dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): -Wl,-Bsymbolic-functions dpkg-buildpackage: source package biococoa dpkg-buildpackage: source version 2.2.2-1build1 dpkg-source --before-build biococoa-2.2.2 dpkg-buildpackage: host architecture armel /usr/bin/fakeroot debian/rules clean test -x debian/rules dh_testroot rm -f debian/stamp-makefile-build debian/stamp-makefile-install GNUSTEP_MAKEFILES=/usr/share/GNUstep/Makefiles /usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="-Wl,-z,defs -Wl,--as-needed" OPTFLAG=-O2 -k clean This is gnustep-make 2.6.0. Type 'make print-gnustep-make-help' for help. make[1]: Entering directory `/build/buildd/biococoa-2.2.2' rm -rf ./*~ ./obj Making clean in subprojects of framework BioCocoa... make[2]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation' rm -rf ./*~ ./obj Making clean in subprojects of subproject BCFoundation... make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' rm -rf ./*~ ./obj make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' rm -rf ./*~ ./obj make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' rm -rf ./*~ ./obj make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' rm -rf ./*~ ./obj make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' rm -rf ./*~ ./obj make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSequence' rm -rf ./*~ ./obj make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' rm -rf ./*~ ./obj make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' rm -rf ./*~ ./obj make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCTools' rm -rf ./*~ ./obj make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCUtils' rm -rf ./*~ ./obj make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCUtils' make[2]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation' Making clean for framework BioCocoa... rm -rf \ \ ./BioCocoa.framework ./derived_src make[1]: Leaving directory `/build/buildd/biococoa-2.2.2' dh_clean rm -f debian/libbiococoa2.install rm -f debian/libbiococoa-dev.install /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/build/buildd/biococoa-2.2.2' make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/build/buildd/biococoa-2.2.2' if [ -d "." ]; then \ cd . && QUILT_PATCHES=/build/buildd/biococoa-2.2.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \ fi Removing patch link-libs.patch Restoring GNUmakefile No patches applied rm -rf ./.pc rm -f debian/stamp-patch* debian/rules build test -x debian/rules mkdir -p "." /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/build/buildd/biococoa-2.2.2' make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/build/buildd/biococoa-2.2.2' cd . && QUILT_PATCHES=/build/buildd/biococoa-2.2.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2 Applying patch link-libs.patch patching file GNUmakefile Hunk #1 succeeded at 39 (offset 6 lines). Now at patch link-libs.patch touch debian/stamp-patched /usr/bin/make -f debian/rules update-config make[1]: Entering directory `/build/buildd/biococoa-2.2.2' make[1]: Nothing to be done for `update-config'. make[1]: Leaving directory `/build/buildd/biococoa-2.2.2' GNUSTEP_MAKEFILES=/usr/share/GNUstep/Makefiles /usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="-Wl,-z,defs -Wl,--as-needed" OPTFLAG=-O2 This is gnustep-make 2.6.0. Type 'make print-gnustep-make-help' for help. make[1]: Entering directory `/build/buildd/biococoa-2.2.2' Making build-headers in subprojects of framework BioCocoa... make[2]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation' Making build-headers in subprojects of subproject BCFoundation... make[3]: Entering directory `/build/buildd/biococoa-2.2.2/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 `/build/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/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 `/build/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/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 `/build/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/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 `/build/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/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 `/build/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/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 `/build/buildd/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/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 `/build/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/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 `/build/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/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 `/build/buildd/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/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 `/build/buildd/biococoa-2.2.2/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 `/build/buildd/biococoa-2.2.2/BCFoundation' Making build-headers for framework BioCocoa... /usr/share/GNUstep/Makefiles/mkinstalldirs ./derived_src; \ touch derived_src/.stamp /usr/share/GNUstep/Makefiles/mkinstalldirs BioCocoa.framework/Versions/2/Resources cd ./BioCocoa.framework/Versions; \ rm -f Current; \ ln -s 2 Current cd ./BioCocoa.framework; \ if [ ! -h "Resources" ]; then \ rm -f Resources; \ ln -s Versions/Current/Resources Resources; \ fi; \ if [ ! -h "Headers" ]; then \ rm -f Headers; \ ln -s Versions/Current/Headers Headers; \ fi cd ./derived_src; \ if [ ! -h "BioCocoa" ]; then \ rm -f ./BioCocoa; \ ln -s ../BioCocoa.framework/Headers \ ./BioCocoa; \ fi cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all in subprojects of framework BioCocoa... make[2]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all in subprojects of subproject BCFoundation... make[3]: Entering directory `/build/buildd/biococoa-2.2.2/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 -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 -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 -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 -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 -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 -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,-z,defs -Wl,--as-needed -shared-libgcc -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 `/build/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/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 -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 -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 intersectToFile:withMCP:]': BCMCP.m:486:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:487:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:489:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:490:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:514:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:515:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:517:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:518:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:735:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:736:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:738:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:739:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:762:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:763:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:765:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:766:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m: In function '-[BCMCP unionToFile:withMCP:]': BCMCP.m:910:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:911:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:913:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:914:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:936:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:937:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:939:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:940:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1093:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1094:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1096:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1097:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1123:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1124:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1126:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1127:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1167:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1168:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1170:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1171:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1186:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1187:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1189:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1190:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1222:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1223:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1225:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1226:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1239:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1240:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1242:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1243:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m: In function '-[BCMCP trimToFile:]': BCMCP.m:1272:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1273:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1275:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1276:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m: In function '-[BCMCP outputFormat:withMinimumLength:]': BCMCP.m:1481:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1482:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1485:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1486:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1603:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1604:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1606:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1607:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m: In function '+[BCMCP mcpToFile:suffixArray:withSuffixArray:lowerBound:]': BCMCP.m:160:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:161:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:163:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:164:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:334:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:335:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:352:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:353:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:358:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:359:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:366:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:367:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] gcc BCSuffixArray.m -c \ -MMD -MP -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 -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 constructFromSequenceArray:strand:]': BCSuffixArray.m:487:13: warning: ignoring return value of 'mktemp', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:513:13: warning: ignoring return value of 'mktemp', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m: In function '-[BCSuffixArray dumpSuffixArray]': BCSuffixArray.m:896:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:897:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:932:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:933:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m: In function '-[BCSuffixArrayUnionEnumerator nextSuffixPosition:sequence:suffixArray:]': BCSuffixArray.m:1464:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:1465:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:1598:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:1599:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -shared-libgcc -fexceptions -o ./obj/subproject.o obj/BCAnalysis.obj/BCMCP.m.o obj/BCAnalysis.obj/BCSuffixArray.m.o ; make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/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 -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 -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 BCSeries.m: In function '+[BCSeries keysForSeries:withInternalKeys:]': BCSeries.m:113:7: warning: 'iKeys' may be used uninitialized in this function [-Wuninitialized] gcc BCSample.m -c \ -MMD -MP -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 -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 -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 -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 -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 -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,-z,defs -Wl,--as-needed -shared-libgcc -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 `/build/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/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 -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 -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 -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 -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 -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 -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 -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 -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] gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -shared-libgcc -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 `/build/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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,-z,defs -Wl,--as-needed -shared-libgcc -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 `/build/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/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 -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 -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 BCAnnotation.m: In function '-[BCAnnotation isEqualToAnnotation:]': BCAnnotation.m:214:2: warning: 'NSObject' may not respond to '-isEqualTo:' [enabled by default] BCAnnotation.m:214:2: warning: (Messages without a matching method signature [enabled by default] BCAnnotation.m:214:2: warning: will be assumed to return 'id' and accept [enabled by default] BCAnnotation.m:214:2: warning: '...' as arguments.) [enabled by default] BCAnnotation.m:214:2: warning: return makes integer from pointer without a cast [enabled by default] gcc BCSequence.m -c \ -MMD -MP -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 -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 -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 -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 -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 -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 [-Wuninitialized] gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -shared-libgcc -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 `/build/buildd/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/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 -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 -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 [enabled by default] BCSequenceReader.m:167:3: warning: (Messages without a matching method signature [enabled by default] BCSequenceReader.m:167:3: warning: will be assumed to return 'id' and accept [enabled by default] BCSequenceReader.m:167:3: warning: '...' as arguments.) [enabled by default] BCSequenceReader.m: In function '-[BCSequenceReader readMacVectorFile:]': BCSequenceReader.m:651:18: warning: variable 'annotationsArray' set but not used [-Wunused-but-set-variable] BCSequenceReader.m: In function '-[BCSequenceReader readClustalFile:]': BCSequenceReader.m:782:9: warning: passing argument 1 of 'isEqualTo:' from distinct Objective-C type [enabled by default] BCSequenceReader.m:798:3: warning: passing argument 2 of 'scanUpToString:intoString:' from incompatible pointer type [enabled by default] BCSequenceReader.m:798:3: note: expected 'struct NSString **' but argument is of type 'id' BCSequenceReader.m: In function '-[BCSequenceReader readGDEFile:]': BCSequenceReader.m:891:9: warning: passing argument 1 of 'isEqualTo:' from distinct Objective-C type [enabled by default] BCSequenceReader.m: In function '-[BCSequenceReader readPirFile:]': BCSequenceReader.m:976:9: warning: passing argument 1 of 'isEqualTo:' from distinct Objective-C type [enabled by default] BCSequenceReader.m: In function '-[BCSequenceReader readPhylipFile:]': BCSequenceReader.m:1130:9: warning: passing argument 1 of 'isEqualTo:' from distinct Objective-C type [enabled by default] BCSequenceReader.m:1113:31: warning: variable 'annotationsArray' set but not used [-Wunused-but-set-variable] BCSequenceReader.m: In function '-[BCSequenceReader readRawFile:]': BCSequenceReader.m:1195:3: warning: passing argument 1 of 'isEqualTo:' from distinct Objective-C type [enabled by default] BCSequenceReader.m: In function '-[BCSequenceReader readSwissProtFile:]': BCSequenceReader.m:426:15: warning: 'sequenceString' may be used uninitialized in this function [-Wuninitialized] BCSequenceReader.m: In function '-[BCSequenceReader readClustalFile:]': BCSequenceReader.m:822:18: warning: 'sequenceRange.location' may be used uninitialized in this function [-Wuninitialized] BCSequenceReader.m: In function '-[BCSequenceReader readFASTQFile:]': BCSequenceReader.m:1310:18: warning: 'seqData' may be used uninitialized in this function [-Wuninitialized] gcc BCSequenceWriter.m -c \ -MMD -MP -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 -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 -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 -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 -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 -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:58:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCCachedFastaFile.m:73:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCCachedFastaFile.m:76:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCCachedFastaFile.m:97:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCCachedFastaFile.m: In function '-[BCCachedFastaFile symbols:ForCurrentSequenceAtPosition:ofLength:]': BCCachedFastaFile.m:149:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCCachedFastaFile.m: In function '-[BCCachedFastaFile initWithContentsOfFile:]': BCCachedFastaFile.m:104:3: warning: 'filePos' may be used uninitialized in this function [-Wuninitialized] gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -shared-libgcc -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 `/build/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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,-z,defs -Wl,--as-needed -shared-libgcc -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 `/build/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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,-z,defs -Wl,--as-needed -shared-libgcc -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 `/build/buildd/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/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 -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 -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 -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 -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 -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 -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 [enabled by default] 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 [enabled by default] BCUtilStrings.m:100:3: note: expected 'int *' but argument is of type 'id' gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -shared-libgcc -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 `/build/buildd/biococoa-2.2.2/BCFoundation/BCUtils' Making all for subproject BCFoundation... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCFoundation.obj/ gcc BCStringDefinitions.m -c \ -MMD -MP -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 -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 -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 -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,-z,defs -Wl,--as-needed -shared-libgcc -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 `/build/buildd/biococoa-2.2.2/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 "$classarray" > ./derived_src/BioCocoa-class-list; \ echo "#include " > derived_src/NSFramework_BioCocoa.m; \ echo "@interface NSFramework_BioCocoa" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkEnv;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkPath;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkVersion;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString **)frameworkClasses;" >> derived_src/NSFramework_BioCocoa.m; \ echo "@end" >> derived_src/NSFramework_BioCocoa.m; \ echo "@implementation NSFramework_BioCocoa" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkEnv { return nil; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkPath { return @\"/usr/local/lib/GNUstep/Frameworks\"; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkVersion { return @\"2\"; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "static NSString *allClasses[] = {$classlist};" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString **)frameworkClasses { return allClasses; }" >> derived_src/NSFramework_BioCocoa.m;\ echo "@end" >> derived_src/NSFramework_BioCocoa.m gcc derived_src/NSFramework_BioCocoa.m -c -MMD -MP -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -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,-z,defs -Wl,--as-needed -shared-libgcc -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) \ 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 `/build/buildd/biococoa-2.2.2' touch debian/stamp-makefile-build DEB_MAKE_CHECK_TARGET unset, not running checks /usr/bin/fakeroot debian/rules binary-arch test -x debian/rules dh_testroot dh_clean -k dh_clean: dh_clean -k is deprecated; use dh_prep instead 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 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="-Wl,-z,defs -Wl,--as-needed" OPTFLAG=-O2 install DESTDIR=/build/buildd/biococoa-2.2.2/debian/tmp/ GNUSTEP_INSTALLATION_DOMAIN=SYSTEM This is gnustep-make 2.6.0. Type 'make print-gnustep-make-help' for help. make[1]: Entering directory `/build/buildd/biococoa-2.2.2' Making build-headers in subprojects of framework BioCocoa... make[2]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation' Making build-headers in subprojects of subproject BCFoundation... make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' Making build-headers for subproject BCAlignment... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' Making build-headers for subproject BCAnalysis... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making build-headers for subproject BCGeneExpression... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making build-headers for subproject BCGeneticCode... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making build-headers for subproject BCProteinStructure... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSequence' Making build-headers for subproject BCSequence... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making build-headers for subproject BCSequenceIO... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' Making build-headers for subproject BCSymbol... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCTools' Making build-headers for subproject BCTools... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCUtils... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCFoundation... make[3]: Nothing to be done for `internal-subproject-build-headers'. make[2]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation' Making build-headers for framework BioCocoa... cd ./BioCocoa.framework; \ if [ ! -h "Resources" ]; then \ rm -f Resources; \ ln -s Versions/Current/Resources Resources; \ fi; \ if [ ! -h "Headers" ]; then \ rm -f Headers; \ ln -s Versions/Current/Headers Headers; \ fi cd ./derived_src; \ if [ ! -h "BioCocoa" ]; then \ rm -f ./BioCocoa; \ ln -s ../BioCocoa.framework/Headers \ ./BioCocoa; \ fi Making all in subprojects of framework BioCocoa... make[2]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation' Making all in subprojects of subproject BCFoundation... make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' Making all for subproject BCAlignment... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' Making all for subproject BCAnalysis... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making all for subproject BCGeneExpression... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making all for subproject BCGeneticCode... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making all for subproject BCProteinStructure... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSequence' Making all for subproject BCSequence... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making all for subproject BCSequenceIO... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' Making all for subproject BCSymbol... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCTools' Making all for subproject BCTools... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCUtils' Making all for subproject BCUtils... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCUtils' Making all for subproject BCFoundation... make[4]: Nothing to be done for `internal-subproject-compile'. make[2]: Leaving directory `/build/buildd/biococoa-2.2.2/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 Making install in subprojects of framework BioCocoa... make[2]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation' Making install in subprojects of subproject BCFoundation... make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' Making install for subproject BCAlignment... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' Making install for subproject BCAnalysis... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making install for subproject BCGeneExpression... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making install for subproject BCGeneticCode... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making install for subproject BCProteinStructure... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSequence' Making install for subproject BCSequence... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making install for subproject BCSequenceIO... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' Making install for subproject BCSymbol... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCTools' Making install for subproject BCTools... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCUtils' Making install for subproject BCUtils... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation/BCUtils' Making install for subproject BCFoundation... make[3]: Nothing to be done for `internal-subproject-install'. make[2]: Leaving directory `/build/buildd/biococoa-2.2.2/BCFoundation' Making install for framework BioCocoa... /usr/share/GNUstep/Makefiles/mkinstalldirs /build/buildd/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks /usr/share/GNUstep/Makefiles/mkinstalldirs /build/buildd/biococoa-2.2.2/debian/tmp///usr/include/GNUstep rm -rf /build/buildd/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework; \ (cd .; tar cfX - /usr/share/GNUstep/Makefiles/tar-exclude-list BioCocoa.framework) | (cd /build/buildd/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks; tar xf -) cd /build/buildd/biococoa-2.2.2/debian/tmp///usr/include/GNUstep; \ rm -f BioCocoa; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /build/buildd/biococoa-2.2.2/debian/tmp///usr/include/GNUstep /build/buildd/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Headers short` BioCocoa; \ cd /build/buildd/biococoa-2.2.2/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 /build/buildd/biococoa-2.2.2/debian/tmp///usr/lib/. /build/buildd/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so short` libBioCocoa.so; \ if test -r "/build/buildd/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so.2"; then \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /build/buildd/biococoa-2.2.2/debian/tmp///usr/lib/. /build/buildd/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so.2 short` libBioCocoa.so.2; \ fi; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /build/buildd/biococoa-2.2.2/debian/tmp///usr/lib/. /build/buildd/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so.2.2.2 short` libBioCocoa.so.2.2.2 make[1]: Leaving directory `/build/buildd/biococoa-2.2.2' 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=/build/buildd/biococoa-2.2.2/debian/tmp/ dh_link -plibbiococoa-dev dh_installmime -plibbiococoa-dev dh_installgsettings -plibbiococoa-dev gsdh_gnustep -plibbiococoa-dev dh_link -plibbiococoa-dev rm -f debian/libbiococoa-dev//usr/lib/GNUstep/Frameworks/*.framework/Versions/Current 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=/build/buildd/biococoa-2.2.2/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: all non-arch-all packages for this build platform armel: libbiococoa-dev libbiococoa2 dh_strip debug symbol extraction: packages to act on: libbiococoa-dev dh_strip debug symbol extraction: ignored packages: libbiococoa-dev is already stripped, ignoring dh_compress -plibbiococoa-dev dh_fixperms -plibbiococoa-dev dh_makeshlibs -plibbiococoa-dev dh_strip -plibbiococoa2 dh_strip debug symbol extraction: all non-arch-all packages for this build platform armel: libbiococoa-dev libbiococoa2 dh_strip debug symbol extraction: packages to act on: libbiococoa2 dh_strip debug symbol extraction: ignored packages: libbiococoa2 is already stripped, 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: debian/libbiococoa2/usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/libBioCocoa.so.2.2.2 contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dh_gencontrol -plibbiococoa-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 101 pkgstriptranslations: processing control file: ./debian/libbiococoa-dev/DEBIAN/control, package libbiococoa-dev, directory ./debian/libbiococoa-dev pkgstriptranslations: libbiococoa-dev does not contain translations, skipping 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 pkgstripfiles: Truncating changelog to topmost ten records 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 dpkg-deb: warning: 'debian/libbiococoa-dev/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `libbiococoa-dev' in `../libbiococoa-dev_2.2.2-1build1_armel.deb'. dh_gencontrol -plibbiococoa2 # 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 101 pkgstriptranslations: processing control file: ./debian/libbiococoa2/DEBIAN/control, package libbiococoa2, directory ./debian/libbiococoa2 pkgstriptranslations: libbiococoa2 does not contain translations, skipping pkgstriptranslations: processing control file: ./debian/libbiococoa-dev/DEBIAN/control, package libbiococoa-dev, directory ./debian/libbiococoa-dev pkgstriptranslations: libbiococoa-dev does not contain translations, skipping 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 changelog to topmost ten records dpkg-deb: warning: 'debian/libbiococoa2/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `libbiococoa2' in `../libbiococoa2_2.2.2-1build1_armel.deb'. dpkg-genchanges -B -mUbuntu/armel Build Daemon >../biococoa_2.2.2-1build1_armel.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build biococoa-2.2.2 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20110814-1828 chroot-autobuild/build/buildd/libbiococoa-dev_2.2.2-1build1_armel.deb: new debian package, version 2.0. size 127648 bytes: control archive= 3681 bytes. 1380 bytes, 25 lines control 9990 bytes, 92 lines md5sums Package: libbiococoa-dev Source: biococoa Version: 2.2.2-1build1 Architecture: armel Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 640 Depends: libbiococoa2 (= 2.2.2-1build1), 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. chroot-autobuild/build/buildd/libbiococoa2_2.2.2-1build1_armel.deb: new debian package, version 2.0. size 125804 bytes: control archive= 1169 bytes. 1348 bytes, 24 lines control 597 bytes, 6 lines md5sums 27 bytes, 1 lines shlibs Package: libbiococoa2 Source: biococoa Version: 2.2.2-1build1 Architecture: armel Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 416 Depends: gnustep-base-runtime (>= 1.22.0), libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libgnustep-base1.22 (>= 1.22.0), libobjc3 (>= 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. chroot-autobuild/build/buildd/libbiococoa-dev_2.2.2-1build1_armel.deb: drwxr-xr-x root/root 0 2011-08-14 18:26 ./ drwxr-xr-x root/root 0 2011-08-14 18:26 ./usr/ drwxr-xr-x root/root 0 2011-08-14 18:26 ./usr/include/ drwxr-xr-x root/root 0 2011-08-14 18:26 ./usr/include/GNUstep/ drwxr-xr-x root/root 0 2011-08-14 18:26 ./usr/include/GNUstep/Frameworks/ drwxr-xr-x root/root 0 2011-08-14 18:26 ./usr/include/GNUstep/Frameworks/BioCocoa.framework/ drwxr-xr-x root/root 0 2011-08-14 18:26 ./usr/include/GNUstep/Frameworks/BioCocoa.framework/Versions/ drwxr-xr-x root/root 0 2011-08-14 18:23 ./usr/include/GNUstep/Frameworks/BioCocoa.framework/Versions/2/ -rw-r--r-- root/root 4773 2009-07-02 23:13 ./usr/include/GNUstep/Frameworks/BioCocoa.framework/Versions/2/BCSequenceReader.h -rw-r--r-- root/root 2130 2009-07-02 23:13 ./usr/include/GNUstep/Frameworks/BioCocoa.framework/Versions/2/BCPlatform.h -rw-r--r-- root/root 1835 2009-07-02 23:13 ./usr/include/GNUstep/Frameworks/BioCocoa.framework/Versions/2/BCProteinStructure.h -rw-r--r-- root/root 3415 2009-07-02 23:13 ./usr/include/GNUstep/Frameworks/BioCocoa.framework/Versions/2/BCCodonRNA.h -rw-r--r-- root/root 1748 2009-07-02 23:13 ./usr/include/GNUstep/Frameworks/BioCocoa.framework/Versions/2/BCSequenceWriter.h -rw-r--r-- root/root 10266 2010-05-07 02:55 ./usr/include/GNUstep/Frameworks/BioCocoa.framework/Versions/2/BCAnnotation.h -rw-r--r-- root/root 1839 2009-07-02 23:13 ./usr/include/GNUstep/Frameworks/BioCocoa.framework/Versions/2/BCSecondaryStructure.h -rw-r--r-- root/root 11462 2009-07-02 23:13 ./usr/include/GNUstep/Frameworks/BioCocoa.framework/Versions/2/BCSymbol.h -rw-r--r-- root/root 6582 2009-07-02 23:13 ./usr/include/GNUstep/Frameworks/BioCocoa.framework/Versions/2/BCAminoAcid.h -rw-r--r-- root/root 3429 2009-07-02 23:13 ./usr/include/GNUstep/Frameworks/BioCocoa.framework/Versions/2/BCCodonDNA.h -rw-r--r-- root/root 3997 2009-07-02 23:13 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GNUstep/Frameworks/BioCocoa.framework/Versions/Current/libBioCocoa.so.2 biococoa_2.2.2-1build1_armel.changes: Format: 1.8 Date: Sun, 14 Aug 2011 17:48:35 +0000 Source: biococoa Binary: libbiococoa-dev libbiococoa2 Architecture: armel Version: 2.2.2-1build1 Distribution: oneiric Urgency: low Maintainer: Ubuntu/armel Build Daemon Changed-By: Matthias Klose Description: libbiococoa-dev - Bioinformatics framework for GNUstep and Cocoa (development files libbiococoa2 - Bioinformatics framework for GNUstep and Cocoa (library files) Changes: biococoa (2.2.2-1build1) oneiric; urgency=low . * Build using GCC 4.6 Checksums-Sha1: 65fa088adcadd563dab67d3483a7d437ef71375c 127648 libbiococoa-dev_2.2.2-1build1_armel.deb fa0b8fb4f30bcb83cd1b275345bad3ff2d9a3b3d 125804 libbiococoa2_2.2.2-1build1_armel.deb Checksums-Sha256: 5ef40c330f8336b3585032ee848edc149a88b2463fa498041633909771e976fc 127648 libbiococoa-dev_2.2.2-1build1_armel.deb 60c422bd62bbd535dea44b7c2a7f91aada29167935b38f7c11a613bfad0f1723 125804 libbiococoa2_2.2.2-1build1_armel.deb Files: 471b7a272111313f47eafb868f7e86cc 127648 libdevel optional libbiococoa-dev_2.2.2-1build1_armel.deb 9160ef0acd4d62021d900c8800456643 125804 libs optional libbiococoa2_2.2.2-1build1_armel.deb ****************************************************************************** Built successfully Purging chroot-autobuild/build/buildd/biococoa-2.2.2 ------------------------------------------------------------------------------ /usr/bin/sudo dpkg --purge groff-base libavahi-common3 libhttp-message-perl mime-support m4 gettext file libhtml-parser-perl intltool libhttp-cookies-perl libwww-perl liburi-perl libicu44 libhtml-tree-perl autotools-dev po-debconf libnet-http-perl libgnustep-base1.22 gnustep-base-runtime gobjc quilt dh-translations libxml-parser-perl libcroco3 libhtml-tagset-perl libxml2 automake python-scour libhttp-date-perl man-db libnet-ssleay-perl libfile-listing-perl libencode-locale-perl gobjc-4.6 libhttp-negotiate-perl intltool-debian python2.7 libavahi-client3 libio-socket-ssl-perl xml-core liblwp-protocol-https-perl gnustep-base-common libobjc3 cdbs diffstat html2text libwww-robotrules-perl gnustep-make gettext-base debhelper sgml-base libunistring0 python libxslt1.1 libavahi-common-data libmagic1 libpipeline1 libexpat1 libsqlite3-0 gnustep-common bsdmainutils liblwp-mediatypes-perl autoconf libgnustep-base-dev (Reading database ... 17389 files and directories currently installed.) Removing quilt ... Purging configuration files for quilt ... Removing cdbs ... Removing diffstat ... Removing libgnustep-base-dev ... Removing gnustep-base-runtime ... invoke-rc.d: policy-rc.d denied execution of stop. Purging configuration files for gnustep-base-runtime ... Removing gobjc ... Removing dh-translations ... Removing python-scour ... Removing gobjc-4.6 ... Removing gnustep-make ... Removing debhelper ... Removing python ... Purging configuration files for python ... Removing intltool ... Removing po-debconf ... Removing libgnustep-base1.22 ... Purging configuration files for libgnustep-base1.22 ... Removing libxml-parser-perl ... Removing automake ... Removing man-db ... Purging configuration files for man-db ... Removing catpages as well as /var/cache/man hierarchy. Removing intltool-debian ... Removing python2.7 ... Purging configuration files for python2.7 ... Removing libavahi-client3 ... Purging configuration files for libavahi-client3 ... Removing gnustep-base-common ... Purging configuration files for gnustep-base-common ... Removing libobjc3 ... Purging configuration files for libobjc3 ... Removing html2text ... Purging configuration files for html2text ... Removing libxslt1.1 ... Purging configuration files for libxslt1.1 ... Removing libpipeline1 ... Purging configuration files for libpipeline1 ... Removing libexpat1 ... Purging configuration files for libexpat1 ... Removing libsqlite3-0 ... Purging configuration files for libsqlite3-0 ... Removing gnustep-common ... Purging configuration files for gnustep-common ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing autoconf ... Purging configuration files for autoconf ... Removing groff-base ... Purging configuration files for groff-base ... Removing libavahi-common3 ... Purging configuration files for libavahi-common3 ... Removing mime-support ... Purging configuration files for mime-support ... Removing m4 ... Removing gettext ... Removing file ... Removing libicu44 ... Purging configuration files for libicu44 ... Removing autotools-dev ... Removing libcroco3 ... Purging configuration files for libcroco3 ... Removing libxml2 ... Purging configuration files for libxml2 ... Removing xml-core ... Purging configuration files for xml-core ... dpkg: warning: while removing xml-core, directory '/etc/sgml' not empty so not removed. Removing gettext-base ... Removing sgml-base ... Purging configuration files for sgml-base ... Removing libunistring0 ... Purging configuration files for libunistring0 ... Removing libavahi-common-data ... Removing libmagic1 ... Purging configuration files for libmagic1 ... Removing liblwp-protocol-https-perl ... Removing libwww-perl ... Removing libhtml-tree-perl ... Removing libnet-http-perl ... Removing libfile-listing-perl ... Removing libhttp-negotiate-perl ... Removing libio-socket-ssl-perl ... Removing libwww-robotrules-perl ... Removing libhttp-cookies-perl ... Removing libnet-ssleay-perl ... Removing libhttp-message-perl ... Removing libhtml-parser-perl ... Removing liburi-perl ... Removing libhtml-tagset-perl ... Removing libhttp-date-perl ... Removing libencode-locale-perl ... Removing liblwp-mediatypes-perl ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place ****************************************************************************** Finished at 20110814-1828 Build needed 00:05:56, 7688k disk space Can't open average time db /var/debbuild/avg-build-times Can't open average space db /var/debbuild/avg-build-space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', 'e0e6c5ab29c07ba7130c0fba08f37c0b274aba27'] Scanning for processes to kill in build /home/buildd/build-e0e6c5ab29c07ba7130c0fba08f37c0b274aba27/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'e0e6c5ab29c07ba7130c0fba08f37c0b274aba27'] Unmounting chroot for build e0e6c5ab29c07ba7130c0fba08f37c0b274aba27... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'e0e6c5ab29c07ba7130c0fba08f37c0b274aba27'] Removing build e0e6c5ab29c07ba7130c0fba08f37c0b274aba27