RUN: /bin/echo ['echo', 'Forking build subprocess...'] Forking build subprocess... RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', '60a9e9a2b60f7bda7323f2353c16429ad2819a0c', '/home/buildd/filecache-default/1072168715032372000a2363264a1d6c9c33a9f2'] Synching the system clock with the buildd NTP service... 27 Nov 17:55:39 ntpdate[23868]: adjust time server 10.211.37.1 offset -0.000001 sec Unpacking chroot for build 60a9e9a2b60f7bda7323f2353c16429ad2819a0c RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', '60a9e9a2b60f7bda7323f2353c16429ad2819a0c'] Mounting chroot for build 60a9e9a2b60f7bda7323f2353c16429ad2819a0c RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', '60a9e9a2b60f7bda7323f2353c16429ad2819a0c', 'deb http://ftpmaster.internal/ubuntu precise main restricted universe multiverse'] Overriding sources.list in build-60a9e9a2b60f7bda7323f2353c16429ad2819a0c RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', '60a9e9a2b60f7bda7323f2353c16429ad2819a0c', 'amd64'] Updating debian chroot for build 60a9e9a2b60f7bda7323f2353c16429ad2819a0c Ign http://ftpmaster.internal precise InRelease Get:1 http://ftpmaster.internal precise Release.gpg [198 B] Get:2 http://ftpmaster.internal precise Release [49.6 kB] Get:3 http://ftpmaster.internal precise/main amd64 Packages [1267 kB] Get:4 http://ftpmaster.internal precise/restricted amd64 Packages [8333 B] Get:5 http://ftpmaster.internal precise/universe amd64 Packages [4658 kB] Get:6 http://ftpmaster.internal precise/multiverse amd64 Packages [120 kB] Get:7 http://ftpmaster.internal precise/main i386 Packages [1267 kB] Get:8 http://ftpmaster.internal precise/restricted i386 Packages [8332 B] Get:9 http://ftpmaster.internal precise/universe i386 Packages [4668 kB] Get:10 http://ftpmaster.internal precise/multiverse i386 Packages [123 kB] Get:11 http://ftpmaster.internal precise/main TranslationIndex [3502 B] Get:12 http://ftpmaster.internal precise/multiverse TranslationIndex [2472 B] Get:13 http://ftpmaster.internal precise/restricted TranslationIndex [2464 B] Get:14 http://ftpmaster.internal precise/universe TranslationIndex [2712 B] Get:15 http://ftpmaster.internal precise/main Translation-en [715 kB] Get:16 http://ftpmaster.internal precise/multiverse Translation-en [95.3 kB] Get:17 http://ftpmaster.internal precise/restricted Translation-en [2229 B] Get:18 http://ftpmaster.internal precise/universe Translation-en [3294 kB] Fetched 16.3 MB in 4s (3365 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: base-files binutils coreutils cpp-4.6 debconf dpkg dpkg-dev g++-4.6 gcc-4.6 gcc-4.6-base gnupg gpgv initramfs-tools initramfs-tools-bin initscripts libacl1 libalgorithm-diff-xs-perl libattr1 libcurl3-gnutls libdpkg-perl libgcc1 libgnutls26 libgomp1 libgssapi-krb5-2 libk5crypto3 libkrb5-3 libkrb5support0 libldap-2.4-2 libmpfr4 libncurses5 libncursesw5 libquadmath0 libreadline6 libsasl2-2 libstdc++6 libstdc++6-4.6-dev libtinfo5 libudev0 linux-libc-dev locales module-init-tools ncurses-base ncurses-bin perl perl-base perl-modules pkg-create-dbgsym pkgbinarymangler procps python-minimal readline-common sysv-rc sysvinit-utils tar ubuntu-keyring udev 56 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 47.5 MB of archives. After this operation, 10.6 MB disk space will be freed. WARNING: The following packages cannot be authenticated! base-files libattr1 libacl1 dpkg coreutils libncursesw5 libtinfo5 libncurses5 ncurses-bin perl libalgorithm-diff-xs-perl perl-base perl-modules tar ncurses-base python-minimal readline-common libreadline6 libgomp1 gcc-4.6-base libstdc++6 cpp-4.6 libquadmath0 libstdc++6-4.6-dev g++-4.6 gcc-4.6 libgcc1 libmpfr4 binutils debconf libudev0 module-init-tools libgnutls26 libk5crypto3 libgssapi-krb5-2 libkrb5-3 libkrb5support0 libsasl2-2 libldap-2.4-2 libcurl3-gnutls gpgv gnupg ubuntu-keyring initramfs-tools initramfs-tools-bin sysvinit-utils sysv-rc initscripts procps udev locales dpkg-dev libdpkg-perl linux-libc-dev pkg-create-dbgsym pkgbinarymangler Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ precise/main base-files amd64 6.5ubuntu3 [67.0 kB] Get:2 http://ftpmaster.internal/ubuntu/ precise/main libattr1 amd64 1:2.4.46-3ubuntu1 [10.9 kB] Get:3 http://ftpmaster.internal/ubuntu/ precise/main libacl1 amd64 2.2.51-4ubuntu1 [18.0 kB] Get:4 http://ftpmaster.internal/ubuntu/ precise/main dpkg amd64 1.16.1.2ubuntu1 [1835 kB] Get:5 http://ftpmaster.internal/ubuntu/ precise/main coreutils amd64 8.13-3ubuntu2 [2610 kB] Get:6 http://ftpmaster.internal/ubuntu/ precise/main libncursesw5 amd64 5.9-4 [137 kB] Get:7 http://ftpmaster.internal/ubuntu/ precise/main libtinfo5 amd64 5.9-4 [95.3 kB] Get:8 http://ftpmaster.internal/ubuntu/ precise/main libncurses5 amd64 5.9-4 [114 kB] Get:9 http://ftpmaster.internal/ubuntu/ precise/main ncurses-bin amd64 5.9-4 [151 kB] Get:10 http://ftpmaster.internal/ubuntu/ precise/main perl amd64 5.14.2-5ubuntu1 [4398 kB] Get:11 http://ftpmaster.internal/ubuntu/ precise/main libalgorithm-diff-xs-perl amd64 0.04-2build2 [12.4 kB] Get:12 http://ftpmaster.internal/ubuntu/ precise/main perl-base amd64 5.14.2-5ubuntu1 [1455 kB] Get:13 http://ftpmaster.internal/ubuntu/ precise/main perl-modules all 5.14.2-5ubuntu1 [3369 kB] Get:14 http://ftpmaster.internal/ubuntu/ precise/main tar amd64 1.26-3ubuntu1 [219 kB] Get:15 http://ftpmaster.internal/ubuntu/ precise/main ncurses-base all 5.9-4 [21.0 kB] Get:16 http://ftpmaster.internal/ubuntu/ precise/main python-minimal all 2.7.2-9ubuntu1 [29.7 kB] Get:17 http://ftpmaster.internal/ubuntu/ precise/main readline-common amd64 6.2-8 [49.9 kB] Get:18 http://ftpmaster.internal/ubuntu/ precise/main libreadline6 amd64 6.2-8 [139 kB] Get:19 http://ftpmaster.internal/ubuntu/ precise/main libgomp1 amd64 4.6.2-5ubuntu1 [25.4 kB] Get:20 http://ftpmaster.internal/ubuntu/ precise/main gcc-4.6-base amd64 4.6.2-5ubuntu1 [15.3 kB] Get:21 http://ftpmaster.internal/ubuntu/ precise/main libstdc++6 amd64 4.6.2-5ubuntu1 [320 kB] Get:22 http://ftpmaster.internal/ubuntu/ precise/main cpp-4.6 amd64 4.6.2-5ubuntu1 [4826 kB] Get:23 http://ftpmaster.internal/ubuntu/ precise/main libquadmath0 amd64 4.6.2-5ubuntu1 [126 kB] Get:24 http://ftpmaster.internal/ubuntu/ precise/main libstdc++6-4.6-dev amd64 4.6.2-5ubuntu1 [1645 kB] Get:25 http://ftpmaster.internal/ubuntu/ precise/main g++-4.6 amd64 4.6.2-5ubuntu1 [6969 kB] Get:26 http://ftpmaster.internal/ubuntu/ precise/main gcc-4.6 amd64 4.6.2-5ubuntu1 [7536 kB] Get:27 http://ftpmaster.internal/ubuntu/ precise/main libgcc1 amd64 1:4.6.2-5ubuntu1 [42.6 kB] Get:28 http://ftpmaster.internal/ubuntu/ precise/main libmpfr4 amd64 3.1.0-3 [201 kB] Get:29 http://ftpmaster.internal/ubuntu/ precise/main binutils amd64 2.22-1ubuntu1 [2637 kB] Get:30 http://ftpmaster.internal/ubuntu/ precise/main debconf amd64 1.5.41ubuntu1 [145 kB] Get:31 http://ftpmaster.internal/ubuntu/ precise/main libudev0 amd64 175-0ubuntu2 [29.4 kB] Get:32 http://ftpmaster.internal/ubuntu/ precise/main module-init-tools amd64 3.16-1ubuntu2 [105 kB] Get:33 http://ftpmaster.internal/ubuntu/ precise/main libgnutls26 amd64 2.12.14-3 [459 kB] Get:34 http://ftpmaster.internal/ubuntu/ precise/main libk5crypto3 amd64 1.9.1+dfsg-3ubuntu1 [81.8 kB] Get:35 http://ftpmaster.internal/ubuntu/ precise/main libgssapi-krb5-2 amd64 1.9.1+dfsg-3ubuntu1 [118 kB] Get:36 http://ftpmaster.internal/ubuntu/ precise/main libkrb5-3 amd64 1.9.1+dfsg-3ubuntu1 [348 kB] Get:37 http://ftpmaster.internal/ubuntu/ precise/main libkrb5support0 amd64 1.9.1+dfsg-3ubuntu1 [23.8 kB] Get:38 http://ftpmaster.internal/ubuntu/ precise/main libsasl2-2 amd64 2.1.24~rc1.dfsg1+cvs2011-05-23-4ubuntu3 [70.3 kB] Get:39 http://ftpmaster.internal/ubuntu/ precise/main libldap-2.4-2 amd64 2.4.25-3ubuntu3 [183 kB] Get:40 http://ftpmaster.internal/ubuntu/ precise/main libcurl3-gnutls amd64 7.22.0-3ubuntu1 [227 kB] Get:41 http://ftpmaster.internal/ubuntu/ precise/main gpgv amd64 1.4.11-3ubuntu2 [185 kB] Get:42 http://ftpmaster.internal/ubuntu/ precise/main gnupg amd64 1.4.11-3ubuntu2 [808 kB] Get:43 http://ftpmaster.internal/ubuntu/ precise/main ubuntu-keyring amd64 2011.11.21 [11.4 kB] Get:44 http://ftpmaster.internal/ubuntu/ precise/main initramfs-tools amd64 0.99ubuntu9 [48.6 kB] Get:45 http://ftpmaster.internal/ubuntu/ precise/main initramfs-tools-bin amd64 0.99ubuntu9 [11.9 kB] Get:46 http://ftpmaster.internal/ubuntu/ precise/main sysvinit-utils amd64 2.88dsf-13.10ubuntu5 [62.5 kB] Get:47 http://ftpmaster.internal/ubuntu/ precise/main sysv-rc all 2.88dsf-13.10ubuntu5 [44.5 kB] Get:48 http://ftpmaster.internal/ubuntu/ precise/main initscripts amd64 2.88dsf-13.10ubuntu5 [27.2 kB] Get:49 http://ftpmaster.internal/ubuntu/ precise/main procps amd64 1:3.2.8-11ubuntu4 [235 kB] Get:50 http://ftpmaster.internal/ubuntu/ precise/main udev amd64 175-0ubuntu2 [323 kB] Get:51 http://ftpmaster.internal/ubuntu/ precise/main locales all 2.13+git20111116-1 [3349 kB] Get:52 http://ftpmaster.internal/ubuntu/ precise/main dpkg-dev amd64 1.16.1.2ubuntu1 [468 kB] Get:53 http://ftpmaster.internal/ubuntu/ precise/main libdpkg-perl amd64 1.16.1.2ubuntu1 [181 kB] Get:54 http://ftpmaster.internal/ubuntu/ precise/main linux-libc-dev amd64 3.2.0-2.4 [848 kB] Get:55 http://ftpmaster.internal/ubuntu/ precise/main pkg-create-dbgsym all 0.50 [8334 B] Get:56 http://ftpmaster.internal/ubuntu/ precise/main pkgbinarymangler all 106 [27.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 47.5 MB in 1s (29.4 MB/s) (Reading database ... 14111 files and directories currently installed.) Preparing to replace base-files 6.5ubuntu2 (using .../base-files_6.5ubuntu3_amd64.deb) ... Unpacking replacement base-files ... Setting up base-files (6.5ubuntu3) ... (Reading database ... 14111 files and directories currently installed.) Preparing to replace libattr1 1:2.4.46-3 (using .../libattr1_1%3a2.4.46-3ubuntu1_amd64.deb) ... Unpacking replacement libattr1 ... Setting up libattr1 (1:2.4.46-3ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 14111 files and directories currently installed.) Preparing to replace libacl1 2.2.51-3 (using .../libacl1_2.2.51-4ubuntu1_amd64.deb) ... Unpacking replacement libacl1 ... Setting up libacl1 (2.2.51-4ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 14111 files and directories currently installed.) Preparing to replace dpkg 1.16.1.1ubuntu3 (using .../dpkg_1.16.1.2ubuntu1_amd64.deb) ... Unpacking replacement dpkg ... Setting up dpkg (1.16.1.2ubuntu1) ... (Reading database ... 14111 files and directories currently installed.) Preparing to replace coreutils 8.13-3ubuntu1 (using .../coreutils_8.13-3ubuntu2_amd64.deb) ... Unpacking replacement coreutils ... Setting up coreutils (8.13-3ubuntu2) ... (Reading database ... 14111 files and directories currently installed.) Preparing to replace libncursesw5 5.9-2 (using .../libncursesw5_5.9-4_amd64.deb) ... Unpacking replacement libncursesw5 ... Preparing to replace libtinfo5 5.9-2 (using .../libtinfo5_5.9-4_amd64.deb) ... Unpacking replacement libtinfo5 ... Replacing files in old package libncurses5 ... Setting up libtinfo5 (5.9-4) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 14109 files and directories currently installed.) Preparing to replace libncurses5 5.9-2 (using .../libncurses5_5.9-4_amd64.deb) ... Unpacking replacement libncurses5 ... Setting up libncurses5 (5.9-4) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 14109 files and directories currently installed.) Preparing to replace ncurses-bin 5.9-2 (using .../ncurses-bin_5.9-4_amd64.deb) ... Unpacking replacement ncurses-bin ... Setting up ncurses-bin (5.9-4) ... (Reading database ... 14109 files and directories currently installed.) Preparing to replace perl 5.12.4-6 (using .../perl_5.14.2-5ubuntu1_amd64.deb) ... Unpacking replacement perl ... Preparing to replace libalgorithm-diff-xs-perl 0.04-2 (using .../libalgorithm-diff-xs-perl_0.04-2build2_amd64.deb) ... Unpacking replacement libalgorithm-diff-xs-perl ... Preparing to replace perl-base 5.12.4-6 (using .../perl-base_5.14.2-5ubuntu1_amd64.deb) ... Unpacking replacement perl-base ... Setting up perl-base (5.14.2-5ubuntu1) ... (Reading database ... 14140 files and directories currently installed.) Preparing to replace perl-modules 5.12.4-6 (using .../perl-modules_5.14.2-5ubuntu1_all.deb) ... Unpacking replacement perl-modules ... Preparing to replace tar 1.25-3 (using .../tar_1.26-3ubuntu1_amd64.deb) ... Unpacking replacement tar ... Setting up tar (1.26-3ubuntu1) ... (Reading database ... 14187 files and directories currently installed.) Preparing to replace ncurses-base 5.9-2 (using .../ncurses-base_5.9-4_all.deb) ... Unpacking replacement ncurses-base ... Setting up ncurses-base (5.9-4) ... Installing new version of config file /etc/terminfo/README ... (Reading database ... 14187 files and directories currently installed.) Preparing to replace python-minimal 2.7.2-7ubuntu4 (using .../python-minimal_2.7.2-9ubuntu1_all.deb) ... Unpacking replacement python-minimal ... Setting up python-minimal (2.7.2-9ubuntu1) ... (Reading database ... 14187 files and directories currently installed.) Preparing to replace readline-common 6.2-7ubuntu1 (using .../readline-common_6.2-8_amd64.deb) ... Unpacking replacement readline-common ... Setting up readline-common (6.2-8) ... (Reading database ... 14187 files and directories currently installed.) Preparing to replace libreadline6 6.2-7ubuntu1 (using .../libreadline6_6.2-8_amd64.deb) ... Unpacking replacement libreadline6 ... Setting up libreadline6 (6.2-8) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 14187 files and directories currently installed.) Preparing to replace libgomp1 4.6.2-2ubuntu1 (using .../libgomp1_4.6.2-5ubuntu1_amd64.deb) ... Unpacking replacement libgomp1 ... Preparing to replace gcc-4.6-base 4.6.2-2ubuntu1 (using .../gcc-4.6-base_4.6.2-5ubuntu1_amd64.deb) ... Unpacking replacement gcc-4.6-base ... Setting up gcc-4.6-base (4.6.2-5ubuntu1) ... (Reading database ... 14187 files and directories currently installed.) Preparing to replace libstdc++6 4.6.2-2ubuntu1 (using .../libstdc++6_4.6.2-5ubuntu1_amd64.deb) ... Unpacking replacement libstdc++6 ... Setting up libstdc++6 (4.6.2-5ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 14187 files and directories currently installed.) Preparing to replace cpp-4.6 4.6.2-2ubuntu1 (using .../cpp-4.6_4.6.2-5ubuntu1_amd64.deb) ... Unpacking replacement cpp-4.6 ... Preparing to replace libquadmath0 4.6.2-2ubuntu1 (using .../libquadmath0_4.6.2-5ubuntu1_amd64.deb) ... Unpacking replacement libquadmath0 ... Preparing to replace libstdc++6-4.6-dev 4.6.2-2ubuntu1 (using .../libstdc++6-4.6-dev_4.6.2-5ubuntu1_amd64.deb) ... Unpacking replacement libstdc++6-4.6-dev ... Preparing to replace g++-4.6 4.6.2-2ubuntu1 (using .../g++-4.6_4.6.2-5ubuntu1_amd64.deb) ... Unpacking replacement g++-4.6 ... Preparing to replace gcc-4.6 4.6.2-2ubuntu1 (using .../gcc-4.6_4.6.2-5ubuntu1_amd64.deb) ... Unpacking replacement gcc-4.6 ... Preparing to replace libgcc1 1:4.6.2-2ubuntu1 (using .../libgcc1_1%3a4.6.2-5ubuntu1_amd64.deb) ... Unpacking replacement libgcc1 ... Setting up libgcc1 (1:4.6.2-5ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 14187 files and directories currently installed.) Preparing to replace libmpfr4 3.1.0-2 (using .../libmpfr4_3.1.0-3_amd64.deb) ... Unpacking replacement libmpfr4 ... Preparing to replace binutils 2.21.90.20111025-1ubuntu1 (using .../binutils_2.22-1ubuntu1_amd64.deb) ... Unpacking replacement binutils ... Preparing to replace debconf 1.5.40ubuntu1 (using .../debconf_1.5.41ubuntu1_amd64.deb) ... Unpacking replacement debconf ... Setting up debconf (1.5.41ubuntu1) ... (Reading database ... 14184 files and directories currently installed.) Preparing to replace libudev0 175-0ubuntu1 (using .../libudev0_175-0ubuntu2_amd64.deb) ... Unpacking replacement libudev0 ... Preparing to replace module-init-tools 3.16-1ubuntu1 (using .../module-init-tools_3.16-1ubuntu2_amd64.deb) ... Unpacking replacement module-init-tools ... Preparing to replace libgnutls26 2.12.11-1 (using .../libgnutls26_2.12.14-3_amd64.deb) ... Unpacking replacement libgnutls26 ... Preparing to replace libk5crypto3 1.9.1+dfsg-1ubuntu2.1 (using .../libk5crypto3_1.9.1+dfsg-3ubuntu1_amd64.deb) ... Unpacking replacement libk5crypto3 ... Preparing to replace libgssapi-krb5-2 1.9.1+dfsg-1ubuntu2.1 (using .../libgssapi-krb5-2_1.9.1+dfsg-3ubuntu1_amd64.deb) ... Unpacking replacement libgssapi-krb5-2 ... Preparing to replace libkrb5-3 1.9.1+dfsg-1ubuntu2.1 (using .../libkrb5-3_1.9.1+dfsg-3ubuntu1_amd64.deb) ... Unpacking replacement libkrb5-3 ... Preparing to replace libkrb5support0 1.9.1+dfsg-1ubuntu2.1 (using .../libkrb5support0_1.9.1+dfsg-3ubuntu1_amd64.deb) ... Unpacking replacement libkrb5support0 ... Preparing to replace libsasl2-2 2.1.24~rc1.dfsg1+cvs2011-05-23-4ubuntu2 (using .../libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-4ubuntu3_amd64.deb) ... Unpacking replacement libsasl2-2 ... Preparing to replace libldap-2.4-2 2.4.25-3ubuntu1 (using .../libldap-2.4-2_2.4.25-3ubuntu3_amd64.deb) ... Unpacking replacement libldap-2.4-2 ... Preparing to replace libcurl3-gnutls 7.21.7-3ubuntu1 (using .../libcurl3-gnutls_7.22.0-3ubuntu1_amd64.deb) ... Unpacking replacement libcurl3-gnutls ... Preparing to replace gpgv 1.4.11-3ubuntu1 (using .../gpgv_1.4.11-3ubuntu2_amd64.deb) ... Unpacking replacement gpgv ... Setting up gpgv (1.4.11-3ubuntu2) ... (Reading database ... 14184 files and directories currently installed.) Preparing to replace gnupg 1.4.11-3ubuntu1 (using .../gnupg_1.4.11-3ubuntu2_amd64.deb) ... Unpacking replacement gnupg ... Setting up gnupg (1.4.11-3ubuntu2) ... (Reading database ... 14184 files and directories currently installed.) Preparing to replace ubuntu-keyring 2010.+09.30 (using .../ubuntu-keyring_2011.11.21_amd64.deb) ... Unpacking replacement ubuntu-keyring ... Setting up ubuntu-keyring (2011.11.21) ... 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 ... 14184 files and directories currently installed.) Preparing to replace initramfs-tools 0.99ubuntu8 (using .../initramfs-tools_0.99ubuntu9_amd64.deb) ... Unpacking replacement initramfs-tools ... Preparing to replace initramfs-tools-bin 0.99ubuntu8 (using .../initramfs-tools-bin_0.99ubuntu9_amd64.deb) ... Unpacking replacement initramfs-tools-bin ... Preparing to replace sysvinit-utils 2.88dsf-13.10ubuntu4 (using .../sysvinit-utils_2.88dsf-13.10ubuntu5_amd64.deb) ... Unpacking replacement sysvinit-utils ... Preparing to replace sysv-rc 2.88dsf-13.10ubuntu4 (using .../sysv-rc_2.88dsf-13.10ubuntu5_all.deb) ... Unpacking replacement sysv-rc ... Preparing to replace initscripts 2.88dsf-13.10ubuntu4 (using .../initscripts_2.88dsf-13.10ubuntu5_amd64.deb) ... Unpacking replacement initscripts ... Preparing to replace procps 1:3.2.8-11ubuntu1 (using .../procps_1%3a3.2.8-11ubuntu4_amd64.deb) ... invoke-rc.d: policy-rc.d denied execution of stop. Unpacking replacement procps ... Preparing to replace udev 175-0ubuntu1 (using .../udev_175-0ubuntu2_amd64.deb) ... Adding 'diversion of /sbin/udevadm to /sbin/udevadm.upgrade by fake-udev' Unpacking replacement udev ... Preparing to replace locales 2.13+git20110622-2 (using .../locales_2.13+git20111116-1_all.deb) ... Unpacking replacement locales ... Preparing to replace dpkg-dev 1.16.1.1ubuntu3 (using .../dpkg-dev_1.16.1.2ubuntu1_amd64.deb) ... Unpacking replacement dpkg-dev ... Preparing to replace libdpkg-perl 1.16.1.1ubuntu3 (using .../libdpkg-perl_1.16.1.2ubuntu1_amd64.deb) ... Unpacking replacement libdpkg-perl ... Preparing to replace linux-libc-dev 3.1.0-2.3 (using .../linux-libc-dev_3.2.0-2.4_amd64.deb) ... Unpacking replacement linux-libc-dev ... Preparing to replace pkg-create-dbgsym 0.49 (using .../pkg-create-dbgsym_0.50_all.deb) ... Unpacking replacement pkg-create-dbgsym ... Preparing to replace pkgbinarymangler 105 (using .../pkgbinarymangler_106_all.deb) ... Unpacking replacement pkgbinarymangler ... Setting up libncursesw5 (5.9-4) ... Setting up libgomp1 (4.6.2-5ubuntu1) ... Setting up libmpfr4 (3.1.0-3) ... Setting up cpp-4.6 (4.6.2-5ubuntu1) ... Setting up libquadmath0 (4.6.2-5ubuntu1) ... Setting up binutils (2.22-1ubuntu1) ... Setting up gcc-4.6 (4.6.2-5ubuntu1) ... Setting up libudev0 (175-0ubuntu2) ... Setting up module-init-tools (3.16-1ubuntu2) ... Setting up libgnutls26 (2.12.14-3) ... Setting up libkrb5support0 (1.9.1+dfsg-3ubuntu1) ... Setting up libk5crypto3 (1.9.1+dfsg-3ubuntu1) ... Setting up libkrb5-3 (1.9.1+dfsg-3ubuntu1) ... Setting up libgssapi-krb5-2 (1.9.1+dfsg-3ubuntu1) ... Setting up libsasl2-2 (2.1.24~rc1.dfsg1+cvs2011-05-23-4ubuntu3) ... Setting up libldap-2.4-2 (2.4.25-3ubuntu3) ... Setting up libcurl3-gnutls (7.22.0-3ubuntu1) ... Setting up initramfs-tools-bin (0.99ubuntu9) ... Setting up sysvinit-utils (2.88dsf-13.10ubuntu5) ... Setting up sysv-rc (2.88dsf-13.10ubuntu5) ... Setting up initscripts (2.88dsf-13.10ubuntu5) ... guest environment detected: Linking /run/shm to /dev/shm Setting up procps (1:3.2.8-11ubuntu4) ... Installing new version of config file /etc/init/procps.conf ... invoke-rc.d: policy-rc.d denied execution of start. Setting up locales (2.13+git20111116-1) ... Setting up linux-libc-dev (3.2.0-2.4) ... Setting up pkg-create-dbgsym (0.50) ... Setting up pkgbinarymangler (106) ... Setting up perl-modules (5.14.2-5ubuntu1) ... Setting up perl (5.14.2-5ubuntu1) ... Setting up libalgorithm-diff-xs-perl (0.04-2build2) ... Setting up libstdc++6-4.6-dev (4.6.2-5ubuntu1) ... Setting up udev (175-0ubuntu2) ... Installing new version of config file /etc/init/udev.conf ... invoke-rc.d: policy-rc.d denied execution of restart. Removing 'diversion of /sbin/udevadm to /sbin/udevadm.upgrade by fake-udev' update-initramfs: deferring update (trigger activated) Setting up initramfs-tools (0.99ubuntu9) ... update-initramfs: deferring update (trigger activated) Setting up libdpkg-perl (1.16.1.2ubuntu1) ... Setting up dpkg-dev (1.16.1.2ubuntu1) ... Setting up g++-4.6 (4.6.2-5ubuntu1) ... 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', '60a9e9a2b60f7bda7323f2353c16429ad2819a0c', 'amd64', 'precise', '--nolog', '--batch', '--archive=ubuntu', '--dist=precise', '--purpose=PRIMARY', '--architecture=amd64', '--comp=multiverse', 'clustalx_2.1+lgpl-2.dsc'] Initiating build 60a9e9a2b60f7bda7323f2353c16429ad2819a0c with 8 processor cores. Automatic build of clustalx_2.1+lgpl-2 on allspice by sbuild/amd64 1.170.5 Build started at 20111127-1756 ****************************************************************************** clustalx_2.1+lgpl-2.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: debhelper (>= 8), libqt4-dev 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... debhelper: missing libqt4-dev: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper libqt4-dev Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils file fontconfig fontconfig-config gettext gettext-base groff-base html2text intltool-debian libaudio2 libcroco3 libexpat1 libfontconfig1 libfreetype6 libgettextpo0 libice6 libjpeg8 liblcms1 libmagic1 libmng1 libpipeline1 libpthread-stubs0 libpthread-stubs0-dev libqt4-dbus libqt4-declarative libqt4-designer libqt4-help libqt4-network libqt4-qt3support libqt4-script libqt4-scripttools libqt4-sql libqt4-svg libqt4-test libqt4-xml libqt4-xmlpatterns libqtcore4 libqtgui4 libsm6 libtiff4 libunistring0 libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext6 libxi6 libxml2 libxrender1 libxt6 man-db po-debconf qdbus qt4-linguist-tools qt4-qmake ttf-dejavu-core ucf x11-common x11proto-core-dev x11proto-input-dev x11proto-kb-dev xorg-sgml-doctools xtrans-dev Suggested packages: wamerican wordlist whois vacation dh-make defoma gettext-doc groff nas liblcms-utils libqt4-declarative-folderlistmodel libqt4-declarative-gestures libqt4-declarative-particles libqt4-declarative-shaders qt4-qmlviewer libmysqlclient-dev libpq-dev libsqlite3-dev qt4-dev-tools qt4-doc unixodbc-dev qt4-qtconfig less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur libqt4-opengl-dev libqtwebkit-dev libqt4-sql-mysql libqt4-sql-odbc libqt4-sql-psql libqt4-sql-sqlite libcups2 libx11-doc xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper file fontconfig fontconfig-config gettext gettext-base groff-base html2text intltool-debian libaudio2 libcroco3 libexpat1 libfontconfig1 libfreetype6 libgettextpo0 libice6 libjpeg8 liblcms1 libmagic1 libmng1 libpipeline1 libpthread-stubs0 libpthread-stubs0-dev libqt4-dbus libqt4-declarative libqt4-designer libqt4-dev libqt4-help libqt4-network libqt4-qt3support libqt4-script libqt4-scripttools libqt4-sql libqt4-svg libqt4-test libqt4-xml libqt4-xmlpatterns libqtcore4 libqtgui4 libsm6 libtiff4 libunistring0 libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext6 libxi6 libxml2 libxrender1 libxt6 man-db po-debconf qdbus qt4-linguist-tools qt4-qmake ttf-dejavu-core ucf x11-common x11proto-core-dev x11proto-input-dev x11proto-kb-dev xorg-sgml-doctools xtrans-dev 0 upgraded, 70 newly installed, 0 to remove and 0 not upgraded. Need to get 30.8 MB of archives. After this operation, 115 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libexpat1 libfreetype6 ucf ttf-dejavu-core fontconfig-config libfontconfig1 libpipeline1 libxau6 libxdmcp6 libxcb1 libx11-data libx11-6 libxext6 libxml2 libxrender1 x11-common libice6 libsm6 libxt6 libaudio2 libcroco3 libunistring0 libgettextpo0 libjpeg8 liblcms1 libmng1 libqtcore4 libqt4-xml qdbus libqt4-dbus libqt4-network libqt4-script libqt4-sql libqt4-xmlpatterns fontconfig libtiff4 libxi6 libqtgui4 libqt4-declarative libqt4-designer libqt4-help libqt4-qt3support libqt4-scripttools libqt4-svg libqt4-test libmagic1 file bsdmainutils gettext-base groff-base man-db html2text gettext intltool-debian po-debconf debhelper libpthread-stubs0 libpthread-stubs0-dev qt4-linguist-tools qt4-qmake xorg-sgml-doctools x11proto-core-dev libxau-dev libxdmcp-dev x11proto-input-dev x11proto-kb-dev xtrans-dev libxcb1-dev libx11-dev libqt4-dev Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ precise/main libexpat1 amd64 2.0.1-7.2 [131 kB] Get:2 http://ftpmaster.internal/ubuntu/ precise/main libfreetype6 amd64 2.4.8-1 [342 kB] Get:3 http://ftpmaster.internal/ubuntu/ precise/main ucf all 3.0025+nmu2ubuntu1 [54.4 kB] Get:4 http://ftpmaster.internal/ubuntu/ precise/main ttf-dejavu-core amd64 2.33-2 [1550 kB] Get:5 http://ftpmaster.internal/ubuntu/ precise/main fontconfig-config amd64 2.8.0-3ubuntu2 [44.5 kB] Get:6 http://ftpmaster.internal/ubuntu/ precise/main libfontconfig1 amd64 2.8.0-3ubuntu2 [124 kB] Get:7 http://ftpmaster.internal/ubuntu/ precise/main libpipeline1 amd64 1.2.0-5 [26.2 kB] Get:8 http://ftpmaster.internal/ubuntu/ precise/main libxau6 amd64 1:1.0.6-4 [8392 B] Get:9 http://ftpmaster.internal/ubuntu/ precise/main libxdmcp6 amd64 1:1.1.0-4 [12.7 kB] Get:10 http://ftpmaster.internal/ubuntu/ precise/main libxcb1 amd64 1.7-4 [40.9 kB] Get:11 http://ftpmaster.internal/ubuntu/ precise/main libx11-data amd64 2:1.4.4-4 [172 kB] Get:12 http://ftpmaster.internal/ubuntu/ precise/main libx11-6 amd64 2:1.4.4-4 [766 kB] Get:13 http://ftpmaster.internal/ubuntu/ precise/main libxext6 amd64 2:1.3.0-3 [34.7 kB] Get:14 http://ftpmaster.internal/ubuntu/ precise/main libxml2 amd64 2.7.8.dfsg-5ubuntu1 [673 kB] Get:15 http://ftpmaster.internal/ubuntu/ precise/main libxrender1 amd64 1:0.9.6-2 [20.8 kB] Get:16 http://ftpmaster.internal/ubuntu/ precise/main x11-common amd64 1:7.6+7ubuntu7 [56.6 kB] Get:17 http://ftpmaster.internal/ubuntu/ precise/main libice6 amd64 2:1.0.7-2 [46.2 kB] Get:18 http://ftpmaster.internal/ubuntu/ precise/main libsm6 amd64 2:1.2.0-2 [18.1 kB] Get:19 http://ftpmaster.internal/ubuntu/ precise/main libxt6 amd64 1:1.1.1-2 [185 kB] Get:20 http://ftpmaster.internal/ubuntu/ precise/main libaudio2 amd64 1.9.3-1 [58.2 kB] Get:21 http://ftpmaster.internal/ubuntu/ precise/main libcroco3 amd64 0.6.2-2 [100 kB] Get:22 http://ftpmaster.internal/ubuntu/ precise/main libunistring0 amd64 0.9.3-5 [427 kB] Get:23 http://ftpmaster.internal/ubuntu/ precise/main libgettextpo0 amd64 0.18.1.1-5ubuntu2 [120 kB] Get:24 http://ftpmaster.internal/ubuntu/ precise/main libjpeg8 amd64 8c-2ubuntu4 [123 kB] Get:25 http://ftpmaster.internal/ubuntu/ precise/main liblcms1 amd64 1.19.dfsg-1ubuntu3 [106 kB] Get:26 http://ftpmaster.internal/ubuntu/ precise/main libmng1 amd64 1.0.10-3 [215 kB] Get:27 http://ftpmaster.internal/ubuntu/ precise/main libqtcore4 amd64 4:4.7.4-1ubuntu4 [1898 kB] Get:28 http://ftpmaster.internal/ubuntu/ precise/main libqt4-xml amd64 4:4.7.4-1ubuntu4 [91.7 kB] Get:29 http://ftpmaster.internal/ubuntu/ precise/main qdbus amd64 4:4.7.4-1ubuntu4 [27.7 kB] Get:30 http://ftpmaster.internal/ubuntu/ precise/main libqt4-dbus amd64 4:4.7.4-1ubuntu4 [170 kB] Get:31 http://ftpmaster.internal/ubuntu/ precise/main libqt4-network amd64 4:4.7.4-1ubuntu4 [518 kB] Get:32 http://ftpmaster.internal/ubuntu/ precise/main libqt4-script amd64 4:4.7.4-1ubuntu4 [758 kB] Get:33 http://ftpmaster.internal/ubuntu/ precise/main libqt4-sql amd64 4:4.7.4-1ubuntu4 [95.3 kB] Get:34 http://ftpmaster.internal/ubuntu/ precise/main libqt4-xmlpatterns amd64 4:4.7.4-1ubuntu4 [1031 kB] Get:35 http://ftpmaster.internal/ubuntu/ precise/main fontconfig amd64 2.8.0-3ubuntu2 [157 kB] Get:36 http://ftpmaster.internal/ubuntu/ precise/main libtiff4 amd64 3.9.5-2 [144 kB] Get:37 http://ftpmaster.internal/ubuntu/ precise/main libxi6 amd64 2:1.4.3-3ubuntu1 [30.6 kB] Get:38 http://ftpmaster.internal/ubuntu/ precise/main libqtgui4 amd64 4:4.7.4-1ubuntu4 [3931 kB] Get:39 http://ftpmaster.internal/ubuntu/ precise/main libqt4-declarative amd64 4:4.7.4-1ubuntu4 [997 kB] Get:40 http://ftpmaster.internal/ubuntu/ precise/main libqt4-designer amd64 4:4.7.4-1ubuntu4 [3646 kB] Get:41 http://ftpmaster.internal/ubuntu/ precise/main libqt4-help amd64 4:4.7.4-1ubuntu4 [197 kB] Get:42 http://ftpmaster.internal/ubuntu/ precise/main libqt4-qt3support amd64 4:4.7.4-1ubuntu4 [1019 kB] Get:43 http://ftpmaster.internal/ubuntu/ precise/main libqt4-scripttools amd64 4:4.7.4-1ubuntu4 [219 kB] Get:44 http://ftpmaster.internal/ubuntu/ precise/main libqt4-svg amd64 4:4.7.4-1ubuntu4 [136 kB] Get:45 http://ftpmaster.internal/ubuntu/ precise/main libqt4-test amd64 4:4.7.4-1ubuntu4 [58.1 kB] Get:46 http://ftpmaster.internal/ubuntu/ precise/main libmagic1 amd64 5.09-2 [217 kB] Get:47 http://ftpmaster.internal/ubuntu/ precise/main file amd64 5.09-2 [19.7 kB] Get:48 http://ftpmaster.internal/ubuntu/ precise/main bsdmainutils amd64 8.2.3 [198 kB] Get:49 http://ftpmaster.internal/ubuntu/ precise/main gettext-base amd64 0.18.1.1-5ubuntu2 [80.1 kB] Get:50 http://ftpmaster.internal/ubuntu/ precise/main groff-base amd64 1.21-6 [1047 kB] Get:51 http://ftpmaster.internal/ubuntu/ precise/main man-db amd64 2.6.0.2-3 [727 kB] Get:52 http://ftpmaster.internal/ubuntu/ precise/main html2text amd64 1.3.2a-15 [104 kB] Get:53 http://ftpmaster.internal/ubuntu/ precise/main gettext amd64 0.18.1.1-5ubuntu2 [1188 kB] Get:54 http://ftpmaster.internal/ubuntu/ precise/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:55 http://ftpmaster.internal/ubuntu/ precise/main po-debconf amd64 1.0.16+nmu1ubuntu1 [211 kB] Get:56 http://ftpmaster.internal/ubuntu/ precise/main debhelper amd64 8.9.9ubuntu1 [477 kB] Get:57 http://ftpmaster.internal/ubuntu/ precise/main libpthread-stubs0 amd64 0.3-2.1ubuntu1 [3358 B] Get:58 http://ftpmaster.internal/ubuntu/ precise/main libpthread-stubs0-dev amd64 0.3-2.1ubuntu1 [2482 B] Get:59 http://ftpmaster.internal/ubuntu/ precise/main qt4-linguist-tools amd64 4:4.7.4-1ubuntu4 [834 kB] Get:60 http://ftpmaster.internal/ubuntu/ precise/main qt4-qmake amd64 4:4.7.4-1ubuntu4 [1224 kB] Get:61 http://ftpmaster.internal/ubuntu/ precise/main xorg-sgml-doctools amd64 1:1.8-2 [10.9 kB] Get:62 http://ftpmaster.internal/ubuntu/ precise/main x11proto-core-dev amd64 7.0.22-1 [299 kB] Get:63 http://ftpmaster.internal/ubuntu/ precise/main libxau-dev amd64 1:1.0.6-4 [10.5 kB] Get:64 http://ftpmaster.internal/ubuntu/ precise/main libxdmcp-dev amd64 1:1.1.0-4 [26.9 kB] Get:65 http://ftpmaster.internal/ubuntu/ precise/main x11proto-input-dev amd64 2.0.2-2ubuntu1 [69.0 kB] Get:66 http://ftpmaster.internal/ubuntu/ precise/main x11proto-kb-dev amd64 1.0.5-2 [27.6 kB] Get:67 http://ftpmaster.internal/ubuntu/ precise/main xtrans-dev amd64 1.2.6-2 [82.9 kB] Get:68 http://ftpmaster.internal/ubuntu/ precise/main libxcb1-dev amd64 1.7-4 [78.0 kB] Get:69 http://ftpmaster.internal/ubuntu/ precise/main libx11-dev amd64 2:1.4.4-4 [912 kB] Get:70 http://ftpmaster.internal/ubuntu/ precise/main libqt4-dev amd64 4:4.7.4-1ubuntu4 [2359 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 30.8 MB in 0s (35.3 MB/s) Selecting previously unselected package libexpat1. (Reading database ... 14186 files and directories currently installed.) Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_amd64.deb) ... Selecting previously unselected package libfreetype6. Unpacking libfreetype6 (from .../libfreetype6_2.4.8-1_amd64.deb) ... Selecting previously unselected package ucf. Unpacking ucf (from .../ucf_3.0025+nmu2ubuntu1_all.deb) ... Moving old data out of the way Selecting previously unselected package ttf-dejavu-core. Unpacking ttf-dejavu-core (from .../ttf-dejavu-core_2.33-2_amd64.deb) ... Selecting previously unselected package fontconfig-config. Unpacking fontconfig-config (from .../fontconfig-config_2.8.0-3ubuntu2_amd64.deb) ... Selecting previously unselected package libfontconfig1. Unpacking libfontconfig1 (from .../libfontconfig1_2.8.0-3ubuntu2_amd64.deb) ... Selecting previously unselected package libpipeline1. Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_amd64.deb) ... Selecting previously unselected package libxau6. 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Selecting previously unselected package libqt4-dev. Unpacking libqt4-dev (from .../libqt4-dev_4%3a4.7.4-1ubuntu4_amd64.deb) ... Setting up libexpat1 (2.0.1-7.2) ... Setting up libfreetype6 (2.4.8-1) ... Setting up ucf (3.0025+nmu2ubuntu1) ... Setting up ttf-dejavu-core (2.33-2) ... Setting up fontconfig-config (2.8.0-3ubuntu2) ... Setting up libfontconfig1 (2.8.0-3ubuntu2) ... Setting up libpipeline1 (1.2.0-5) ... Setting up libxau6 (1:1.0.6-4) ... Setting up libxdmcp6 (1:1.1.0-4) ... Setting up libxcb1 (1.7-4) ... Setting up libx11-data (2:1.4.4-4) ... Setting up libx11-6 (2:1.4.4-4) ... Setting up libxext6 (2:1.3.0-3) ... Setting up libxml2 (2.7.8.dfsg-5ubuntu1) ... Setting up libxrender1 (1:0.9.6-2) ... Setting up x11-common (1:7.6+7ubuntu7) ... invoke-rc.d: policy-rc.d denied execution of start. Setting up libice6 (2:1.0.7-2) ... Setting up libsm6 (2:1.2.0-2) ... Setting up libxt6 (1:1.1.1-2) ... Setting up libaudio2 (1.9.3-1) ... Setting up libcroco3 (0.6.2-2) ... Setting up libunistring0 (0.9.3-5) ... Setting up libgettextpo0 (0.18.1.1-5ubuntu2) ... Setting up libjpeg8 (8c-2ubuntu4) ... Setting up liblcms1 (1.19.dfsg-1ubuntu3) ... Setting up libmng1 (1.0.10-3) ... Setting up libqtcore4 (4:4.7.4-1ubuntu4) ... Setting up libqt4-xml (4:4.7.4-1ubuntu4) ... Setting up libqt4-sql (4:4.7.4-1ubuntu4) ... Setting up fontconfig (2.8.0-3ubuntu2) ... Cleaning up old fontconfig caches... done. Regenerating fonts cache... done. Setting up libtiff4 (3.9.5-2) ... Setting up libxi6 (2:1.4.3-3ubuntu1) ... Setting up libqt4-test (4:4.7.4-1ubuntu4) ... Setting up libmagic1 (5.09-2) ... Setting up file (5.09-2) ... 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 (0.18.1.1-5ubuntu2) ... Setting up groff-base (1.21-6) ... Setting up man-db (2.6.0.2-3) ... Building database of manual pages ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu1ubuntu1) ... Setting up debhelper (8.9.9ubuntu1) ... Setting up libpthread-stubs0 (0.3-2.1ubuntu1) ... Setting up libpthread-stubs0-dev (0.3-2.1ubuntu1) ... Setting up qt4-linguist-tools (4:4.7.4-1ubuntu4) ... update-alternatives: using /usr/bin/lupdate-qt4 to provide /usr/bin/lupdate (lupdate) in auto mode. update-alternatives: using /usr/bin/lrelease-qt4 to provide /usr/bin/lrelease (lrelease) in auto mode. Setting up qt4-qmake (4:4.7.4-1ubuntu4) ... update-alternatives: using /usr/bin/qmake-qt4 to provide /usr/bin/qmake (qmake) in auto mode. Setting up xorg-sgml-doctools (1:1.8-2) ... Setting up x11proto-core-dev (7.0.22-1) ... Setting up libxau-dev (1:1.0.6-4) ... Setting up libxdmcp-dev (1:1.1.0-4) ... Setting up x11proto-input-dev (2.0.2-2ubuntu1) ... Setting up x11proto-kb-dev (1.0.5-2) ... Setting up xtrans-dev (1.2.6-2) ... Setting up libxcb1-dev (1.7-4) ... Setting up libx11-dev (2:1.4.4-4) ... Setting up qdbus (4:4.7.4-1ubuntu4) ... Setting up libqtgui4 (4:4.7.4-1ubuntu4) ... Setting up libqt4-svg (4:4.7.4-1ubuntu4) ... Setting up libqt4-dbus (4:4.7.4-1ubuntu4) ... Setting up libqt4-network (4:4.7.4-1ubuntu4) ... Setting up libqt4-script (4:4.7.4-1ubuntu4) ... Setting up libqt4-xmlpatterns (4:4.7.4-1ubuntu4) ... Setting up libqt4-declarative (4:4.7.4-1ubuntu4) ... Setting up libqt4-designer (4:4.7.4-1ubuntu4) ... Setting up libqt4-help (4:4.7.4-1ubuntu4) ... Setting up libqt4-qt3support (4:4.7.4-1ubuntu4) ... Setting up libqt4-scripttools (4:4.7.4-1ubuntu4) ... Setting up libqt4-dev (4:4.7.4-1ubuntu4) ... update-alternatives: using /usr/bin/moc-qt4 to provide /usr/bin/moc (moc) in auto mode. update-alternatives: using /usr/bin/uic-qt4 to provide /usr/bin/uic (uic) in auto mode. update-alternatives: warning: skip creation of /usr/share/man/man1/uic.1.gz because associated file /usr/share/man/man1/uic-qt4.1.gz (of link group uic) doesn't exist. Processing triggers for libc-bin ... ldconfig deferred processing now taking place Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.13-20ubuntu5 make_3.81-8.1ubuntu1 dpkg-dev_1.16.1.2ubuntu1 gcc-4.6_4.6.2-5ubuntu1 g++-4.6_4.6.2-5ubuntu1 binutils_2.22-1ubuntu1 libstdc++6-4.6-dev_4.6.2-5ubuntu1 libstdc++6_4.6.2-5ubuntu1 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt gpgv: Signature made Wed Nov 16 06:30:25 2011 UTC using RSA key ID 2295D502 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./clustalx_2.1+lgpl-2.dsc dpkg-source: info: extracting clustalx in clustalx-2.1+lgpl dpkg-source: info: unpacking clustalx_2.1+lgpl.orig.tar.gz dpkg-source: info: unpacking clustalx_2.1+lgpl-2.debian.tar.gz dpkg-source: info: applying hardcode-accessory-file-locations.patch dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): -D_FORTIFY_SOURCE=2 dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): -Wl,-Bsymbolic-functions -Wl,-z,relro dpkg-buildpackage: source package clustalx dpkg-buildpackage: source version 2.1+lgpl-2 dpkg-source --before-build clustalx-2.1+lgpl dpkg-buildpackage: host architecture amd64 /usr/bin/fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean debian/rules override_dh_clean make[1]: Entering directory `/build/buildd/clustalx-2.1+lgpl' rm -f moc_* dh_clean make[1]: Leaving directory `/build/buildd/clustalx-2.1+lgpl' debian/rules build dh build dh_testdir debian/rules override_dh_auto_configure make[1]: Entering directory `/build/buildd/clustalx-2.1+lgpl' qmake-qt4 make[1]: Leaving directory `/build/buildd/clustalx-2.1+lgpl' dh_auto_build make[1]: Entering directory `/build/buildd/clustalx-2.1+lgpl' g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignmentFormatOptions.o AlignmentFormatOptions.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignmentParameters.o AlignmentParameters.cpp AlignmentParameters.cpp:48:6: warning: unused parameter 'event' [-Wunused-parameter] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignmentViewerWidget.o AlignmentViewerWidget.cpp AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeGapPenaltyData()': AlignmentViewerWidget.cpp:588:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeSecStructData()': AlignmentViewerWidget.cpp:645:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] AlignmentViewerWidget.cpp:652:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] AlignmentViewerWidget.cpp: At global scope: AlignmentViewerWidget.cpp:781:6: warning: unused parameter 'event' [-Wunused-parameter] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignmentWidget.o AlignmentWidget.cpp AlignmentWidget.h: In constructor 'AlignmentWidget::AlignmentWidget(int, int, QFont*, QWidget*)': AlignmentWidget.h:170:10: warning: 'AlignmentWidget::blackAndWhite' will be initialized after [-Wreorder] AlignmentWidget.h:161:27: warning: 'std::vector >* AlignmentWidget::selectedColoredRes' [-Wreorder] AlignmentWidget.cpp:65:1: warning: when initialized here [-Wreorder] AlignmentWidget.cpp: In member function 'void AlignmentWidget::calculatePixMaps()': AlignmentWidget.cpp:225:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] AlignmentWidget.cpp:235:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] AlignmentWidget.cpp:268:78: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] AlignmentWidget.cpp:280:81: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] AlignmentWidget.cpp:291:88: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] AlignmentWidget.cpp:215:9: warning: unused variable 'codeForSpace' [-Wunused-variable] AlignmentWidget.cpp: In member function 'void AlignmentWidget::generateSecStructurePixmaps()': AlignmentWidget.cpp:333:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] AlignmentWidget.cpp: In member function 'void AlignmentWidget::drawContents(QPainter*, int, int, int, int)': AlignmentWidget.cpp:569:64: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] AlignmentWidget.cpp: In member function 'void AlignmentWidget::calcConserveInfo()': AlignmentWidget.cpp:689:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] AlignmentWidget.cpp:693:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] AlignmentWidget.cpp:700:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] AlignmentWidget.cpp:701:62: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] AlignmentWidget.cpp:725:62: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] AlignmentWidget.cpp:737:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] AlignmentWidget.cpp:760:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] AlignmentWidget.cpp:771:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] AlignmentWidget.cpp: In member function 'void AlignmentWidget::makeColorMask(clustalw::Array2D*, ColorParameters*)': AlignmentWidget.cpp:878:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] AlignmentWidget.cpp: In member function 'QString AlignmentWidget::initConsensus()': AlignmentWidget.cpp:927:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] AlignmentWidget.cpp: In member function 'void AlignmentWidget::generatePixMaps()': AlignmentWidget.cpp:1039:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignOutputFileNames.o AlignOutputFileNames.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o BootstrapTreeDialog.o BootstrapTreeDialog.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ColorFileXmlParser.o ColorFileXmlParser.cpp ColorFileXmlParser.cpp:74:13: warning: multi-line comment [-Wcomment] ColorFileXmlParser.cpp:84:5: warning: unused parameter 'parentItem' [-Wunused-parameter] ColorFileXmlParser.cpp:138:6: warning: unused parameter 'parentItem' [-Wunused-parameter] ColorFileXmlParser.cpp:175:5: warning: unused parameter 'parentItem' [-Wunused-parameter] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ColorParameters.o ColorParameters.cpp ColorParameters.cpp: In member function 'QColor ColorParameters::getResidueColor(QChar, QChar)': ColorParameters.cpp:160:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] ColorParameters.cpp:174:26: warning: unused variable 'temp' [-Wunused-variable] ColorParameters.cpp:157:10: warning: unused variable 'showRes' [-Wunused-variable] ColorParameters.cpp:158:10: warning: unused variable 'showCon' [-Wunused-variable] ColorParameters.cpp: In member function 'int ColorParameters::getResidueColorNum(QChar, QChar)': ColorParameters.cpp:197:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] ColorParameters.cpp:211:26: warning: unused variable 'temp' [-Wunused-variable] ColorParameters.cpp:194:10: warning: unused variable 'showRes' [-Wunused-variable] ColorParameters.cpp:195:10: warning: unused variable 'showCon' [-Wunused-variable] ColorParameters.cpp: In member function 'void ColorParameters::printColorInfo()': ColorParameters.cpp:229:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] ColorParameters.cpp: In member function 'int ColorParameters::getIndexOfColor(QColor)': ColorParameters.cpp:238:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] ColorParameters.cpp: In member function 'QColor ColorParameters::getColorFromNum(int)': ColorParameters.cpp:251:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ColumnScoreParams.o ColumnScoreParams.cpp ColumnScoreParams.cpp:51:6: warning: unused parameter 'event' [-Wunused-parameter] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o FileDialog.o FileDialog.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o HardCodedColorScheme.o HardCodedColorScheme.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o HelpDisplayWidget.o HelpDisplayWidget.cpp HelpDisplayWidget.cpp: In member function 'std::string* HelpDisplayWidget::loadHelpInformation(char)': HelpDisplayWidget.cpp:61:13: warning: variable 'number' set but not used [-Wunused-but-set-variable] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o HistogramWidget.o HistogramWidget.cpp HistogramWidget.cpp: In member function 'void HistogramWidget::drawContents(QPainter*, int, int, int, int)': HistogramWidget.cpp:180:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] HistogramWidget.cpp:198:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o KeyController.o KeyController.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o LowScoringSegParams.o LowScoringSegParams.cpp LowScoringSegParams.cpp:51:6: warning: unused parameter 'event' [-Wunused-parameter] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o main.o main.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o mainwindow.o mainwindow.cpp mainwindow.cpp:198:6: warning: unused parameter 'event' [-Wunused-parameter] mainwindow.cpp:1454:6: warning: unused parameter 'type' [-Wunused-parameter] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o PairwiseParams.o PairwiseParams.cpp PairwiseParams.cpp:74:6: warning: unused parameter 'event' [-Wunused-parameter] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o PostscriptFileParams.o PostscriptFileParams.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ProteinGapParameters.o ProteinGapParameters.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o PSPrinter.o PSPrinter.cpp PSPrinter.cpp: In member function 'void PSPrinter::writePSFile(PostscriptFileParams*)': PSPrinter.cpp:207:67: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] PSPrinter.cpp:307:69: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] PSPrinter.cpp:421:69: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] PSPrinter.cpp:55:9: warning: unused variable 'err' [-Wunused-variable] PSPrinter.cpp:73:9: warning: unused variable 'gapPos1' [-Wunused-variable] PSPrinter.cpp:74:9: warning: unused variable 'gapPos2' [-Wunused-variable] PSPrinter.cpp: In member function 'void PSPrinter::printHeaderLine(std::ofstream*, int, int, int)': PSPrinter.cpp:587:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] PSPrinter.cpp: In member function 'void PSPrinter::printFooterLine(std::ofstream*, int, int)': PSPrinter.cpp:730:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] PSPrinter.cpp: In member function 'void PSPrinter::printQualityCurve(std::ofstream*, int, int, int)': PSPrinter.cpp:789:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] PSPrinter.cpp:781:14: warning: unused variable 'psY' [-Wunused-variable] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o QTUtility.o QTUtility.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Resources.o Resources.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o SaveSeqFile.o SaveSeqFile.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o SearchForString.o SearchForString.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o SecStructOptions.o SecStructOptions.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o SeqNameWidget.o SeqNameWidget.cpp SeqNameWidget.cpp: In member function 'virtual void SeqNameWidget::paintEvent(QPaintEvent*)': SeqNameWidget.cpp:375:11: warning: variable 'redrawRect' set but not used [-Wunused-but-set-variable] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o TreeFormatOptions.o TreeFormatOptions.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o TreeOutputFileNames.o TreeOutputFileNames.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o WritePostscriptFile.o WritePostscriptFile.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Clustal.o clustalW/Clustal.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Help.o clustalW/Help.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Alignment.o clustalW/alignment/Alignment.cpp clustalW/alignment/Alignment.cpp: In member function 'bool clustalw::Alignment::keepPortionOfSeqArray(int, int)': clustalW/alignment/Alignment.cpp:1715:24: warning: variable 'posToAddTo' set but not used [-Wunused-but-set-variable] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignmentOutput.o clustalW/alignment/AlignmentOutput.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ObjectiveScore.o clustalW/alignment/ObjectiveScore.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Sequence.o clustalW/alignment/Sequence.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ClustalFileParser.o clustalW/fileInput/ClustalFileParser.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o EMBLFileParser.o clustalW/fileInput/EMBLFileParser.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o FileParser.o clustalW/fileInput/FileParser.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o FileReader.o clustalW/fileInput/FileReader.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o GDEFileParser.o clustalW/fileInput/GDEFileParser.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o InFileStream.o clustalW/fileInput/InFileStream.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o MSFFileParser.o clustalW/fileInput/MSFFileParser.cpp clustalW/fileInput/MSFFileParser.cpp:34:22: warning: unused parameter 'offendingSeq' [-Wunused-parameter] clustalW/fileInput/MSFFileParser.cpp:246:6: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] clustalW/fileInput/MSFFileParser.cpp:246:6: warning: unused parameter 'secStructMask' [-Wunused-parameter] clustalW/fileInput/MSFFileParser.cpp:246:6: warning: unused parameter 'secStructName' [-Wunused-parameter] clustalW/fileInput/MSFFileParser.cpp:246:6: warning: unused parameter 'length' [-Wunused-parameter] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o PearsonFileParser.o clustalW/fileInput/PearsonFileParser.cpp clustalW/fileInput/PearsonFileParser.cpp:199:14: warning: unused parameter 'offendingSeq' [-Wunused-parameter] clustalW/fileInput/PearsonFileParser.cpp:444:6: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] clustalW/fileInput/PearsonFileParser.cpp:444:6: warning: unused parameter 'secStructMask' [-Wunused-parameter] clustalW/fileInput/PearsonFileParser.cpp:444:6: warning: unused parameter 'secStructName' [-Wunused-parameter] clustalW/fileInput/PearsonFileParser.cpp:444:6: warning: unused parameter 'length' [-Wunused-parameter] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o PIRFileParser.o clustalW/fileInput/PIRFileParser.cpp clustalW/fileInput/PIRFileParser.cpp:292:6: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] clustalW/fileInput/PIRFileParser.cpp:292:6: warning: unused parameter 'secStructMask' [-Wunused-parameter] clustalW/fileInput/PIRFileParser.cpp:292:6: warning: unused parameter 'secStructName' [-Wunused-parameter] clustalW/fileInput/PIRFileParser.cpp:292:6: warning: unused parameter 'length' [-Wunused-parameter] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o RSFFileParser.o clustalW/fileInput/RSFFileParser.cpp clustalW/fileInput/RSFFileParser.cpp:240:6: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ClustalWResources.o clustalW/general/ClustalWResources.cpp clustalW/general/ClustalWResources.cpp: In member function 'std::string clustalw::ClustalWResources::findFile(std::string, clustalw::ClustalWResourcePathType) const': clustalW/general/ClustalWResources.cpp:106:12: warning: array subscript is above array bounds [-Warray-bounds] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o DebugLog.o clustalW/general/DebugLog.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o OutputFile.o clustalW/general/OutputFile.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Stats.o clustalW/general/Stats.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o SymMatrix.o clustalW/general/SymMatrix.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o UserParameters.o clustalW/general/UserParameters.cpp clustalW/general/UserParameters.cpp:33:1: warning: unused parameter 'log' [-Wunused-parameter] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Utility.o clustalW/general/Utility.cpp clustalW/general/Utility.cpp: In member function 'bool clustalw::Utility::lineType(char*, const char*)': clustalW/general/Utility.cpp:251:8: warning: variable 'n' set but not used [-Wunused-but-set-variable] clustalW/general/Utility.cpp: At global scope: clustalW/general/Utility.cpp:519:6: warning: unused parameter 'ptrToLabelObj' [-Wunused-parameter] clustalW/general/Utility.cpp: In member function 'int clustalw::Utility::getInt(const char*, int, int, int)': clustalW/general/Utility.cpp:221:36: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] clustalW/general/Utility.cpp: In member function 'double clustalw::Utility::getReal(const char*, double, double, double)': clustalW/general/Utility.cpp:183:36: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o VectorOutOfRange.o clustalW/general/VectorOutOfRange.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o CommandLineParser.o clustalW/interface/CommandLineParser.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o InteractiveMenu.o clustalW/interface/InteractiveMenu.cpp clustalW/interface/InteractiveMenu.cpp: In member function 'void clustalw::InteractiveMenu::doSystem()': clustalW/interface/InteractiveMenu.cpp:1190:29: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Iteration.o clustalW/multipleAlign/Iteration.cpp clustalW/multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': clustalW/multipleAlign/Iteration.cpp:170:9: warning: variable 'count' set but not used [-Wunused-but-set-variable] clustalW/multipleAlign/Iteration.cpp:231:32: warning: ignoring return value of 'char* tmpnam(char*)', declared with attribute warn_unused_result [-Wunused-result] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o LowScoreSegProfile.o clustalW/multipleAlign/LowScoreSegProfile.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o MSA.o clustalW/multipleAlign/MSA.cpp clustalW/multipleAlign/MSA.cpp: In member function 'int clustalw::MSA::multiSeqAlign(clustalw::Alignment*, clustalw::DistMatrix*, std::vector*, clustalw::AlignmentSteps*, int)': clustalW/multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable] clustalW/multipleAlign/MSA.cpp: At global scope: clustalW/multipleAlign/MSA.cpp:358:5: warning: unused parameter 'phylipName' [-Wunused-parameter] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o MyersMillerProfileAlign.o clustalW/multipleAlign/MyersMillerProfileAlign.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ProfileBase.o clustalW/multipleAlign/ProfileBase.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ProfileStandard.o clustalW/multipleAlign/ProfileStandard.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ProfileWithSub.o clustalW/multipleAlign/ProfileWithSub.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o FastPairwiseAlign.o clustalW/pairwise/FastPairwiseAlign.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o FullPairwiseAlign.o clustalW/pairwise/FullPairwiseAlign.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o SubMatrix.o clustalW/substitutionMatrix/SubMatrix.cpp clustalW/substitutionMatrix/SubMatrix.cpp:1613:6: warning: unused parameter 'alignResidueType' [-Wunused-parameter] clustalW/substitutionMatrix/SubMatrix.cpp:1613:6: warning: unused parameter 'alignType' [-Wunused-parameter] clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForHistogram(int (*)[32])': clustalW/substitutionMatrix/SubMatrix.cpp:1657:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable] clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForLowScoreSeg(int (*)[32])': clustalW/substitutionMatrix/SubMatrix.cpp:1717:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable] clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeries(const char*, clustalw::Matrix&, clustalw::Xref&)': clustalW/substitutionMatrix/SubMatrix.cpp:998:9: warning: 'n' may be used uninitialized in this function [-Wuninitialized] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignmentSteps.o clustalW/tree/AlignmentSteps.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ClusterTree.o clustalW/tree/ClusterTree.cpp clustalW/tree/ClusterTree.cpp: In member function 'void clustalw::ClusterTree::calcPercIdentity(std::ofstream*, clustalw::Alignment*)': clustalW/tree/ClusterTree.cpp:580:9: warning: variable 'rs' set but not used [-Wunused-but-set-variable] clustalW/tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ClusterTreeOutput.o clustalW/tree/ClusterTreeOutput.cpp clustalW/tree/../alignment/../general/SymMatrix.h: In member function 'void clustalw::ClusterTreeOutput::printPhylipTree(clustalw::PhyloTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*, std::vector*)': clustalW/tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] clustalW/tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] clustalW/tree/../alignment/../general/SymMatrix.h: In member function 'void clustalw::ClusterTreeOutput::printNexusTree(clustalw::PhyloTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*, std::vector*)': clustalW/tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] clustalW/tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o NJTree.o clustalW/tree/NJTree.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o RandomGenerator.o clustalW/tree/RandomGenerator.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Tree.o clustalW/tree/Tree.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o TreeInterface.o clustalW/tree/TreeInterface.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o UnRootedClusterTree.o clustalW/tree/UnRootedClusterTree.cpp clustalW/tree/../alignment/../general/SymMatrix.h: In member function 'void clustalw::UnRootedClusterTree::treeFromDistMatrix(clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string&)': clustalW/tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Node.o clustalW/tree/UPGMA/Node.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o RootedClusterTree.o clustalW/tree/UPGMA/RootedClusterTree.cpp clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h: In member function 'std::auto_ptr clustalw::RootedClusterTree::treeFromDistMatrix(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string&)': clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o RootedGuideTree.o clustalW/tree/UPGMA/RootedGuideTree.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o RootedTreeOutput.o clustalW/tree/UPGMA/RootedTreeOutput.cpp clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h: In member function 'void clustalw::RootedTreeOutput::printPhylipTree(clustalw::RootedGuideTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*)': clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h: In member function 'void clustalw::RootedTreeOutput::printNexusTree(clustalw::RootedGuideTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*)': clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o UPGMAAlgorithm.o clustalW/tree/UPGMA/UPGMAAlgorithm.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. AlignmentFormatOptions.h -o moc_AlignmentFormatOptions.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_AlignmentFormatOptions.o moc_AlignmentFormatOptions.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. AlignmentParameters.h -o moc_AlignmentParameters.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_AlignmentParameters.o moc_AlignmentParameters.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. AlignmentViewerWidget.h -o moc_AlignmentViewerWidget.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_AlignmentViewerWidget.o moc_AlignmentViewerWidget.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. AlignmentWidget.h -o moc_AlignmentWidget.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_AlignmentWidget.o moc_AlignmentWidget.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. AlignOutputFileNames.h -o moc_AlignOutputFileNames.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_AlignOutputFileNames.o moc_AlignOutputFileNames.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. BootstrapTreeDialog.h -o moc_BootstrapTreeDialog.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_BootstrapTreeDialog.o moc_BootstrapTreeDialog.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. ColorFileXmlParser.h -o moc_ColorFileXmlParser.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_ColorFileXmlParser.o moc_ColorFileXmlParser.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. ColumnScoreParams.h -o moc_ColumnScoreParams.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_ColumnScoreParams.o moc_ColumnScoreParams.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. FileDialog.h -o moc_FileDialog.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_FileDialog.o moc_FileDialog.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. HelpDisplayWidget.h -o moc_HelpDisplayWidget.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_HelpDisplayWidget.o moc_HelpDisplayWidget.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. HistogramWidget.h -o moc_HistogramWidget.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_HistogramWidget.o moc_HistogramWidget.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. LowScoringSegParams.h -o moc_LowScoringSegParams.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_LowScoringSegParams.o moc_LowScoringSegParams.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. mainwindow.h -o moc_mainwindow.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_mainwindow.o moc_mainwindow.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. PairwiseParams.h -o moc_PairwiseParams.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_PairwiseParams.o moc_PairwiseParams.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. ProteinGapParameters.h -o moc_ProteinGapParameters.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_ProteinGapParameters.o moc_ProteinGapParameters.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. PSPrinter.h -o moc_PSPrinter.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_PSPrinter.o moc_PSPrinter.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. SaveSeqFile.h -o moc_SaveSeqFile.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_SaveSeqFile.o moc_SaveSeqFile.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. SearchForString.h -o moc_SearchForString.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_SearchForString.o moc_SearchForString.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. SecStructOptions.h -o moc_SecStructOptions.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_SecStructOptions.o moc_SecStructOptions.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. SeqNameWidget.h -o moc_SeqNameWidget.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_SeqNameWidget.o moc_SeqNameWidget.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. TreeFormatOptions.h -o moc_TreeFormatOptions.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_TreeFormatOptions.o moc_TreeFormatOptions.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. TreeOutputFileNames.h -o moc_TreeOutputFileNames.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_TreeOutputFileNames.o moc_TreeOutputFileNames.cpp /usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. WritePostscriptFile.h -o moc_WritePostscriptFile.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_WritePostscriptFile.o moc_WritePostscriptFile.cpp g++ -m64 -Wl,-O1 -o clustalx AlignmentFormatOptions.o AlignmentParameters.o AlignmentViewerWidget.o AlignmentWidget.o AlignOutputFileNames.o BootstrapTreeDialog.o ColorFileXmlParser.o ColorParameters.o ColumnScoreParams.o FileDialog.o HardCodedColorScheme.o HelpDisplayWidget.o HistogramWidget.o KeyController.o LowScoringSegParams.o main.o mainwindow.o PairwiseParams.o PostscriptFileParams.o ProteinGapParameters.o PSPrinter.o QTUtility.o Resources.o SaveSeqFile.o SearchForString.o SecStructOptions.o SeqNameWidget.o TreeFormatOptions.o TreeOutputFileNames.o WritePostscriptFile.o Clustal.o Help.o Alignment.o AlignmentOutput.o ObjectiveScore.o Sequence.o ClustalFileParser.o EMBLFileParser.o FileParser.o FileReader.o GDEFileParser.o InFileStream.o MSFFileParser.o PearsonFileParser.o PIRFileParser.o RSFFileParser.o ClustalWResources.o DebugLog.o OutputFile.o Stats.o SymMatrix.o UserParameters.o Utility.o VectorOutOfRange.o CommandLineParser.o InteractiveMenu.o Iteration.o LowScoreSegProfile.o MSA.o MyersMillerProfileAlign.o ProfileBase.o ProfileStandard.o ProfileWithSub.o FastPairwiseAlign.o FullPairwiseAlign.o SubMatrix.o AlignmentSteps.o ClusterTree.o ClusterTreeOutput.o NJTree.o RandomGenerator.o Tree.o TreeInterface.o UnRootedClusterTree.o Node.o RootedClusterTree.o RootedGuideTree.o RootedTreeOutput.o UPGMAAlgorithm.o moc_AlignmentFormatOptions.o moc_AlignmentParameters.o moc_AlignmentViewerWidget.o moc_AlignmentWidget.o moc_AlignOutputFileNames.o moc_BootstrapTreeDialog.o moc_ColorFileXmlParser.o moc_ColumnScoreParams.o moc_FileDialog.o moc_HelpDisplayWidget.o moc_HistogramWidget.o moc_LowScoringSegParams.o moc_mainwindow.o moc_PairwiseParams.o moc_ProteinGapParameters.o moc_PSPrinter.o moc_SaveSeqFile.o moc_SearchForString.o moc_SecStructOptions.o moc_SeqNameWidget.o moc_TreeFormatOptions.o moc_TreeOutputFileNames.o moc_WritePostscriptFile.o -L/usr/lib/x86_64-linux-gnu -lQtXml -lQtGui -lQtCore -lpthread make[1]: Leaving directory `/build/buildd/clustalx-2.1+lgpl' dh_auto_test /usr/bin/fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_installdirs -a dh_auto_install -a dh_install -a dh_installdocs -a debian/rules override_dh_installchangelogs make[1]: Entering directory `/build/buildd/clustalx-2.1+lgpl' dh_installchangelogs debian/CHANGELOG.upstream make[1]: Leaving directory `/build/buildd/clustalx-2.1+lgpl' dh_installexamples -a dh_installman -a dh_installcatalogs -a dh_installcron -a dh_installdebconf -a dh_installemacsen -a dh_installifupdown -a dh_installinfo -a dh_installinit -a dh_installmenu -a dh_installmime -a dh_installmodules -a dh_installlogcheck -a dh_installlogrotate -a dh_installpam -a dh_installppp -a dh_installudev -a dh_installwm -a dh_installxfonts -a dh_installgsettings -a dh_bugfiles -a dh_ucf -a dh_lintian -a dh_gconf -a dh_icons -a dh_perl -a dh_usrlocal -a dh_link -a dh_compress -a dh_fixperms -a dh_strip -a dh_strip debug symbol extraction: all non-arch-all packages for this build platform amd64: clustalx dh_strip debug symbol extraction: packages to act on: clustalx dh_strip debug symbol extraction: ignored packages: clustalx is already stripped, ignoring dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 106 pkgstriptranslations: processing clustalx (in debian/clustalx); do_strip: , oemstrip: debian/clustalx/usr/share/applications/clustalx.desktop: does not have gettext domain, not stripping pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/clustalx/DEBIAN/control, package clustalx, directory debian/clustalx .. removing usr/share/doc/clustalx/changelog.gz pkgstripfiles: Truncating usr/share/doc/clustalx/changelog.Debian.gz to topmost ten records dpkg-deb: warning: 'debian/clustalx/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `clustalx' in `../clustalx_2.1+lgpl-2_amd64.deb'. dpkg-genchanges -B -mUbuntu/amd64 Build Daemon >../clustalx_2.1+lgpl-2_amd64.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 clustalx-2.1+lgpl dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20111127-1758 chroot-autobuild/build/buildd/clustalx_2.1+lgpl-2_amd64.deb: new debian package, version 2.0. size 563466 bytes: control archive= 1671 bytes. 1586 bytes, 28 lines control 862 bytes, 13 lines md5sums 551 bytes, 17 lines * postinst #!/bin/sh 467 bytes, 13 lines * postrm #!/bin/sh Package: clustalx Version: 2.1+lgpl-2 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1373 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libqt4-xml (>= 4:4.5.3), libqtcore4 (>= 4:4.6.1), libqtgui4 (>= 4:4.5.3), libstdc++6 (>= 4.6) Suggests: clustalw, texshade | texlive-latex-extra, boxshade Section: science Priority: optional Homepage: http://www.clustal.org/clustal2/ Description: Multiple alignment of nucleic acid and protein sequences (graphical interface) This package offers a GUI interface for the Clustal multiple sequence alignment program. It provides an integrated environment for performing multiple sequence- and profile-alignments to analyse the results. The sequence alignment is displayed in a window on the screen. A versatile coloring scheme has been incorporated to highlight conserved features in the alignment. For professional presentations, one should use the texshade LaTeX package or boxshade. . The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment. You can cut-and-paste sequences to change the order of the alignment; you can select a subset of sequences to be aligned; you can select a sub-range of the alignment to be realigned and inserted back into the original alignment. . An alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. chroot-autobuild/build/buildd/clustalx_2.1+lgpl-2_amd64.deb: drwxr-xr-x root/root 0 2011-11-27 17:57 ./ drwxr-xr-x root/root 0 2011-11-27 17:57 ./usr/ drwxr-xr-x root/root 0 2011-11-27 17:57 ./usr/share/ drwxr-xr-x root/root 0 2011-11-27 17:57 ./usr/share/doc/ drwxr-xr-x root/root 0 2011-11-27 17:58 ./usr/share/doc/clustalx/ -rw-r--r-- root/root 1794 2011-11-16 05:48 ./usr/share/doc/clustalx/copyright -rw-r--r-- root/root 2617 2011-11-27 17:58 ./usr/share/doc/clustalx/changelog.Debian.gz -rw-r--r-- root/root 410 2011-11-16 05:48 ./usr/share/doc/clustalx/README.Debian drwxr-xr-x root/root 0 2011-11-27 17:57 ./usr/share/menu/ -rw-r--r-- root/root 163 2011-11-16 05:48 ./usr/share/menu/clustalx drwxr-xr-x root/root 0 2011-11-27 17:57 ./usr/share/man/ drwxr-xr-x root/root 0 2011-11-27 17:57 ./usr/share/man/man1/ -rw-r--r-- root/root 797 2011-11-27 17:57 ./usr/share/man/man1/clustalx.1.gz drwxr-xr-x root/root 0 2011-11-27 17:57 ./usr/share/clustalx/ -rw-r--r-- root/root 69428 2010-11-17 10:12 ./usr/share/clustalx/clustalx.hlp -rw-r--r-- root/root 1276 2010-11-17 10:12 ./usr/share/clustalx/colprint.xml -rw-r--r-- root/root 847 2010-11-17 10:12 ./usr/share/clustalx/coldna.xml -rw-r--r-- root/root 5047 2010-11-17 10:12 ./usr/share/clustalx/colprot.xml drwxr-xr-x root/root 0 2011-11-27 17:57 ./usr/share/applications/ -rw-r--r-- root/root 873 2011-11-16 05:48 ./usr/share/applications/clustalx.desktop drwxr-xr-x root/root 0 2011-11-27 17:57 ./usr/share/mime/ drwxr-xr-x root/root 0 2011-11-27 17:57 ./usr/share/mime/packages/ -rw-r--r-- root/root 513 2011-11-16 05:48 ./usr/share/mime/packages/clustalx.xml drwxr-xr-x root/root 0 2011-11-27 17:57 ./usr/bin/ -rwxr-xr-x root/root 1246168 2011-11-27 17:57 ./usr/bin/clustalx drwxr-xr-x root/root 0 2011-11-27 17:57 ./usr/lib/ drwxr-xr-x root/root 0 2011-11-27 17:57 ./usr/lib/mime/ drwxr-xr-x root/root 0 2011-11-27 17:57 ./usr/lib/mime/packages/ -rw-r--r-- root/root 114 2011-11-16 05:48 ./usr/lib/mime/packages/clustalx clustalx_2.1+lgpl-2_amd64.changes: Format: 1.8 Date: Wed, 16 Nov 2011 14:37:03 +0900 Source: clustalx Binary: clustalx Architecture: amd64 Version: 2.1+lgpl-2 Distribution: precise Urgency: low Maintainer: Ubuntu/amd64 Build Daemon Changed-By: Charles Plessy Description: clustalx - Multiple alignment of nucleic acid and protein sequences (graphic Closes: 648812 Changes: clustalx (2.1+lgpl-2) unstable; urgency=low . [8b9662e] Update providing upgrade path to backports (Closes: #648812). [727f540] Corrected and normalised copyright file with config-edit. [fa455a0] Conforms to Policy version 3.9.2 (no changes needed). [9cd039b] Updated Homepage. [a36daf1] Rely on dpkg-dev for patching and removed build-dependancy on quilt. [51bde59] Support build-arch and build-indep targets through dh. [c3b9f16] Signal and configure the use of git-buildpackage. Checksums-Sha1: f022e3176a33c579aaec0f7e229292d98173414b 563466 clustalx_2.1+lgpl-2_amd64.deb Checksums-Sha256: 1d61d167b319d0e299b6661b69617d0d3f15ee6935402a54ce68af7c7d82488d 563466 clustalx_2.1+lgpl-2_amd64.deb Files: 423c5915659d4f72e81a7cea7a264ef0 563466 science optional clustalx_2.1+lgpl-2_amd64.deb ****************************************************************************** Built successfully Purging chroot-autobuild/build/buildd/clustalx-2.1+lgpl ------------------------------------------------------------------------------ /usr/bin/sudo dpkg --purge groff-base libx11-data libxdmcp-dev fontconfig-config ttf-dejavu-core gettext file libqt4-sql libqt4-help fontconfig libqtgui4 x11-common libqt4-qt3support libx11-dev libcroco3 libxi6 libfreetype6 libgettextpo0 libxcb1 x11proto-input-dev html2text libqtcore4 debhelper libfontconfig1 libpthread-stubs0 libqt4-xmlpatterns libmagic1 libqt4-script libtiff4 libexpat1 qt4-qmake bsdmainutils libxau6 libx11-6 xtrans-dev xorg-sgml-doctools x11proto-core-dev libqt4-dbus libxcb1-dev libqt4-dev libxt6 libmng1 libxdmcp6 qt4-linguist-tools po-debconf qdbus libqt4-xml libxml2 libjpeg8 liblcms1 man-db libice6 x11proto-kb-dev intltool-debian libqt4-svg libxrender1 libpthread-stubs0-dev libxau-dev ucf libqt4-declarative gettext-base libqt4-network libqt4-designer libqt4-scripttools libunistring0 libqt4-test libsm6 libpipeline1 libxext6 libaudio2 (Reading database ... 19662 files and directories currently installed.) 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Purging configuration files for libxt6 ... Removing qdbus ... Removing libqt4-xml ... Purging configuration files for libqt4-xml ... Removing libsm6 ... Purging configuration files for libsm6 ... Removing fontconfig-config ... Purging configuration files for fontconfig-config ... Removing ttf-dejavu-core ... Removing libfreetype6 ... Purging configuration files for libfreetype6 ... Removing libqtcore4 ... Purging configuration files for libqtcore4 ... Removing libx11-6 ... Purging configuration files for libx11-6 ... Removing libice6 ... Purging configuration files for libice6 ... Removing ucf ... Purging configuration files for ucf ... Removing libx11-data ... Removing x11-common ... invoke-rc.d: policy-rc.d denied execution of stop. Purging configuration files for x11-common ... Removing libxcb1 ... Purging configuration files for libxcb1 ... Removing libxau6 ... Purging configuration files for libxau6 ... Removing libxdmcp6 ... Purging configuration files for libxdmcp6 ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place ****************************************************************************** Finished at 20111127-1758 Build needed 00:01:47, 9556k 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', '60a9e9a2b60f7bda7323f2353c16429ad2819a0c'] Scanning for processes to kill in build /home/buildd/build-60a9e9a2b60f7bda7323f2353c16429ad2819a0c/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', '60a9e9a2b60f7bda7323f2353c16429ad2819a0c'] Unmounting chroot for build 60a9e9a2b60f7bda7323f2353c16429ad2819a0c... none /home/buildd/build-60a9e9a2b60f7bda7323f2353c16429ad2819a0c/chroot-autobuild/proc proc rw,relatime 0 0 none /home/buildd/build-60a9e9a2b60f7bda7323f2353c16429ad2819a0c/chroot-autobuild/dev/pts devpts rw,relatime 0 0 none /home/buildd/build-60a9e9a2b60f7bda7323f2353c16429ad2819a0c/chroot-autobuild/sys sysfs rw,relatime 0 0 none /home/buildd/build-60a9e9a2b60f7bda7323f2353c16429ad2819a0c/chroot-autobuild/dev/shm tmpfs rw,relatime 0 0 RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', '60a9e9a2b60f7bda7323f2353c16429ad2819a0c'] Removing build 60a9e9a2b60f7bda7323f2353c16429ad2819a0c