RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: 2.6.24-32-xen #1 SMP Thu Jul 12 14:30:40 UTC 2012 x86_64 Buildd toolchain package versions: launchpad-buildd_113~0.IS.08.04 python-lpbuildd_113~0.IS.08.04 bzr-builder_0.7.2+bzr156-0ubuntu1~1.IS.8.04 bzr_2.4.0-0ubuntu2~11.IS.8.04. Syncing the system clock with the buildd NTP service... 20 Aug 21:00:11 ntpdate[3376]: step time server 10.211.37.1 offset -16011.603513 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', '7e40fb86ebd52dedeb3f5dedec4d6ea8404a8d23', '/home/buildd/filecache-default/8eacd1245734d394a672d9a8221787a881f94c87'] Uncompressing the tarball... Unpacking chroot for build 7e40fb86ebd52dedeb3f5dedec4d6ea8404a8d23 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', '7e40fb86ebd52dedeb3f5dedec4d6ea8404a8d23'] Mounting chroot for build 7e40fb86ebd52dedeb3f5dedec4d6ea8404a8d23 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', '7e40fb86ebd52dedeb3f5dedec4d6ea8404a8d23', 'deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main', 'deb http://ftpmaster.internal/ubuntu precise main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu precise-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu precise-updates main restricted universe multiverse'] Overriding sources.list in build-7e40fb86ebd52dedeb3f5dedec4d6ea8404a8d23 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', '7e40fb86ebd52dedeb3f5dedec4d6ea8404a8d23', 'i386'] Updating debian chroot for build 7e40fb86ebd52dedeb3f5dedec4d6ea8404a8d23 Ign http://ftpmaster.internal precise InRelease Ign http://ftpmaster.internal precise-security InRelease Ign http://ftpmaster.internal precise-updates InRelease Get:1 http://ftpmaster.internal precise Release.gpg [198 B] Get:2 http://ftpmaster.internal precise-security Release.gpg [198 B] Ign http://ppa.launchpad.net precise InRelease Get:3 http://ftpmaster.internal precise-updates Release.gpg [198 B] Get:4 http://ftpmaster.internal precise Release [49.6 kB] Get:5 http://ppa.launchpad.net precise Release.gpg [316 B] Get:6 http://ppa.launchpad.net precise Release [11.9 kB] Get:7 http://ftpmaster.internal precise-security Release [49.6 kB] Ign http://ppa.launchpad.net precise Release Get:8 http://ftpmaster.internal precise-updates Release [49.6 kB] Get:9 http://ppa.launchpad.net precise/main i386 Packages [8704 B] Ign http://ppa.launchpad.net precise/main TranslationIndex Get:10 http://ftpmaster.internal precise/main i386 Packages [1274 kB] Ign http://ppa.launchpad.net precise/main Translation-en Get:11 http://ftpmaster.internal precise/restricted i386 Packages [8431 B] Get:12 http://ftpmaster.internal precise/universe i386 Packages [4796 kB] Get:13 http://ftpmaster.internal precise/multiverse i386 Packages [121 kB] Get:14 http://ftpmaster.internal precise/main TranslationIndex [3706 B] Get:15 http://ftpmaster.internal precise/multiverse TranslationIndex [2676 B] Get:16 http://ftpmaster.internal precise/restricted TranslationIndex [2596 B] Get:17 http://ftpmaster.internal precise/universe TranslationIndex [2922 B] Get:18 http://ftpmaster.internal precise-security/main i386 Packages [160 kB] Get:19 http://ftpmaster.internal precise-security/restricted i386 Packages [3968 B] Get:20 http://ftpmaster.internal precise-security/universe i386 Packages [39.6 kB] Get:21 http://ftpmaster.internal precise-security/multiverse i386 Packages [2369 B] Get:22 http://ftpmaster.internal precise-security/main TranslationIndex [73 B] Get:23 http://ftpmaster.internal precise-security/multiverse TranslationIndex [71 B] Get:24 http://ftpmaster.internal precise-security/restricted TranslationIndex [71 B] Get:25 http://ftpmaster.internal precise-security/universe TranslationIndex [73 B] Get:26 http://ftpmaster.internal precise-updates/main i386 Packages [376 kB] Get:27 http://ftpmaster.internal precise-updates/restricted i386 Packages [6732 B] Get:28 http://ftpmaster.internal precise-updates/universe i386 Packages [123 kB] Get:29 http://ftpmaster.internal precise-updates/multiverse i386 Packages [9672 B] Get:30 http://ftpmaster.internal precise-updates/main TranslationIndex [3564 B] Get:31 http://ftpmaster.internal precise-updates/multiverse TranslationIndex [2605 B] Get:32 http://ftpmaster.internal precise-updates/restricted TranslationIndex [2461 B] Get:33 http://ftpmaster.internal precise-updates/universe TranslationIndex [2850 B] Get:34 http://ftpmaster.internal precise/main Translation-en [726 kB] Get:35 http://ftpmaster.internal precise/multiverse Translation-en [93.4 kB] Get:36 http://ftpmaster.internal precise/restricted Translation-en [2395 B] Get:37 http://ftpmaster.internal precise/universe Translation-en [3341 kB] Get:38 http://ftpmaster.internal precise-security/main Translation-en [74.2 kB] Get:39 http://ftpmaster.internal precise-security/multiverse Translation-en [995 B] Get:40 http://ftpmaster.internal precise-security/restricted Translation-en [978 B] Get:41 http://ftpmaster.internal precise-security/universe Translation-en [24.5 kB] Get:42 http://ftpmaster.internal precise-updates/main Translation-en [180 kB] Get:43 http://ftpmaster.internal precise-updates/multiverse Translation-en [5414 B] Get:44 http://ftpmaster.internal precise-updates/restricted Translation-en [1484 B] Get:45 http://ftpmaster.internal precise-updates/universe Translation-en [73.5 kB] Fetched 11.6 MB in 18s (636 kB/s) Reading package lists... W: GPG error: http://ppa.launchpad.net precise Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 759A8E0E5BA15160 Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: apt apt-transport-https base-files initscripts libapt-pkg4.12 libgcrypt11 libglib2.0-0 libgnutls26 libgssapi-krb5-2 libk5crypto3 libkrb5-3 libkrb5support0 libldap-2.4-2 libsasl2-2 libsqlite3-0 libssl1.0.0 libtasn1-3 libudev0 linux-libc-dev openssl perl perl-base perl-modules python2.7-minimal sysv-rc sysvinit-utils tzdata udev upstart 29 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 19.2 MB of archives. After this operation, 39.9 kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! base-files perl perl-base perl-modules libapt-pkg4.12 apt libssl1.0.0 libsqlite3-0 libglib2.0-0 libudev0 libgcrypt11 libtasn1-3 libgnutls26 libk5crypto3 libgssapi-krb5-2 libkrb5-3 libkrb5support0 libsasl2-2 libldap-2.4-2 python2.7-minimal tzdata sysvinit-utils sysv-rc initscripts upstart udev apt-transport-https linux-libc-dev openssl Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ precise-updates/main base-files i386 6.5ubuntu6.2 [65.1 kB] Get:2 http://ftpmaster.internal/ubuntu/ precise-updates/main perl i386 5.14.2-6ubuntu2.1 [3685 kB] Get:3 http://ftpmaster.internal/ubuntu/ precise-updates/main perl-base i386 5.14.2-6ubuntu2.1 [1472 kB] Get:4 http://ftpmaster.internal/ubuntu/ precise-updates/main perl-modules all 5.14.2-6ubuntu2.1 [3396 kB] Get:5 http://ftpmaster.internal/ubuntu/ precise-security/main libapt-pkg4.12 i386 0.8.16~exp12ubuntu10.2 [940 kB] Get:6 http://ftpmaster.internal/ubuntu/ precise-security/main apt i386 0.8.16~exp12ubuntu10.2 [1102 kB] Get:7 http://ftpmaster.internal/ubuntu/ precise-security/main libssl1.0.0 i386 1.0.1-4ubuntu5.3 [1006 kB] Get:8 http://ftpmaster.internal/ubuntu/ precise-updates/main libsqlite3-0 i386 3.7.9-2ubuntu1.1 [354 kB] Get:9 http://ftpmaster.internal/ubuntu/ precise-updates/main libglib2.0-0 i386 2.32.3-0ubuntu1 [1187 kB] Get:10 http://ftpmaster.internal/ubuntu/ precise-updates/main libudev0 i386 175-0ubuntu9.1 [33.6 kB] Get:11 http://ftpmaster.internal/ubuntu/ precise-updates/main libgcrypt11 i386 1.5.0-3ubuntu0.1 [281 kB] Get:12 http://ftpmaster.internal/ubuntu/ precise-security/main libtasn1-3 i386 2.10-1ubuntu1.1 [43.8 kB] Get:13 http://ftpmaster.internal/ubuntu/ precise-updates/main libgnutls26 i386 2.12.14-5ubuntu3.1 [448 kB] Get:14 http://ftpmaster.internal/ubuntu/ precise-security/main libk5crypto3 i386 1.10+dfsg~beta1-2ubuntu0.3 [77.4 kB] Get:15 http://ftpmaster.internal/ubuntu/ precise-security/main libgssapi-krb5-2 i386 1.10+dfsg~beta1-2ubuntu0.3 [120 kB] Get:16 http://ftpmaster.internal/ubuntu/ precise-security/main libkrb5-3 i386 1.10+dfsg~beta1-2ubuntu0.3 [366 kB] Get:17 http://ftpmaster.internal/ubuntu/ precise-security/main libkrb5support0 i386 1.10+dfsg~beta1-2ubuntu0.3 [23.9 kB] Get:18 http://ftpmaster.internal/ubuntu/ precise-updates/main libsasl2-2 i386 2.1.25.dfsg1-3ubuntu0.1 [69.0 kB] Get:19 http://ftpmaster.internal/ubuntu/ precise-updates/main libldap-2.4-2 i386 2.4.28-1.1ubuntu4.1 [186 kB] Get:20 http://ftpmaster.internal/ubuntu/ precise-updates/main python2.7-minimal i386 2.7.3-0ubuntu3.1 [1693 kB] Get:21 http://ftpmaster.internal/ubuntu/ precise-updates/main tzdata all 2012e-0ubuntu0.12.04 [438 kB] Get:22 http://ftpmaster.internal/ubuntu/ precise-updates/main sysvinit-utils i386 2.88dsf-13.10ubuntu11.1 [58.4 kB] Get:23 http://ftpmaster.internal/ubuntu/ precise-updates/main sysv-rc all 2.88dsf-13.10ubuntu11.1 [44.6 kB] Get:24 http://ftpmaster.internal/ubuntu/ precise-updates/main initscripts i386 2.88dsf-13.10ubuntu11.1 [28.1 kB] Get:25 http://ftpmaster.internal/ubuntu/ precise-updates/main upstart i386 1.5-0ubuntu7 [313 kB] Get:26 http://ftpmaster.internal/ubuntu/ precise-updates/main udev i386 175-0ubuntu9.1 [349 kB] Get:27 http://ftpmaster.internal/ubuntu/ precise-security/main apt-transport-https i386 0.8.16~exp12ubuntu10.2 [16.3 kB] Get:28 http://ftpmaster.internal/ubuntu/ precise-security/main linux-libc-dev i386 3.2.0-29.46 [871 kB] Get:29 http://ftpmaster.internal/ubuntu/ precise-security/main openssl i386 1.0.1-4ubuntu5.3 [520 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.2 MB in 22s (867 kB/s) (Reading database ... 12281 files and directories currently installed.) Preparing to replace base-files 6.5ubuntu6 (using .../base-files_6.5ubuntu6.2_i386.deb) ... Unpacking replacement base-files ... Setting up base-files (6.5ubuntu6.2) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... (Reading database ... 12281 files and directories currently installed.) Preparing to replace perl 5.14.2-6ubuntu2 (using .../perl_5.14.2-6ubuntu2.1_i386.deb) ... Unpacking replacement perl ... Preparing to replace perl-base 5.14.2-6ubuntu2 (using .../perl-base_5.14.2-6ubuntu2.1_i386.deb) ... Unpacking replacement perl-base ... Setting up perl-base (5.14.2-6ubuntu2.1) ... (Reading database ... 12281 files and directories currently installed.) Preparing to replace perl-modules 5.14.2-6ubuntu2 (using .../perl-modules_5.14.2-6ubuntu2.1_all.deb) ... Unpacking replacement perl-modules ... Preparing to replace libapt-pkg4.12 0.8.16~exp12ubuntu10 (using .../libapt-pkg4.12_0.8.16~exp12ubuntu10.2_i386.deb) ... Unpacking replacement libapt-pkg4.12 ... Setting up libapt-pkg4.12 (0.8.16~exp12ubuntu10.2) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12281 files and directories currently installed.) Preparing to replace apt 0.8.16~exp12ubuntu10 (using .../apt_0.8.16~exp12ubuntu10.2_i386.deb) ... Unpacking replacement apt ... Setting up apt (0.8.16~exp12ubuntu10.2) ... 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 ... 12281 files and directories currently installed.) Preparing to replace libssl1.0.0 1.0.1-4ubuntu3 (using .../libssl1.0.0_1.0.1-4ubuntu5.3_i386.deb) ... Unpacking replacement libssl1.0.0 ... Setting up libssl1.0.0 (1.0.1-4ubuntu5.3) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12281 files and directories currently installed.) Preparing to replace libsqlite3-0 3.7.9-2ubuntu1 (using .../libsqlite3-0_3.7.9-2ubuntu1.1_i386.deb) ... Unpacking replacement libsqlite3-0 ... Preparing to replace libglib2.0-0 2.32.1-0ubuntu2 (using .../libglib2.0-0_2.32.3-0ubuntu1_i386.deb) ... Unpacking replacement libglib2.0-0 ... Preparing to replace libudev0 175-0ubuntu9 (using .../libudev0_175-0ubuntu9.1_i386.deb) ... Unpacking replacement libudev0 ... Preparing to replace libgcrypt11 1.5.0-3 (using .../libgcrypt11_1.5.0-3ubuntu0.1_i386.deb) ... Unpacking replacement libgcrypt11 ... Preparing to replace libtasn1-3 2.10-1ubuntu1 (using .../libtasn1-3_2.10-1ubuntu1.1_i386.deb) ... Unpacking replacement libtasn1-3 ... Preparing to replace libgnutls26 2.12.14-5ubuntu3 (using .../libgnutls26_2.12.14-5ubuntu3.1_i386.deb) ... Unpacking replacement libgnutls26 ... Preparing to replace libk5crypto3 1.10+dfsg~beta1-2 (using .../libk5crypto3_1.10+dfsg~beta1-2ubuntu0.3_i386.deb) ... Unpacking replacement libk5crypto3 ... Preparing to replace libgssapi-krb5-2 1.10+dfsg~beta1-2 (using .../libgssapi-krb5-2_1.10+dfsg~beta1-2ubuntu0.3_i386.deb) ... Unpacking replacement libgssapi-krb5-2 ... Preparing to replace libkrb5-3 1.10+dfsg~beta1-2 (using .../libkrb5-3_1.10+dfsg~beta1-2ubuntu0.3_i386.deb) ... Unpacking replacement libkrb5-3 ... Preparing to replace libkrb5support0 1.10+dfsg~beta1-2 (using .../libkrb5support0_1.10+dfsg~beta1-2ubuntu0.3_i386.deb) ... Unpacking replacement libkrb5support0 ... Preparing to replace libsasl2-2 2.1.25.dfsg1-3 (using .../libsasl2-2_2.1.25.dfsg1-3ubuntu0.1_i386.deb) ... Unpacking replacement libsasl2-2 ... Preparing to replace libldap-2.4-2 2.4.28-1.1ubuntu4 (using .../libldap-2.4-2_2.4.28-1.1ubuntu4.1_i386.deb) ... Unpacking replacement libldap-2.4-2 ... Preparing to replace python2.7-minimal 2.7.3-0ubuntu3 (using .../python2.7-minimal_2.7.3-0ubuntu3.1_i386.deb) ... Unpacking replacement python2.7-minimal ... Setting up python2.7-minimal (2.7.3-0ubuntu3.1) ... (Reading database ... 12281 files and directories currently installed.) Preparing to replace tzdata 2012b-1 (using .../tzdata_2012e-0ubuntu0.12.04_all.deb) ... Unpacking replacement tzdata ... Setting up tzdata (2012e-0ubuntu0.12.04) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Aug 20 16:36:09 UTC 2012. Universal Time is now: Mon Aug 20 16:36:09 UTC 2012. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 12281 files and directories currently installed.) Preparing to replace sysvinit-utils 2.88dsf-13.10ubuntu11 (using .../sysvinit-utils_2.88dsf-13.10ubuntu11.1_i386.deb) ... Unpacking replacement sysvinit-utils ... Preparing to replace sysv-rc 2.88dsf-13.10ubuntu11 (using .../sysv-rc_2.88dsf-13.10ubuntu11.1_all.deb) ... Unpacking replacement sysv-rc ... Preparing to replace initscripts 2.88dsf-13.10ubuntu11 (using .../initscripts_2.88dsf-13.10ubuntu11.1_i386.deb) ... Unpacking replacement initscripts ... Preparing to replace upstart 1.5-0ubuntu5 (using .../upstart_1.5-0ubuntu7_i386.deb) ... Unpacking replacement upstart ... Preparing to replace udev 175-0ubuntu9 (using .../udev_175-0ubuntu9.1_i386.deb) ... Adding 'diversion of /sbin/udevadm to /sbin/udevadm.upgrade by fake-udev' Unpacking replacement udev ... Preparing to replace apt-transport-https 0.8.16~exp12ubuntu10 (using .../apt-transport-https_0.8.16~exp12ubuntu10.2_i386.deb) ... Unpacking replacement apt-transport-https ... Preparing to replace linux-libc-dev 3.2.0-23.36 (using .../linux-libc-dev_3.2.0-29.46_i386.deb) ... Unpacking replacement linux-libc-dev ... Preparing to replace openssl 1.0.1-4ubuntu3 (using .../openssl_1.0.1-4ubuntu5.3_i386.deb) ... Unpacking replacement openssl ... Setting up libsqlite3-0 (3.7.9-2ubuntu1.1) ... Setting up libglib2.0-0 (2.32.3-0ubuntu1) ... No schema files found: doing nothing. Setting up libudev0 (175-0ubuntu9.1) ... Setting up libgcrypt11 (1.5.0-3ubuntu0.1) ... Setting up libtasn1-3 (2.10-1ubuntu1.1) ... Setting up libgnutls26 (2.12.14-5ubuntu3.1) ... Setting up libkrb5support0 (1.10+dfsg~beta1-2ubuntu0.3) ... Setting up libk5crypto3 (1.10+dfsg~beta1-2ubuntu0.3) ... Setting up libkrb5-3 (1.10+dfsg~beta1-2ubuntu0.3) ... Setting up libgssapi-krb5-2 (1.10+dfsg~beta1-2ubuntu0.3) ... Setting up libsasl2-2 (2.1.25.dfsg1-3ubuntu0.1) ... Setting up libldap-2.4-2 (2.4.28-1.1ubuntu4.1) ... Setting up sysvinit-utils (2.88dsf-13.10ubuntu11.1) ... Setting up sysv-rc (2.88dsf-13.10ubuntu11.1) ... Setting up apt-transport-https (0.8.16~exp12ubuntu10.2) ... Setting up linux-libc-dev (3.2.0-29.46) ... Setting up openssl (1.0.1-4ubuntu5.3) ... Setting up perl-modules (5.14.2-6ubuntu2.1) ... Setting up upstart (1.5-0ubuntu7) ... Installing new version of config file /etc/logrotate.d/upstart ... Setting up udev (175-0ubuntu9.1) ... 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 perl (5.14.2-6ubuntu2.1) ... Setting up initscripts (2.88dsf-13.10ubuntu11.1) ... 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', '7e40fb86ebd52dedeb3f5dedec4d6ea8404a8d23', 'i386', 'precise', '--nolog', '--batch', '--archive=ubuntu', '--dist=precise', '-A', '--purpose=PPA', '--architecture=i386', '--comp=main', 'mothur_1.27.0+repack-precise2.dsc'] Initiating build 7e40fb86ebd52dedeb3f5dedec4d6ea8404a8d23 with 2 jobs across 2 processor cores. Automatic build of mothur_1.27.0+repack-precise2 on dubnium by sbuild/i386 1.170.5 Build started at 20120820-1636 ****************************************************************************** mothur_1.27.0+repack-precise2.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 8), libreadline-dev, gfortran, quilt, libopenmpi-dev Checking for already installed source dependencies... debhelper: missing libreadline-dev: missing gfortran: missing quilt: missing libopenmpi-dev: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper libreadline-dev gfortran quilt libopenmpi-dev Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils dh-apparmor diffstat file gettext gettext-base gfortran-4.6 groff-base html2text intltool-debian libcroco3 libgettextpo0 libgfortran3 libibverbs-dev libibverbs1 libmagic1 libnuma1 libopenmpi1.3 libpipeline1 libreadline6-dev libtinfo-dev libtorque2 libunistring0 libxml2 man-db openmpi-common po-debconf Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc gfortran-multilib gfortran-doc gfortran-4.6-multilib gfortran-4.6-doc libgfortran3-dbg groff less www-browser libmail-box-perl procmail graphviz default-mta mail-transport-agent Recommended packages: curl wget lynx-cur xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper dh-apparmor diffstat file gettext gettext-base gfortran gfortran-4.6 groff-base html2text intltool-debian libcroco3 libgettextpo0 libgfortran3 libibverbs-dev libibverbs1 libmagic1 libnuma1 libopenmpi-dev libopenmpi1.3 libpipeline1 libreadline-dev libreadline6-dev libtinfo-dev libtorque2 libunistring0 libxml2 man-db openmpi-common po-debconf quilt 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 16.3 MB of archives. After this operation, 50.2 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libxml2 libcroco3 libunistring0 libgettextpo0 libgfortran3 libmagic1 file bsdmainutils gettext-base groff-base man-db html2text gettext intltool-debian po-debconf dh-apparmor debhelper diffstat gfortran-4.6 gfortran libnuma1 libtinfo-dev libreadline6-dev libreadline-dev libtorque2 openmpi-common quilt libibverbs1 libibverbs-dev libopenmpi1.3 libopenmpi-dev Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ precise/main libpipeline1 i386 1.2.1-1 [26.1 kB] Get:2 http://ftpmaster.internal/ubuntu/ precise-security/main libxml2 i386 2.7.8.dfsg-5.1ubuntu4.1 [662 kB] Get:3 http://ftpmaster.internal/ubuntu/ precise/main libcroco3 i386 0.6.5-1 [99.7 kB] Get:4 http://ftpmaster.internal/ubuntu/ precise/main libunistring0 i386 0.9.3-5 [432 kB] Get:5 http://ftpmaster.internal/ubuntu/ precise/main libgettextpo0 i386 0.18.1.1-5ubuntu3 [118 kB] Get:6 http://ftpmaster.internal/ubuntu/ precise/main libgfortran3 i386 4.6.3-1ubuntu5 [355 kB] Get:7 http://ftpmaster.internal/ubuntu/ precise/main libmagic1 i386 5.09-2 [219 kB] Get:8 http://ftpmaster.internal/ubuntu/ precise/main file i386 5.09-2 [19.4 kB] Get:9 http://ftpmaster.internal/ubuntu/ precise/main bsdmainutils i386 8.2.3ubuntu1 [194 kB] Get:10 http://ftpmaster.internal/ubuntu/ precise/main gettext-base i386 0.18.1.1-5ubuntu3 [58.2 kB] Get:11 http://ftpmaster.internal/ubuntu/ precise/main groff-base i386 1.21-7 [1024 kB] Get:12 http://ftpmaster.internal/ubuntu/ precise/main man-db i386 2.6.1-2 [747 kB] Get:13 http://ftpmaster.internal/ubuntu/ precise/main html2text i386 1.3.2a-15 [101 kB] Get:14 http://ftpmaster.internal/ubuntu/ precise/main gettext i386 0.18.1.1-5ubuntu3 [1122 kB] Get:15 http://ftpmaster.internal/ubuntu/ precise/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:16 http://ftpmaster.internal/ubuntu/ precise/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:17 http://ftpmaster.internal/ubuntu/ precise-security/main dh-apparmor all 2.7.102-0ubuntu3.1 [9546 B] Get:18 http://ftpmaster.internal/ubuntu/ precise/main debhelper all 9.20120115ubuntu3 [616 kB] Get:19 http://ftpmaster.internal/ubuntu/ precise/main diffstat i386 1.54-1 [21.3 kB] Get:20 http://ftpmaster.internal/ubuntu/ precise/main gfortran-4.6 i386 4.6.3-1ubuntu5 [5367 kB] Get:21 http://ftpmaster.internal/ubuntu/ precise/main gfortran i386 4:4.6.3-1ubuntu5 [1202 B] Get:22 http://ftpmaster.internal/ubuntu/ precise/main libnuma1 i386 2.0.8~rc3-1 [23.5 kB] Get:23 http://ftpmaster.internal/ubuntu/ precise/main libtinfo-dev i386 5.9-4 [93.5 kB] Get:24 http://ftpmaster.internal/ubuntu/ precise/main libreadline6-dev i386 6.2-8 [249 kB] Get:25 http://ftpmaster.internal/ubuntu/ precise/main libreadline-dev i386 6.2-8 [932 B] Get:26 http://ftpmaster.internal/ubuntu/ precise/universe libtorque2 i386 2.4.16+dfsg-1build1 [87.4 kB] Get:27 http://ftpmaster.internal/ubuntu/ precise/universe openmpi-common all 1.4.3-2.1ubuntu3 [84.4 kB] Get:28 http://ftpmaster.internal/ubuntu/ precise/main quilt all 0.50-2 [287 kB] Get:29 http://ftpmaster.internal/ubuntu/ precise/main libibverbs1 i386 1.1.5-1ubuntu1 [28.5 kB] Get:30 http://ftpmaster.internal/ubuntu/ precise/main libibverbs-dev i386 1.1.5-1ubuntu1 [74.4 kB] Get:31 http://ftpmaster.internal/ubuntu/ precise/universe libopenmpi1.3 i386 1.4.3-2.1ubuntu3 [1290 kB] Get:32 http://ftpmaster.internal/ubuntu/ precise/universe libopenmpi-dev i386 1.4.3-2.1ubuntu3 [2623 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.3 MB in 28s (563 kB/s) Selecting previously unselected package libpipeline1. (Reading database ... 12283 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_i386.deb) ... Selecting previously unselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1ubuntu4.1_i386.deb) ... Selecting previously unselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.5-1_i386.deb) ... Selecting previously unselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-5_i386.deb) ... Selecting previously unselected package libgettextpo0. Unpacking libgettextpo0 (from .../libgettextpo0_0.18.1.1-5ubuntu3_i386.deb) ... Selecting previously unselected package libgfortran3. Unpacking libgfortran3 (from .../libgfortran3_4.6.3-1ubuntu5_i386.deb) ... Selecting previously unselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.09-2_i386.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.09-2_i386.deb) ... 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Unpacking libopenmpi-dev (from .../libopenmpi-dev_1.4.3-2.1ubuntu3_i386.deb) ... Setting up libpipeline1 (1.2.1-1) ... Setting up libxml2 (2.7.8.dfsg-5.1ubuntu4.1) ... Setting up libcroco3 (0.6.5-1) ... Setting up libunistring0 (0.9.3-5) ... Setting up libgettextpo0 (0.18.1.1-5ubuntu3) ... Setting up libgfortran3 (4.6.3-1ubuntu5) ... Setting up libmagic1 (5.09-2) ... Setting up file (5.09-2) ... Setting up bsdmainutils (8.2.3ubuntu1) ... 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 (0.18.1.1-5ubuntu3) ... Setting up groff-base (1.21-7) ... Setting up man-db (2.6.1-2) ... Building database of manual pages ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2ubuntu1) ... Setting up dh-apparmor (2.7.102-0ubuntu3.1) ... Setting up debhelper (9.20120115ubuntu3) ... Setting up diffstat (1.54-1) ... Setting up gfortran-4.6 (4.6.3-1ubuntu5) ... Setting up gfortran (4:4.6.3-1ubuntu5) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode. Setting up libnuma1 (2.0.8~rc3-1) ... Setting up libtinfo-dev (5.9-4) ... Setting up libreadline6-dev (6.2-8) ... Setting up libreadline-dev (6.2-8) ... Setting up libtorque2 (2.4.16+dfsg-1build1) ... Setting up openmpi-common (1.4.3-2.1ubuntu3) ... Setting up quilt (0.50-2) ... Setting up libibverbs1 (1.1.5-1ubuntu1) ... Setting up libibverbs-dev (1.1.5-1ubuntu1) ... Setting up libopenmpi1.3 (1.4.3-2.1ubuntu3) ... Setting up libopenmpi-dev (1.4.3-2.1ubuntu3) ... update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode. Processing triggers for libc-bin ... ldconfig deferred processing now taking place Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.15-0ubuntu10 make_3.81-8.1ubuntu1 dpkg-dev_1.16.1.2ubuntu7 gcc-4.6_4.6.3-1ubuntu5 g++-4.6_4.6.3-1ubuntu5 binutils_2.22-6ubuntu1 libstdc++6-4.6-dev_4.6.3-1ubuntu5 libstdc++6_4.6.3-1ubuntu5 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt gpgv: Signature made Thu Aug 16 14:20:59 2012 UTC using DSA key ID 113960C5 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./mothur_1.27.0+repack-precise2.dsc dpkg-source: info: extracting mothur in mothur-1.27.0+repack dpkg-source: info: unpacking mothur_1.27.0+repack.orig.tar.gz dpkg-source: info: unpacking mothur_1.27.0+repack-precise2.debian.tar.gz dpkg-source: info: applying makefile.patch dpkg-source: info: applying no_lcurses.patch dpkg-source: info: applying drop_sse_option.patch dpkg-source: info: applying catchall_fix.patch dpkg-source: info: applying build_without_tty.patch dpkg-source: info: applying uchime_link_dynamically 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 mothur dpkg-buildpackage: source version 1.27.0+repack-precise2 dpkg-source --before-build mothur-1.27.0+repack dpkg-buildpackage: host architecture i386 /usr/bin/fakeroot debian/rules clean dh clean --with quilt dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory `/build/buildd/mothur-1.27.0+repack' rm -f mothur mothur-mpi *.o mothur.*.logfile make clean make[2]: Entering directory `/build/buildd/mothur-1.27.0+repack' make[2]: Leaving directory `/build/buildd/mothur-1.27.0+repack' ( cd uchime_src && rm -f *.o mk.stdout mk.stderr tmp.stderr ) make[1]: Leaving directory `/build/buildd/mothur-1.27.0+repack' dh_quilt_unpatch Removing patch uchime_link_dynamically Restoring uchime_src/mk Removing patch build_without_tty.patch Restoring uchime_src/mk Removing patch catchall_fix.patch Restoring catchallcommand.cpp Removing patch drop_sse_option.patch Restoring uchime_src/mk Removing patch no_lcurses.patch Restoring makefile Removing patch makefile.patch Restoring makefile No patches applied dh_clean debian/rules build dh build --with quilt dh_testdir dh_quilt_patch Applying patch makefile.patch patching file makefile Applying patch no_lcurses.patch patching file makefile Applying patch drop_sse_option.patch patching file uchime_src/mk Applying patch catchall_fix.patch patching file catchallcommand.cpp Applying patch build_without_tty.patch patching file uchime_src/mk Applying patch uchime_link_dynamically patching file uchime_src/mk Now at patch uchime_link_dynamically dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory `/build/buildd/mothur-1.27.0+repack' if [ 32 -eq 64 ] ; then \ dh_auto_build -- 64BIT_VERSION=yes USEMPI=yes && \ mv mothur mothur-mpi && make clean && \ dh_auto_build -- 64BIT_VERSION=yes USEMPI=no ; \ else \ dh_auto_build -- 64BIT_VERSION=no ; \ fi make[2]: Entering directory `/build/buildd/mothur-1.27.0+repack' gfortran -c *.f g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o ace.o ace.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o aligncommand.o aligncommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o alignment.o alignment.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o alignmentcell.o alignmentcell.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o alignmentdb.o alignmentdb.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o amovacommand.o amovacommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o anosimcommand.o anosimcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o averagelinkage.o averagelinkage.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o bayesian.o bayesian.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o bellerophon.o bellerophon.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o bergerparker.o bergerparker.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o binsequencecommand.o binsequencecommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o blastalign.o blastalign.cpp blastalign.cpp: In member function 'virtual void BlastAlignment::align(std::string, std::string)': blastalign.cpp:63:30: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o blastdb.o blastdb.cpp blastdb.cpp: In member function 'virtual void BlastDB::generateDB()': blastdb.cpp:376:34: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] blastdb.cpp: In member function 'virtual std::vector BlastDB::findClosestMegaBlast(Sequence*, int, int)': blastdb.cpp:305:31: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] blastdb.cpp: In member function 'virtual std::vector BlastDB::findClosestSequences(Sequence*, int)': blastdb.cpp:240:31: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o boneh.o boneh.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o bootstrap.o bootstrap.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o bootstrapsharedcommand.o bootstrapsharedcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o bstick.o bstick.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o calculator.o calculator.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o canberra.o canberra.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o catchallcommand.o catchallcommand.cpp catchallcommand.cpp: In member function 'virtual int CatchAllCommand::execute()': catchallcommand.cpp:303:38: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] catchallcommand.cpp:356:38: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] catchallcommand.cpp:431:36: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o ccode.o ccode.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chao1.o chao1.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimera.o chimera.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimerabellerophoncommand.o chimerabellerophoncommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimeraccodecommand.o chimeraccodecommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimeracheckcommand.o chimeracheckcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimeracheckrdp.o chimeracheckrdp.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimeraperseuscommand.o chimeraperseuscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimerapintailcommand.o chimerapintailcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimerarealigner.o chimerarealigner.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimeraslayer.o chimeraslayer.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimeraslayercommand.o chimeraslayercommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimerauchimecommand.o chimerauchimecommand.cpp chimerauchimecommand.cpp: In member function 'int ChimeraUchimeCommand::driver(std::string, std::string, std::string, std::string, int&)': chimerauchimecommand.cpp:1297:32: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chopseqscommand.o chopseqscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o classify.o classify.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o classifyotucommand.o classifyotucommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o classifyseqscommand.o classifyseqscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o classifytreecommand.o classifytreecommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o clearcut.o clearcut.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o clearcutcommand.o clearcutcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o clearmemorycommand.o clearmemorycommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o cluster.o cluster.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o clusterclassic.o clusterclassic.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o clustercommand.o clustercommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o clusterdoturcommand.o clusterdoturcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o clusterfragmentscommand.o clusterfragmentscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o clustersplitcommand.o clustersplitcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o cmdargs.o cmdargs.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o collect.o collect.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o collectcommand.o collectcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o collectsharedcommand.o collectsharedcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o commandfactory.o commandfactory.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o commandoptionparser.o commandoptionparser.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o completelinkage.o completelinkage.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o consensuscommand.o consensuscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o consensusseqscommand.o consensusseqscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o cooccurrencecommand.o cooccurrencecommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o corraxescommand.o corraxescommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o countgroupscommand.o countgroupscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o countseqscommand.o countseqscommand.cpp countseqscommand.cpp: In member function 'int CountSeqsCommand::processLarge(std::string)': countseqscommand.cpp:322:40: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] countseqscommand.cpp:324:40: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o counttable.o counttable.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o createdatabasecommand.o createdatabasecommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o database.o database.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o decalc.o decalc.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o deconvolutecommand.o deconvolutecommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o degapseqscommand.o degapseqscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o deuniqueseqscommand.o deuniqueseqscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o deuniquetreecommand.o deuniquetreecommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o distancecommand.o distancecommand.cpp distancecommand.cpp: In member function 'virtual int DistanceCommand::execute()': distancecommand.cpp:517:45: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o distancedb.o distancedb.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o distclearcut.o distclearcut.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o dlibshuff.o dlibshuff.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o dmat.o dmat.cpp dmat.cpp: In function 'DMAT* NJ_parse_distance_matrix(NJ_ARGS*)': dmat.cpp:476:36: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o efron.o efron.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o engine.o engine.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o fasta.o fasta.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o fastamap.o fastamap.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o fileoutput.o fileoutput.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o filterseqscommand.o filterseqscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o flowdata.o flowdata.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o formatcolumn.o formatcolumn.cpp formatcolumn.cpp: In member function 'virtual int FormatColumnMatrix::read(NameAssignment*)': formatcolumn.cpp:87:27: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o formatphylip.o formatphylip.cpp formatphylip.cpp: In member function 'virtual int FormatPhylipMatrix::read(NameAssignment*)': formatphylip.cpp:101:29: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o fullmatrix.o fullmatrix.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o geom.o geom.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getcommandinfocommand.o getcommandinfocommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getcoremicrobiomecommand.o getcoremicrobiomecommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getcurrentcommand.o getcurrentcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getgroupcommand.o getgroupcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getgroupscommand.o getgroupscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getlabelcommand.o getlabelcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getlineagecommand.o getlineagecommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getlistcountcommand.o getlistcountcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getopt_long.o getopt_long.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getotulabelscommand.o getotulabelscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getoturepcommand.o getoturepcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getotuscommand.o getotuscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getrabundcommand.o getrabundcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getrelabundcommand.o getrelabundcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getsabundcommand.o getsabundcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getseqscommand.o getseqscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getsharedotucommand.o getsharedotucommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o goodscoverage.o goodscoverage.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o gotohoverlap.o gotohoverlap.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o gower.o gower.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o groupmap.o groupmap.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o hamming.o hamming.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o hcluster.o hcluster.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o hclustercommand.o hclustercommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o heatmap.o heatmap.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o heatmapcommand.o heatmapcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o heatmapsim.o heatmapsim.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o heatmapsimcommand.o heatmapsimcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o heip.o heip.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o hellinger.o hellinger.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o helpcommand.o helpcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o homovacommand.o homovacommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o indicatorcommand.o indicatorcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o inputdata.o inputdata.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o invsimpson.o invsimpson.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o jackknife.o jackknife.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o kmer.o kmer.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o kmerdb.o kmerdb.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o knn.o knn.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o kruskalwalliscommand.o kruskalwalliscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o libshuff.o libshuff.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o libshuffcommand.o libshuffcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o linearalgebra.o linearalgebra.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o listotulabelscommand.o listotulabelscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o listseqscommand.o listseqscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o listvector.o listvector.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o loadlogfilecommand.o loadlogfilecommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o logsd.o logsd.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o makebiomcommand.o makebiomcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o makecontigscommand.o makecontigscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o makefastqcommand.o makefastqcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o makegroupcommand.o makegroupcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o maligner.o maligner.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o manhattan.o manhattan.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o mantelcommand.o mantelcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o matrixoutputcommand.o matrixoutputcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o memchi2.o memchi2.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o memchord.o memchord.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o memeuclidean.o memeuclidean.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o mempearson.o mempearson.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o mergefilecommand.o mergefilecommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o mergegroupscommand.o mergegroupscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o metastatscommand.o metastatscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o mgclustercommand.o mgclustercommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o mothur.o mothur.cpp mothur.cpp: In function 'int main(int, char**)': mothur.cpp:50:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o mothurfisher.o mothurfisher.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o mothurmetastats.o mothurmetastats.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o mothurout.o mothurout.cpp mothurout.cpp: In member function 'std::string MothurOut::sortFile(std::string, std::string)': mothurout.cpp:1171:27: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] mothurout.cpp: In member function 'int MothurOut::renameFile(std::string, std::string)': mothurout.cpp:1065:27: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] mothurout.cpp:1069:26: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o myPerseus.o myPerseus.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o myseqdist.o myseqdist.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o nameassignment.o nameassignment.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o nast.o nast.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o nastreport.o nastreport.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o needlemanoverlap.o needlemanoverlap.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o newcommandtemplate.o newcommandtemplate.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o nmdscommand.o nmdscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o noalign.o noalign.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o nocommands.o nocommands.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o normalizesharedcommand.o normalizesharedcommand.cpp g++ -g -O2 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-D_FORTIFY_SOURCE=2 -c -o otuassociationcommand.o otuassociationcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o otuhierarchycommand.o otuhierarchycommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o overlap.o overlap.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o pairwiseseqscommand.o pairwiseseqscommand.cpp pairwiseseqscommand.cpp: In member function 'virtual int PairwiseSeqsCommand::execute()': pairwiseseqscommand.cpp:475:46: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] g++ -g -O2 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seqerrorcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o seqnoise.o seqnoise.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o seqsummarycommand.o seqsummarycommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sequence.o sequence.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sequencedb.o sequencedb.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" 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-DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o spearman.o spearman.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o speciesprofile.o speciesprofile.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o spline.o spline.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o splitabundcommand.o splitabundcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o splitgroupscommand.o splitgroupscommand.cpp g++ -g -O2 -fstack-protector 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summarysharedcommand.o summarysharedcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o summarytaxcommand.o summarytaxcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o systemcommand.o systemcommand.cpp systemcommand.cpp: In member function 'virtual int SystemCommand::execute()': systemcommand.cpp:101:26: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o taxonomyequalizer.o taxonomyequalizer.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o tree.o tree.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o treegroupscommand.o treegroupscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o treemap.o treemap.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o treenode.o treenode.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o treereader.o treereader.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o trialSwap2.o trialSwap2.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o trimflowscommand.o trimflowscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o trimoligos.o trimoligos.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o trimseqscommand.o trimseqscommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o unifracunweightedcommand.o unifracunweightedcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o unifracweightedcommand.o unifracweightedcommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o unweighted.o unweighted.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o uvest.o uvest.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o validcalculator.o validcalculator.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o validparameter.o validparameter.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o venn.o venn.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o venncommand.o venncommand.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o weighted.o weighted.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o weightedlinkage.o weightedlinkage.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -O3 -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o whittaker.o whittaker.cpp cd uchime_src && ./mk && mv uchime .. && cd .. addtargets2 alignchime alignchimel alnparams alpha alpha2 fractid getparents globalalign2 make3way mx myutils path searchchime seqdb setnucmx sfasta tracebackbit uchime_main usort viterbifast writechhit -rwxrwxr-x 1 buildd buildd 180K Aug 20 16:50 uchime 49429 180 g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -o mothur ace.o aligncommand.o alignment.o alignmentcell.o alignmentdb.o amovacommand.o anosimcommand.o averagelinkage.o bayesian.o bellerophon.o bergerparker.o binsequencecommand.o blastalign.o blastdb.o boneh.o bootstrap.o bootstrapsharedcommand.o bstick.o calculator.o canberra.o catchallcommand.o ccode.o chao1.o chimera.o chimerabellerophoncommand.o chimeraccodecommand.o chimeracheckcommand.o chimeracheckrdp.o chimeraperseuscommand.o chimerapintailcommand.o chimerarealigner.o chimeraslayer.o chimeraslayercommand.o chimerauchimecommand.o chopseqscommand.o classify.o classifyotucommand.o classifyseqscommand.o classifytreecommand.o clearcut.o clearcutcommand.o clearmemorycommand.o cluster.o clusterclassic.o clustercommand.o clusterdoturcommand.o clusterfragmentscommand.o clustersplitcommand.o cmdargs.o collect.o collectcommand.o collectsharedcommand.o commandfactory.o commandoptionparser.o completelinkage.o consensus.o consensuscommand.o consensusseqscommand.o cooccurrencecommand.o corraxescommand.o countgroupscommand.o countseqscommand.o counttable.o coverage.o createdatabasecommand.o database.o decalc.o deconvolutecommand.o degapseqscommand.o deuniqueseqscommand.o deuniquetreecommand.o distancecommand.o distancedb.o distclearcut.o dlibshuff.o dmat.o efron.o engine.o fasta.o fastamap.o fileoutput.o filterseqscommand.o flowdata.o formatcolumn.o formatphylip.o fullmatrix.o geom.o getcommandinfocommand.o getcoremicrobiomecommand.o getcurrentcommand.o getgroupcommand.o getgroupscommand.o getlabelcommand.o getlineagecommand.o getlistcountcommand.o getopt_long.o getotulabelscommand.o getoturepcommand.o getotuscommand.o getrabundcommand.o getrelabundcommand.o getsabundcommand.o getseqscommand.o getsharedotucommand.o goodscoverage.o gotohoverlap.o gower.o groupmap.o hamming.o hcluster.o hclustercommand.o heatmap.o heatmapcommand.o heatmapsim.o heatmapsimcommand.o heip.o hellinger.o helpcommand.o homovacommand.o indicatorcommand.o inputdata.o invsimpson.o jackknife.o kmer.o kmerdb.o knn.o kruskalwalliscommand.o libshuff.o libshuffcommand.o linearalgebra.o listotulabelscommand.o listseqscommand.o listvector.o loadlogfilecommand.o logsd.o makebiomcommand.o makecontigscommand.o makefastqcommand.o makegroupcommand.o maligner.o manhattan.o mantelcommand.o matrixoutputcommand.o memchi2.o memchord.o memeuclidean.o mempearson.o mergefilecommand.o mergegroupscommand.o metastatscommand.o mgclustercommand.o mothur.o mothurfisher.o mothurmetastats.o mothurout.o myPerseus.o myseqdist.o nameassignment.o nast.o nastreport.o needlemanoverlap.o newcommandtemplate.o nmdscommand.o noalign.o nocommands.o normalizesharedcommand.o npshannon.o odum.o optionparser.o ordervector.o otuassociationcommand.o otuhierarchycommand.o overlap.o pairwiseseqscommand.o parsefastaqcommand.o parselistscommand.o parsimony.o parsimonycommand.o pcacommand.o pcoacommand.o phylodiversity.o phylodiversitycommand.o phylosummary.o phylotree.o phylotypecommand.o pintail.o pipelinepdscommand.o prcseqscommand.o preclustercommand.o prng.o progress.o qstat.o qualityscores.o quitcommand.o rabundvector.o rarecalc.o raredisplay.o rarefact.o rarefactcommand.o rarefactsharedcommand.o readblast.o readcluster.o readcolumn.o readdistcommand.o readotucommand.o readphylip.o readphylipvector.o readtree.o readtreecommand.o refchimeratest.o referencedb.o removegroupscommand.o removelineagecommand.o removeotulabelscommand.o removeotuscommand.o removerarecommand.o removeseqscommand.o reportfile.o reversecommand.o sabundvector.o screenseqscommand.o secondarystructurecommand.o sensspeccommand.o seqerrorcommand.o seqnoise.o seqsummarycommand.o sequence.o sequencedb.o sequenceparser.o setcurrentcommand.o setdircommand.o setlogfilecommand.o sffinfocommand.o shannon.o shannoneven.o sharedace.o sharedanderbergs.o sharedbraycurtis.o sharedchao1.o sharedcommand.o sharedjabund.o sharedjackknife.o sharedjclass.o sharedjest.o sharedkstest.o sharedkulczynski.o sharedkulczynskicody.o sharedlennon.o sharedlistvector.o sharedmarczewski.o sharedmorisitahorn.o sharedochiai.o sharedordervector.o sharedrabundfloatvector.o sharedrabundvector.o sharedsabundvector.o sharedsobs.o sharedsobscollectsummary.o sharedsorabund.o sharedsorclass.o sharedsorest.o sharedthetan.o sharedthetayc.o sharedutilities.o shen.o shhhercommand.o shhhseqscommand.o simpson.o simpsoneven.o singlelinkage.o slayer.o slibshuff.o smithwilson.o soergel.o solow.o sortseqscommand.o sparsedistancematrix.o sparsematrix.o spearman.o speciesprofile.o spline.o splitabundcommand.o splitgroupscommand.o splitmatrix.o structchi2.o structchord.o structeuclidean.o structkulczynski.o structpearson.o subsample.o subsamplecommand.o suffixdb.o suffixnodes.o suffixtree.o summarycommand.o summaryqualcommand.o summarysharedcommand.o summarytaxcommand.o systemcommand.o taxonomyequalizer.o tree.o treegroupscommand.o treemap.o treenode.o treereader.o trialSwap2.o trimflowscommand.o trimoligos.o trimseqscommand.o unifracunweightedcommand.o unifracweightedcommand.o unweighted.o uvest.o validcalculator.o validparameter.o venn.o venncommand.o weighted.o weightedlinkage.o whittaker.o bsplvb.o bsplvd.o bvalue.o daxpy.o ddot.o dpbfa.o dpbsl.o interv.o intrv.o sgram.o sinerp.o sslvrg.o stxwx.o -lreadline strip mothur make[2]: Leaving directory `/build/buildd/mothur-1.27.0+repack' make[1]: Leaving directory `/build/buildd/mothur-1.27.0+repack' dh_auto_test /usr/bin/fakeroot debian/rules binary dh binary --with quilt dh_testroot dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory `/build/buildd/mothur-1.27.0+repack' true make[1]: Leaving directory `/build/buildd/mothur-1.27.0+repack' dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_installcatalogs dh_installcron dh_installdebconf dh_installemacsen dh_installifupdown dh_installinfo dh_installinit dh_installmenu dh_installmime dh_installmodules dh_installlogcheck dh_installlogrotate dh_installpam dh_installppp dh_installudev dh_installwm dh_installxfonts dh_installgsettings dh_bugfiles dh_ucf dh_lintian dh_gconf dh_icons dh_perl dh_usrlocal dh_link dh_compress dh_fixperms dh_strip dh_strip debug symbol extraction: disabling for PPA build dh_strip debug symbol extraction: not doing anything since NO_PKG_MANGLE is given dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb INFO: pkgstriptranslations version 116 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build INFO: Disabling pkgstripfiles for PPA build dpkg-deb: building package `mothur' in `../mothur_1.27.0+repack-precise2_i386.deb'. dpkg-genchanges -b -mUbuntu Build Daemon >../mothur_1.27.0+repack-precise2_i386.changes dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build mothur-1.27.0+repack dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20120820-1651 chroot-autobuild/build/buildd/mothur_1.27.0+repack-precise2_i386.deb: new debian package, version 2.0. size 5312844 bytes: control archive= 1102 bytes. 831 bytes, 18 lines control 428 bytes, 7 lines md5sums 185 bytes, 7 lines * postinst #!/bin/sh 160 bytes, 5 lines * postrm #!/bin/sh Package: mothur Version: 1.27.0+repack-precise2 Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 11811 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libreadline6 (>= 6.0), libstdc++6 (>= 4.6) Conflicts: uchime Provides: uchime Section: science Priority: optional Homepage: http://www.mothur.org Description: sequence analysis suite for research on microbiota Mothur seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. It has incorporated the functionality of dotur, sons, treeclimber, s-libshuff, unifrac, and much more. In addition to improving the flexibility of these algorithms, a number of other features including calculators and visualization tools were added. chroot-autobuild/build/buildd/mothur_1.27.0+repack-precise2_i386.deb: drwxr-xr-x root/root 0 2012-08-20 16:51 ./ drwxr-xr-x root/root 0 2012-08-20 16:51 ./usr/ drwxr-xr-x root/root 0 2012-08-20 16:51 ./usr/share/ drwxr-xr-x root/root 0 2012-08-20 16:51 ./usr/share/menu/ -rw-r--r-- root/root 176 2012-03-01 17:42 ./usr/share/menu/mothur drwxr-xr-x root/root 0 2012-08-20 16:51 ./usr/share/man/ drwxr-xr-x root/root 0 2012-08-20 16:51 ./usr/share/man/man1/ -rw-r--r-- root/root 568 2012-08-20 16:51 ./usr/share/man/man1/mothur.1.gz drwxr-xr-x root/root 0 2012-08-20 16:51 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-08-20 16:51 ./usr/share/doc/mothur/ -rw-r--r-- root/root 4545 2012-05-09 10:16 ./usr/share/doc/mothur/copyright -rw-r--r-- root/root 259 2012-03-01 17:42 ./usr/share/doc/mothur/README.Debian -rw-r--r-- root/root 1787 2012-08-16 14:20 ./usr/share/doc/mothur/changelog.Debian.gz drwxr-xr-x root/root 0 2012-08-20 16:51 ./usr/bin/ -rwxr-xr-x root/root 184060 2012-08-20 16:51 ./usr/bin/uchime -rwxr-xr-x root/root 11860976 2012-08-20 16:51 ./usr/bin/mothur mothur_1.27.0+repack-precise2_i386.changes: Format: 1.8 Date: Thu, 16 Aug 2012 15:20:15 +0100 Source: mothur Binary: mothur mothur-mpi Architecture: i386 Version: 1.27.0+repack-precise2 Distribution: precise Urgency: low Maintainer: Ubuntu Build Daemon Changed-By: Tim Booth Description: mothur - sequence analysis suite for research on microbiota mothur-mpi - mpi-enabled binary for mothur Changes: mothur (1.27.0+repack-precise2) precise; urgency=low . * New minor release from upstream * Build MPI version alongside regular version * ...but only for 64-bit Checksums-Sha1: a240c2832e071f5e223a2802342d7c4afce0b06e 5312844 mothur_1.27.0+repack-precise2_i386.deb Checksums-Sha256: 3f8489ca6b9850a11af1404b369ef1d932dc9f5d169eac4224d55adb05f2fa96 5312844 mothur_1.27.0+repack-precise2_i386.deb Files: ec96241fcf8223e87a5b653b3b6818b7 5312844 science optional mothur_1.27.0+repack-precise2_i386.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20120820-1651 Build needed 00:14:17, 230896k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', '7e40fb86ebd52dedeb3f5dedec4d6ea8404a8d23'] Scanning for processes to kill in build /home/buildd/build-7e40fb86ebd52dedeb3f5dedec4d6ea8404a8d23/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', '7e40fb86ebd52dedeb3f5dedec4d6ea8404a8d23'] Unmounting chroot for build 7e40fb86ebd52dedeb3f5dedec4d6ea8404a8d23... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', '7e40fb86ebd52dedeb3f5dedec4d6ea8404a8d23'] Removing build 7e40fb86ebd52dedeb3f5dedec4d6ea8404a8d23