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... 25 Jan 04:15:06 ntpdate[3408]: step time server 10.211.37.1 offset -6953812.817147 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'fbed6d25bba59083cf01932877e0382811d31d78', '/home/buildd/filecache-default/c021ff3d3373fb2201b3008c0ece6808393ff246'] Uncompressing the tarball... Unpacking chroot for build fbed6d25bba59083cf01932877e0382811d31d78 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'fbed6d25bba59083cf01932877e0382811d31d78'] Mounting chroot for build fbed6d25bba59083cf01932877e0382811d31d78 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'fbed6d25bba59083cf01932877e0382811d31d78', 'deb http://ppa.launchpad.net/l.c.karssen/genabel-ppa/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-fbed6d25bba59083cf01932877e0382811d31d78 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'fbed6d25bba59083cf01932877e0382811d31d78', 'amd64'] Updating debian chroot for build fbed6d25bba59083cf01932877e0382811d31d78 Ign http://ftpmaster.internal precise InRelease Ign http://ftpmaster.internal precise-security InRelease Ign http://ftpmaster.internal precise-updates InRelease Ign http://ppa.launchpad.net precise InRelease Get:1 http://ftpmaster.internal precise Release.gpg [198 B] Get:2 http://ppa.launchpad.net precise Release.gpg [316 B] Get:3 http://ftpmaster.internal precise-security Release.gpg [198 B] Get:4 http://ftpmaster.internal precise-updates Release.gpg [198 B] Get:5 http://ftpmaster.internal precise Release [49.6 kB] Get:6 http://ftpmaster.internal precise-security Release [49.6 kB] Get:7 http://ppa.launchpad.net precise Release [11.9 kB] Get:8 http://ftpmaster.internal precise-updates Release [49.6 kB] Ign http://ppa.launchpad.net precise Release Get:9 http://ftpmaster.internal precise/main amd64 Packages [1273 kB] Get:10 http://ppa.launchpad.net precise/main amd64 Packages [542 B] Ign http://ppa.launchpad.net precise/main TranslationIndex Ign http://ppa.launchpad.net precise/main Translation-en Get:11 http://ftpmaster.internal precise/restricted amd64 Packages [8452 B] Get:12 http://ftpmaster.internal precise/universe amd64 Packages [4786 kB] Get:13 http://ftpmaster.internal precise/multiverse amd64 Packages [119 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 amd64 Packages [181 kB] Get:19 http://ftpmaster.internal precise-security/restricted amd64 Packages [3969 B] Get:20 http://ftpmaster.internal precise-security/universe amd64 Packages [49.0 kB] Get:21 http://ftpmaster.internal precise-security/multiverse amd64 Packages [2188 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 amd64 Packages [420 kB] Get:27 http://ftpmaster.internal precise-updates/restricted amd64 Packages [8366 B] Get:28 http://ftpmaster.internal precise-updates/universe amd64 Packages [150 kB] Get:29 http://ftpmaster.internal precise-updates/multiverse amd64 Packages [8664 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 [89.3 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 [30.5 kB] Get:42 http://ftpmaster.internal precise-updates/main Translation-en [207 kB] Get:43 http://ftpmaster.internal precise-updates/multiverse Translation-en [5414 B] Get:44 http://ftpmaster.internal precise-updates/restricted Translation-en [2082 B] Get:45 http://ftpmaster.internal precise-updates/universe Translation-en [90.3 kB] Fetched 11.8 MB in 4s (2724 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 DF3D4F8F9D453130 Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: apt apt-transport-https base-files build-essential coreutils gnupg gpgv initscripts libapt-pkg4.12 libc-bin libc-dev-bin libc6 libc6-dev libdbus-1-3 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 login lsb-base multiarch-support openssl passwd perl perl-base perl-modules python2.7-minimal sysv-rc sysvinit-utils tzdata ubuntu-keyring udev upstart 43 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 33.5 MB of archives. After this operation, 20.5 kB disk space will be freed. WARNING: The following packages cannot be authenticated! base-files coreutils login perl perl-base perl-modules sysv-rc initscripts upstart libc-dev-bin libc6-dev libc-bin libc6 sysvinit-utils lsb-base passwd libdbus-1-3 libudev0 linux-libc-dev tzdata libapt-pkg4.12 ubuntu-keyring gpgv gnupg apt libssl1.0.0 libsqlite3-0 libglib2.0-0 libgcrypt11 libtasn1-3 libgnutls26 libk5crypto3 libgssapi-krb5-2 libkrb5-3 libkrb5support0 libsasl2-2 libldap-2.4-2 multiarch-support python2.7-minimal udev apt-transport-https openssl build-essential Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ precise-updates/main base-files amd64 6.5ubuntu6.4 [69.9 kB] Get:2 http://ftpmaster.internal/ubuntu/ precise-updates/main coreutils amd64 8.13-3ubuntu3.1 [2216 kB] Get:3 http://ftpmaster.internal/ubuntu/ precise-updates/main login amd64 1:4.1.4.2+svn3283-3ubuntu5.1 [291 kB] Get:4 http://ftpmaster.internal/ubuntu/ precise-updates/main perl amd64 5.14.2-6ubuntu2.1 [4416 kB] Get:5 http://ftpmaster.internal/ubuntu/ precise-updates/main perl-base amd64 5.14.2-6ubuntu2.1 [1498 kB] Get:6 http://ftpmaster.internal/ubuntu/ precise-updates/main perl-modules all 5.14.2-6ubuntu2.1 [3396 kB] Get:7 http://ftpmaster.internal/ubuntu/ precise-updates/main sysv-rc all 2.88dsf-13.10ubuntu11.1 [44.6 kB] Get:8 http://ftpmaster.internal/ubuntu/ precise-updates/main initscripts amd64 2.88dsf-13.10ubuntu11.1 [28.1 kB] Get:9 http://ftpmaster.internal/ubuntu/ precise-updates/main upstart amd64 1.5-0ubuntu7 [311 kB] Get:10 http://ftpmaster.internal/ubuntu/ precise-updates/main libc-dev-bin amd64 2.15-0ubuntu10.3 [84.5 kB] Get:11 http://ftpmaster.internal/ubuntu/ precise-updates/main libc6-dev amd64 2.15-0ubuntu10.3 [2945 kB] Get:12 http://ftpmaster.internal/ubuntu/ precise-updates/main libc-bin amd64 2.15-0ubuntu10.3 [1181 kB] Get:13 http://ftpmaster.internal/ubuntu/ precise-updates/main libc6 amd64 2.15-0ubuntu10.3 [4653 kB] Get:14 http://ftpmaster.internal/ubuntu/ precise-updates/main sysvinit-utils amd64 2.88dsf-13.10ubuntu11.1 [60.2 kB] Get:15 http://ftpmaster.internal/ubuntu/ precise-updates/main lsb-base all 4.0-0ubuntu20.2 [10.4 kB] Get:16 http://ftpmaster.internal/ubuntu/ precise-updates/main passwd amd64 1:4.1.4.2+svn3283-3ubuntu5.1 [959 kB] Get:17 http://ftpmaster.internal/ubuntu/ precise-security/main libdbus-1-3 amd64 1.4.18-1ubuntu1.3 [145 kB] Get:18 http://ftpmaster.internal/ubuntu/ precise-updates/main libudev0 amd64 175-0ubuntu9.2 [29.2 kB] Get:19 http://ftpmaster.internal/ubuntu/ precise-security/main linux-libc-dev amd64 3.2.0-32.51 [868 kB] Get:20 http://ftpmaster.internal/ubuntu/ precise-security/main tzdata all 2012e-0ubuntu0.12.04.1 [474 kB] Get:21 http://ftpmaster.internal/ubuntu/ precise-updates/main libapt-pkg4.12 amd64 0.8.16~exp12ubuntu10.5 [939 kB] Get:22 http://ftpmaster.internal/ubuntu/ precise-updates/main ubuntu-keyring all 2011.11.21.1 [16.7 kB] Get:23 http://ftpmaster.internal/ubuntu/ precise-security/main gpgv amd64 1.4.11-3ubuntu2.1 [185 kB] Get:24 http://ftpmaster.internal/ubuntu/ precise-security/main gnupg amd64 1.4.11-3ubuntu2.1 [808 kB] Get:25 http://ftpmaster.internal/ubuntu/ precise-updates/main apt amd64 0.8.16~exp12ubuntu10.5 [1100 kB] Get:26 http://ftpmaster.internal/ubuntu/ precise-updates/main libssl1.0.0 amd64 1.0.1-4ubuntu5.5 [1011 kB] Get:27 http://ftpmaster.internal/ubuntu/ precise-updates/main libsqlite3-0 amd64 3.7.9-2ubuntu1.1 [349 kB] Get:28 http://ftpmaster.internal/ubuntu/ precise-updates/main libglib2.0-0 amd64 2.32.3-0ubuntu1 [1199 kB] Get:29 http://ftpmaster.internal/ubuntu/ precise-updates/main libgcrypt11 amd64 1.5.0-3ubuntu0.1 [280 kB] Get:30 http://ftpmaster.internal/ubuntu/ precise-security/main libtasn1-3 amd64 2.10-1ubuntu1.1 [43.3 kB] Get:31 http://ftpmaster.internal/ubuntu/ precise-updates/main libgnutls26 amd64 2.12.14-5ubuntu3.1 [459 kB] Get:32 http://ftpmaster.internal/ubuntu/ precise-security/main libk5crypto3 amd64 1.10+dfsg~beta1-2ubuntu0.3 [80.1 kB] Get:33 http://ftpmaster.internal/ubuntu/ precise-security/main libgssapi-krb5-2 amd64 1.10+dfsg~beta1-2ubuntu0.3 [118 kB] Get:34 http://ftpmaster.internal/ubuntu/ precise-security/main libkrb5-3 amd64 1.10+dfsg~beta1-2ubuntu0.3 [355 kB] Get:35 http://ftpmaster.internal/ubuntu/ precise-security/main libkrb5support0 amd64 1.10+dfsg~beta1-2ubuntu0.3 [23.8 kB] Get:36 http://ftpmaster.internal/ubuntu/ precise-updates/main libsasl2-2 amd64 2.1.25.dfsg1-3ubuntu0.1 [69.1 kB] Get:37 http://ftpmaster.internal/ubuntu/ precise-updates/main libldap-2.4-2 amd64 2.4.28-1.1ubuntu4.2 [186 kB] Get:38 http://ftpmaster.internal/ubuntu/ precise-updates/main multiarch-support amd64 2.15-0ubuntu10.3 [4480 B] Get:39 http://ftpmaster.internal/ubuntu/ precise-updates/main python2.7-minimal amd64 2.7.3-0ubuntu3.1 [1741 kB] Get:40 http://ftpmaster.internal/ubuntu/ precise-updates/main udev amd64 175-0ubuntu9.2 [323 kB] Get:41 http://ftpmaster.internal/ubuntu/ precise-updates/main apt-transport-https amd64 0.8.16~exp12ubuntu10.5 [16.3 kB] Get:42 http://ftpmaster.internal/ubuntu/ precise-updates/main openssl amd64 1.0.1-4ubuntu5.5 [523 kB] Get:43 http://ftpmaster.internal/ubuntu/ precise-updates/main build-essential amd64 11.5ubuntu2.1 [5816 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 33.5 MB in 1s (21.2 MB/s) (Reading database ... 12243 files and directories currently installed.) Preparing to replace base-files 6.5ubuntu6 (using .../base-files_6.5ubuntu6.4_amd64.deb) ... Unpacking replacement base-files ... Setting up base-files (6.5ubuntu6.4) ... 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 ... 12244 files and directories currently installed.) Preparing to replace coreutils 8.13-3ubuntu3 (using .../coreutils_8.13-3ubuntu3.1_amd64.deb) ... Unpacking replacement coreutils ... Setting up coreutils (8.13-3ubuntu3.1) ... (Reading database ... 12244 files and directories currently installed.) Preparing to replace login 1:4.1.4.2+svn3283-3ubuntu5 (using .../login_1%3a4.1.4.2+svn3283-3ubuntu5.1_amd64.deb) ... Unpacking replacement login ... Setting up login (1:4.1.4.2+svn3283-3ubuntu5.1) ... (Reading database ... 12244 files and directories currently installed.) Preparing to replace perl 5.14.2-6ubuntu2 (using .../perl_5.14.2-6ubuntu2.1_amd64.deb) ... Unpacking replacement perl ... Preparing to replace perl-base 5.14.2-6ubuntu2 (using .../perl-base_5.14.2-6ubuntu2.1_amd64.deb) ... Unpacking replacement perl-base ... Setting up perl-base (5.14.2-6ubuntu2.1) ... (Reading database ... 12244 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 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_amd64.deb) ... Unpacking replacement initscripts ... Preparing to replace upstart 1.5-0ubuntu5 (using .../upstart_1.5-0ubuntu7_amd64.deb) ... Unpacking replacement upstart ... Preparing to replace libc-dev-bin 2.15-0ubuntu10 (using .../libc-dev-bin_2.15-0ubuntu10.3_amd64.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libc6-dev 2.15-0ubuntu10 (using .../libc6-dev_2.15-0ubuntu10.3_amd64.deb) ... Unpacking replacement libc6-dev ... Preparing to replace libc-bin 2.15-0ubuntu10 (using .../libc-bin_2.15-0ubuntu10.3_amd64.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.15-0ubuntu10.3) ... (Reading database ... 12244 files and directories currently installed.) Preparing to replace libc6 2.15-0ubuntu10 (using .../libc6_2.15-0ubuntu10.3_amd64.deb) ... Unpacking replacement libc6 ... Setting up libc6 (2.15-0ubuntu10.3) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12244 files and directories currently installed.) Preparing to replace sysvinit-utils 2.88dsf-13.10ubuntu11 (using .../sysvinit-utils_2.88dsf-13.10ubuntu11.1_amd64.deb) ... Unpacking replacement sysvinit-utils ... Preparing to replace lsb-base 4.0-0ubuntu20 (using .../lsb-base_4.0-0ubuntu20.2_all.deb) ... Unpacking replacement lsb-base ... Setting up lsb-base (4.0-0ubuntu20.2) ... (Reading database ... 12244 files and directories currently installed.) Preparing to replace passwd 1:4.1.4.2+svn3283-3ubuntu5 (using .../passwd_1%3a4.1.4.2+svn3283-3ubuntu5.1_amd64.deb) ... Unpacking replacement passwd ... Setting up sysvinit-utils (2.88dsf-13.10ubuntu11.1) ... Setting up sysv-rc (2.88dsf-13.10ubuntu11.1) ... Setting up passwd (1:4.1.4.2+svn3283-3ubuntu5.1) ... Setting up initscripts (2.88dsf-13.10ubuntu11.1) ... Setting up upstart (1.5-0ubuntu7) ... Installing new version of config file /etc/logrotate.d/upstart ... (Reading database ... 12246 files and directories currently installed.) Preparing to replace libdbus-1-3 1.4.18-1ubuntu1 (using .../libdbus-1-3_1.4.18-1ubuntu1.3_amd64.deb) ... Unpacking replacement libdbus-1-3 ... Preparing to replace libudev0 175-0ubuntu9 (using .../libudev0_175-0ubuntu9.2_amd64.deb) ... Unpacking replacement libudev0 ... Preparing to replace linux-libc-dev 3.2.0-23.36 (using .../linux-libc-dev_3.2.0-32.51_amd64.deb) ... Unpacking replacement linux-libc-dev ... Preparing to replace tzdata 2012b-1 (using .../tzdata_2012e-0ubuntu0.12.04.1_all.deb) ... Unpacking replacement tzdata ... Setting up tzdata (2012e-0ubuntu0.12.04.1) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Nov 5 16:42:14 UTC 2012. Universal Time is now: Mon Nov 5 16:42:14 UTC 2012. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 12248 files and directories currently installed.) Preparing to replace libapt-pkg4.12 0.8.16~exp12ubuntu10 (using .../libapt-pkg4.12_0.8.16~exp12ubuntu10.5_amd64.deb) ... Unpacking replacement libapt-pkg4.12 ... Setting up libapt-pkg4.12 (0.8.16~exp12ubuntu10.5) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12248 files and directories currently installed.) Preparing to replace ubuntu-keyring 2011.11.21 (using .../ubuntu-keyring_2011.11.21.1_all.deb) ... Unpacking replacement ubuntu-keyring ... Setting up ubuntu-keyring (2011.11.21.1) ... gpg: key 437D05B5: "Ubuntu Archive Automatic Signing Key " not changed gpg: key FBB75451: "Ubuntu CD Image Automatic Signing Key " not changed gpg: key C0B21F32: public key "Ubuntu Archive Automatic Signing Key (2012) " imported gpg: key EFE21092: public key "Ubuntu CD Image Automatic Signing Key (2012) " imported gpg: Total number processed: 4 gpg: imported: 2 (RSA: 2) gpg: unchanged: 2 gpg: no ultimately trusted keys found (Reading database ... 12248 files and directories currently installed.) Preparing to replace gpgv 1.4.11-3ubuntu2 (using .../gpgv_1.4.11-3ubuntu2.1_amd64.deb) ... Unpacking replacement gpgv ... Setting up gpgv (1.4.11-3ubuntu2.1) ... (Reading database ... 12248 files and directories currently installed.) Preparing to replace gnupg 1.4.11-3ubuntu2 (using .../gnupg_1.4.11-3ubuntu2.1_amd64.deb) ... Unpacking replacement gnupg ... Setting up gnupg (1.4.11-3ubuntu2.1) ... (Reading database ... 12248 files and directories currently installed.) Preparing to replace apt 0.8.16~exp12ubuntu10 (using .../apt_0.8.16~exp12ubuntu10.5_amd64.deb) ... Unpacking replacement apt ... Setting up apt (0.8.16~exp12ubuntu10.5) ... gpg: key 437D05B5: "Ubuntu Archive Automatic Signing Key " not changed gpg: key FBB75451: "Ubuntu CD Image Automatic Signing Key " not changed gpg: key C0B21F32: "Ubuntu Archive Automatic Signing Key (2012) " not changed gpg: key EFE21092: "Ubuntu CD Image Automatic Signing Key (2012) " not changed gpg: Total number processed: 4 gpg: unchanged: 4 (Reading database ... 12248 files and directories currently installed.) Preparing to replace libssl1.0.0 1.0.1-4ubuntu3 (using .../libssl1.0.0_1.0.1-4ubuntu5.5_amd64.deb) ... Unpacking replacement libssl1.0.0 ... Setting up libssl1.0.0 (1.0.1-4ubuntu5.5) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12248 files and directories currently installed.) Preparing to replace libsqlite3-0 3.7.9-2ubuntu1 (using .../libsqlite3-0_3.7.9-2ubuntu1.1_amd64.deb) ... Unpacking replacement libsqlite3-0 ... Preparing to replace libglib2.0-0 2.32.1-0ubuntu2 (using .../libglib2.0-0_2.32.3-0ubuntu1_amd64.deb) ... Unpacking replacement libglib2.0-0 ... Preparing to replace libgcrypt11 1.5.0-3 (using .../libgcrypt11_1.5.0-3ubuntu0.1_amd64.deb) ... Unpacking replacement libgcrypt11 ... Preparing to replace libtasn1-3 2.10-1ubuntu1 (using .../libtasn1-3_2.10-1ubuntu1.1_amd64.deb) ... Unpacking replacement libtasn1-3 ... Preparing to replace libgnutls26 2.12.14-5ubuntu3 (using .../libgnutls26_2.12.14-5ubuntu3.1_amd64.deb) ... Unpacking replacement libgnutls26 ... Preparing to replace libk5crypto3 1.10+dfsg~beta1-2 (using .../libk5crypto3_1.10+dfsg~beta1-2ubuntu0.3_amd64.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_amd64.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_amd64.deb) ... Unpacking replacement libkrb5-3 ... Preparing to replace libkrb5support0 1.10+dfsg~beta1-2 (using .../libkrb5support0_1.10+dfsg~beta1-2ubuntu0.3_amd64.deb) ... Unpacking replacement libkrb5support0 ... Preparing to replace libsasl2-2 2.1.25.dfsg1-3 (using .../libsasl2-2_2.1.25.dfsg1-3ubuntu0.1_amd64.deb) ... Unpacking replacement libsasl2-2 ... Preparing to replace libldap-2.4-2 2.4.28-1.1ubuntu4 (using .../libldap-2.4-2_2.4.28-1.1ubuntu4.2_amd64.deb) ... Unpacking replacement libldap-2.4-2 ... Preparing to replace multiarch-support 2.15-0ubuntu10 (using .../multiarch-support_2.15-0ubuntu10.3_amd64.deb) ... Unpacking replacement multiarch-support ... Setting up multiarch-support (2.15-0ubuntu10.3) ... (Reading database ... 12248 files and directories currently installed.) Preparing to replace python2.7-minimal 2.7.3-0ubuntu3 (using .../python2.7-minimal_2.7.3-0ubuntu3.1_amd64.deb) ... Unpacking replacement python2.7-minimal ... Setting up python2.7-minimal (2.7.3-0ubuntu3.1) ... (Reading database ... 12248 files and directories currently installed.) Preparing to replace udev 175-0ubuntu9 (using .../udev_175-0ubuntu9.2_amd64.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~exp12ubuntu10.5_amd64.deb) ... Unpacking replacement apt-transport-https ... Preparing to replace openssl 1.0.1-4ubuntu3 (using .../openssl_1.0.1-4ubuntu5.5_amd64.deb) ... Unpacking replacement openssl ... Preparing to replace build-essential 11.5ubuntu2 (using .../build-essential_11.5ubuntu2.1_amd64.deb) ... Unpacking replacement build-essential ... Setting up libc-dev-bin (2.15-0ubuntu10.3) ... Setting up linux-libc-dev (3.2.0-32.51) ... Setting up libc6-dev (2.15-0ubuntu10.3) ... Setting up libdbus-1-3 (1.4.18-1ubuntu1.3) ... Setting up libudev0 (175-0ubuntu9.2) ... 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 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 (2.4.28-1.1ubuntu4.2) ... Setting up udev (175-0ubuntu9.2) ... 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 apt-transport-https (0.8.16~exp12ubuntu10.5) ... Setting up openssl (1.0.1-4ubuntu5.5) ... Setting up build-essential (11.5ubuntu2.1) ... Setting up perl-modules (5.14.2-6ubuntu2.1) ... Setting up perl (5.14.2-6ubuntu2.1) ... 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', 'fbed6d25bba59083cf01932877e0382811d31d78', 'amd64', 'precise', '--nolog', '--batch', '--archive=ubuntu', '--dist=precise', '--purpose=PPA', '--architecture=amd64', '--comp=main', 'probabel_0.2.0.99-0ubuntu1~precise1.dsc'] Initiating build fbed6d25bba59083cf01932877e0382811d31d78 with 2 jobs across 2 processor cores. Automatic build of probabel_0.2.0.99-0ubuntu1~precise1 on louvi by sbuild/amd64 1.170.5 Build started at 20121105-1642 ****************************************************************************** probabel_0.2.0.99-0ubuntu1~precise1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 7.0.50~), autotools-dev, texlive-latex-base Checking for already installed source dependencies... debhelper: missing autotools-dev: missing texlive-latex-base: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper autotools-dev texlive-latex-base Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils dh-apparmor ed file fontconfig-config gettext gettext-base groff-base html2text intltool-debian libcroco3 libexpat1 libfontconfig1 libfreetype6 libgettextpo0 libice6 libjpeg-turbo8 libjpeg8 libkpathsea5 liblcms2-2 libmagic1 libpaper-utils libpaper1 libpipeline1 libpoppler19 libsm6 libtiff4 libunistring0 libx11-6 libx11-data libxau6 libxaw7 libxcb1 libxdmcp6 libxext6 libxml2 libxmu6 libxpm4 libxt6 luatex man-db mime-support po-debconf tex-common texlive-base texlive-binaries texlive-common texlive-doc-base ttf-dejavu-core ucf x11-common Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff liblcms2-utils poppler-data less www-browser libmail-box-perl perl-tk ghostscript xpdf-reader pdf-viewer gv postscript-viewer Recommended packages: curl wget lynx-cur xml-core texlive-luatex libmail-sendmail-perl lmodern texlive-latex-base-doc The following NEW packages will be installed: autotools-dev bsdmainutils debhelper dh-apparmor ed file fontconfig-config gettext gettext-base groff-base html2text intltool-debian libcroco3 libexpat1 libfontconfig1 libfreetype6 libgettextpo0 libice6 libjpeg-turbo8 libjpeg8 libkpathsea5 liblcms2-2 libmagic1 libpaper-utils libpaper1 libpipeline1 libpoppler19 libsm6 libtiff4 libunistring0 libx11-6 libx11-data libxau6 libxaw7 libxcb1 libxdmcp6 libxext6 libxml2 libxmu6 libxpm4 libxt6 luatex man-db mime-support po-debconf tex-common texlive-base texlive-binaries texlive-common texlive-doc-base texlive-latex-base ttf-dejavu-core ucf x11-common 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. Need to get 39.8 MB of archives. After this operation, 95.1 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libxau6 libxdmcp6 libxcb1 libx11-data libx11-6 libxext6 libxml2 libcroco3 libexpat1 libfreetype6 ucf ttf-dejavu-core fontconfig-config libfontconfig1 libunistring0 libgettextpo0 x11-common libice6 libjpeg-turbo8 liblcms2-2 libjpeg8 libtiff4 libpoppler19 libsm6 libxt6 libxmu6 libxpm4 libxaw7 libmagic1 file mime-support bsdmainutils ed gettext-base groff-base man-db autotools-dev html2text gettext intltool-debian po-debconf dh-apparmor debhelper libkpathsea5 libpaper1 libpaper-utils luatex tex-common texlive-common texlive-doc-base texlive-binaries texlive-base texlive-latex-base Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ precise/main libpipeline1 amd64 1.2.1-1 [26.5 kB] Get:2 http://ftpmaster.internal/ubuntu/ precise/main libxau6 amd64 1:1.0.6-4 [8392 B] Get:3 http://ftpmaster.internal/ubuntu/ precise/main libxdmcp6 amd64 1:1.1.0-4 [12.7 kB] Get:4 http://ftpmaster.internal/ubuntu/ precise-updates/main libxcb1 amd64 1.8.1-1ubuntu0.1 [44.8 kB] Get:5 http://ftpmaster.internal/ubuntu/ precise/main libx11-data all 2:1.4.99.1-0ubuntu2 [168 kB] Get:6 http://ftpmaster.internal/ubuntu/ precise/main libx11-6 amd64 2:1.4.99.1-0ubuntu2 [762 kB] Get:7 http://ftpmaster.internal/ubuntu/ precise/main libxext6 amd64 2:1.3.0-3build1 [33.2 kB] Get:8 http://ftpmaster.internal/ubuntu/ precise-security/main libxml2 amd64 2.7.8.dfsg-5.1ubuntu4.2 [673 kB] Get:9 http://ftpmaster.internal/ubuntu/ precise/main libcroco3 amd64 0.6.5-1 [99.3 kB] Get:10 http://ftpmaster.internal/ubuntu/ precise-security/main libexpat1 amd64 2.0.1-7.2ubuntu1.1 [131 kB] Get:11 http://ftpmaster.internal/ubuntu/ precise/main libfreetype6 amd64 2.4.8-1ubuntu2 [343 kB] Get:12 http://ftpmaster.internal/ubuntu/ precise/main ucf all 3.0025+nmu2ubuntu1 [54.4 kB] Get:13 http://ftpmaster.internal/ubuntu/ precise/main ttf-dejavu-core all 2.33-2ubuntu1 [1552 kB] Get:14 http://ftpmaster.internal/ubuntu/ precise-updates/main fontconfig-config all 2.8.0-3ubuntu9.1 [44.4 kB] Get:15 http://ftpmaster.internal/ubuntu/ precise-updates/main libfontconfig1 amd64 2.8.0-3ubuntu9.1 [125 kB] Get:16 http://ftpmaster.internal/ubuntu/ precise/main libunistring0 amd64 0.9.3-5 [427 kB] Get:17 http://ftpmaster.internal/ubuntu/ precise/main libgettextpo0 amd64 0.18.1.1-5ubuntu3 [120 kB] Get:18 http://ftpmaster.internal/ubuntu/ precise/main x11-common all 1:7.6+12ubuntu1 [57.7 kB] Get:19 http://ftpmaster.internal/ubuntu/ precise/main libice6 amd64 2:1.0.7-2build1 [46.1 kB] Get:20 http://ftpmaster.internal/ubuntu/ precise-updates/main libjpeg-turbo8 amd64 1.1.90+svn733-0ubuntu4.1 [111 kB] Get:21 http://ftpmaster.internal/ubuntu/ precise/main liblcms2-2 amd64 2.2+git20110628-2ubuntu3 [142 kB] Get:22 http://ftpmaster.internal/ubuntu/ precise/main libjpeg8 amd64 8c-2ubuntu7 [2112 B] Get:23 http://ftpmaster.internal/ubuntu/ precise-security/main libtiff4 amd64 3.9.5-2ubuntu1.2 [144 kB] Get:24 http://ftpmaster.internal/ubuntu/ precise/main libpoppler19 amd64 0.18.4-1ubuntu2 [773 kB] Get:25 http://ftpmaster.internal/ubuntu/ precise/main libsm6 amd64 2:1.2.0-2build1 [18.1 kB] Get:26 http://ftpmaster.internal/ubuntu/ precise/main libxt6 amd64 1:1.1.1-2build1 [186 kB] Get:27 http://ftpmaster.internal/ubuntu/ precise/main libxmu6 amd64 2:1.1.0-3 [52.7 kB] Get:28 http://ftpmaster.internal/ubuntu/ precise/main libxpm4 amd64 1:3.5.9-4 [37.0 kB] Get:29 http://ftpmaster.internal/ubuntu/ precise/main libxaw7 amd64 2:1.0.9-3ubuntu1 [201 kB] Get:30 http://ftpmaster.internal/ubuntu/ precise/main libmagic1 amd64 5.09-2 [217 kB] Get:31 http://ftpmaster.internal/ubuntu/ precise/main file amd64 5.09-2 [19.7 kB] Get:32 http://ftpmaster.internal/ubuntu/ precise/main mime-support all 3.51-1ubuntu1 [30.7 kB] Get:33 http://ftpmaster.internal/ubuntu/ precise/main bsdmainutils amd64 8.2.3ubuntu1 [200 kB] Get:34 http://ftpmaster.internal/ubuntu/ precise/main ed amd64 1.5-3 [57.9 kB] Get:35 http://ftpmaster.internal/ubuntu/ precise/main gettext-base amd64 0.18.1.1-5ubuntu3 [80.0 kB] Get:36 http://ftpmaster.internal/ubuntu/ precise/main groff-base amd64 1.21-7 [1046 kB] Get:37 http://ftpmaster.internal/ubuntu/ precise/main man-db amd64 2.6.1-2 [756 kB] Get:38 http://ftpmaster.internal/ubuntu/ precise/main autotools-dev all 20120210.1ubuntu1 [42.4 kB] Get:39 http://ftpmaster.internal/ubuntu/ precise/main html2text amd64 1.3.2a-15 [104 kB] Get:40 http://ftpmaster.internal/ubuntu/ precise/main gettext amd64 0.18.1.1-5ubuntu3 [1188 kB] Get:41 http://ftpmaster.internal/ubuntu/ precise/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:42 http://ftpmaster.internal/ubuntu/ precise/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:43 http://ftpmaster.internal/ubuntu/ precise-security/main dh-apparmor all 2.7.102-0ubuntu3.4 [8952 B] Get:44 http://ftpmaster.internal/ubuntu/ precise/main debhelper all 9.20120115ubuntu3 [616 kB] Get:45 http://ftpmaster.internal/ubuntu/ precise/main libkpathsea5 amd64 2009-11ubuntu2 [56.7 kB] Get:46 http://ftpmaster.internal/ubuntu/ precise/main libpaper1 amd64 1.1.24+nmu1build1 [14.2 kB] Get:47 http://ftpmaster.internal/ubuntu/ precise/main libpaper-utils amd64 1.1.24+nmu1build1 [9040 B] Get:48 http://ftpmaster.internal/ubuntu/ precise/main luatex amd64 0.70.1-1ubuntu1 [2458 kB] Get:49 http://ftpmaster.internal/ubuntu/ precise/main tex-common all 2.10 [709 kB] Get:50 http://ftpmaster.internal/ubuntu/ precise/main texlive-common all 2009-15 [94.4 kB] Get:51 http://ftpmaster.internal/ubuntu/ precise/main texlive-doc-base all 2009-2 [1339 kB] Get:52 http://ftpmaster.internal/ubuntu/ precise/main texlive-binaries amd64 2009-11ubuntu2 [8054 kB] Get:53 http://ftpmaster.internal/ubuntu/ precise/main texlive-base all 2009-15 [14.7 MB] Get:54 http://ftpmaster.internal/ubuntu/ precise/main texlive-latex-base all 2009-15 [1406 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 39.8 MB in 3s (10.9 MB/s) Selecting previously unselected package libpipeline1. (Reading database ... 12248 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_amd64.deb) ... Selecting previously unselected package libxau6. Unpacking libxau6 (from .../libxau6_1%3a1.0.6-4_amd64.deb) ... Selecting previously unselected package libxdmcp6. Unpacking libxdmcp6 (from .../libxdmcp6_1%3a1.1.0-4_amd64.deb) ... Selecting previously unselected package libxcb1. Unpacking libxcb1 (from .../libxcb1_1.8.1-1ubuntu0.1_amd64.deb) ... Selecting previously unselected package libx11-data. Unpacking libx11-data (from .../libx11-data_2%3a1.4.99.1-0ubuntu2_all.deb) ... Selecting previously unselected package libx11-6. Unpacking libx11-6 (from .../libx11-6_2%3a1.4.99.1-0ubuntu2_amd64.deb) ... Selecting previously unselected package libxext6. Unpacking libxext6 (from .../libxext6_2%3a1.3.0-3build1_amd64.deb) ... Selecting previously unselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1ubuntu4.2_amd64.deb) ... Selecting previously unselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.5-1_amd64.deb) ... Selecting previously unselected package libexpat1. Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2ubuntu1.1_amd64.deb) ... Selecting previously unselected package libfreetype6. Unpacking libfreetype6 (from .../libfreetype6_2.4.8-1ubuntu2_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_2.33-2ubuntu1_all.deb) ... Selecting previously unselected package fontconfig-config. Unpacking fontconfig-config (from .../fontconfig-config_2.8.0-3ubuntu9.1_all.deb) ... Selecting previously unselected package libfontconfig1. Unpacking libfontconfig1 (from .../libfontconfig1_2.8.0-3ubuntu9.1_amd64.deb) ... Selecting previously unselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-5_amd64.deb) ... Selecting previously unselected package libgettextpo0. Unpacking libgettextpo0 (from .../libgettextpo0_0.18.1.1-5ubuntu3_amd64.deb) ... Selecting previously unselected package x11-common. Unpacking x11-common (from .../x11-common_1%3a7.6+12ubuntu1_all.deb) ... Selecting previously unselected package libice6. Unpacking libice6 (from .../libice6_2%3a1.0.7-2build1_amd64.deb) ... Selecting previously unselected package libjpeg-turbo8. Unpacking libjpeg-turbo8 (from .../libjpeg-turbo8_1.1.90+svn733-0ubuntu4.1_amd64.deb) ... Selecting previously unselected package liblcms2-2. Unpacking liblcms2-2 (from .../liblcms2-2_2.2+git20110628-2ubuntu3_amd64.deb) ... Selecting previously unselected package libjpeg8. Unpacking libjpeg8 (from .../libjpeg8_8c-2ubuntu7_amd64.deb) ... Selecting previously unselected package libtiff4. Unpacking libtiff4 (from .../libtiff4_3.9.5-2ubuntu1.2_amd64.deb) ... Selecting previously unselected package libpoppler19. Unpacking libpoppler19 (from .../libpoppler19_0.18.4-1ubuntu2_amd64.deb) ... Selecting previously unselected package libsm6. Unpacking libsm6 (from .../libsm6_2%3a1.2.0-2build1_amd64.deb) ... Selecting previously unselected package libxt6. Unpacking libxt6 (from .../libxt6_1%3a1.1.1-2build1_amd64.deb) ... Selecting previously unselected package libxmu6. Unpacking libxmu6 (from .../libxmu6_2%3a1.1.0-3_amd64.deb) ... Selecting previously unselected package libxpm4. Unpacking libxpm4 (from .../libxpm4_1%3a3.5.9-4_amd64.deb) ... Selecting previously unselected package libxaw7. Unpacking libxaw7 (from .../libxaw7_2%3a1.0.9-3ubuntu1_amd64.deb) ... Selecting previously unselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.09-2_amd64.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.09-2_amd64.deb) ... Selecting previously unselected package mime-support. Unpacking mime-support (from .../mime-support_3.51-1ubuntu1_all.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3ubuntu1_amd64.deb) ... Selecting previously unselected package ed. Unpacking ed (from .../archives/ed_1.5-3_amd64.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-5ubuntu3_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-7_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.1-2_amd64.deb) ... Selecting previously unselected package autotools-dev. Unpacking autotools-dev (from .../autotools-dev_20120210.1ubuntu1_all.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-5ubuntu3_amd64.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2ubuntu1_all.deb) ... Selecting previously unselected package dh-apparmor. Unpacking dh-apparmor (from .../dh-apparmor_2.7.102-0ubuntu3.4_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_9.20120115ubuntu3_all.deb) ... Selecting previously unselected package libkpathsea5. Unpacking libkpathsea5 (from .../libkpathsea5_2009-11ubuntu2_amd64.deb) ... Selecting previously unselected package libpaper1. Unpacking libpaper1 (from .../libpaper1_1.1.24+nmu1build1_amd64.deb) ... Selecting previously unselected package libpaper-utils. Unpacking libpaper-utils (from .../libpaper-utils_1.1.24+nmu1build1_amd64.deb) ... Selecting previously unselected package luatex. Unpacking luatex (from .../luatex_0.70.1-1ubuntu1_amd64.deb) ... Selecting previously unselected package tex-common. Unpacking tex-common (from .../tex-common_2.10_all.deb) ... Selecting previously unselected package texlive-common. Unpacking texlive-common (from .../texlive-common_2009-15_all.deb) ... Selecting previously unselected package texlive-doc-base. Unpacking texlive-doc-base (from .../texlive-doc-base_2009-2_all.deb) ... Selecting previously unselected package texlive-binaries. Unpacking texlive-binaries (from .../texlive-binaries_2009-11ubuntu2_amd64.deb) ... Selecting previously unselected package texlive-base. Unpacking texlive-base (from .../texlive-base_2009-15_all.deb) ... Selecting previously unselected package texlive-latex-base. Unpacking texlive-latex-base (from .../texlive-latex-base_2009-15_all.deb) ... Setting up libpipeline1 (1.2.1-1) ... Setting up libxau6 (1:1.0.6-4) ... Setting up libxdmcp6 (1:1.1.0-4) ... Setting up libxcb1 (1.8.1-1ubuntu0.1) ... Setting up libx11-data (2:1.4.99.1-0ubuntu2) ... Setting up libx11-6 (2:1.4.99.1-0ubuntu2) ... Setting up libxext6 (2:1.3.0-3build1) ... Setting up libxml2 (2.7.8.dfsg-5.1ubuntu4.2) ... Setting up libcroco3 (0.6.5-1) ... Setting up libexpat1 (2.0.1-7.2ubuntu1.1) ... Setting up libfreetype6 (2.4.8-1ubuntu2) ... Setting up ucf (3.0025+nmu2ubuntu1) ... Setting up ttf-dejavu-core (2.33-2ubuntu1) ... Setting up fontconfig-config (2.8.0-3ubuntu9.1) ... Setting up libfontconfig1 (2.8.0-3ubuntu9.1) ... Setting up libunistring0 (0.9.3-5) ... Setting up libgettextpo0 (0.18.1.1-5ubuntu3) ... Setting up x11-common (1:7.6+12ubuntu1) ... invoke-rc.d: policy-rc.d denied execution of start. Setting up libice6 (2:1.0.7-2build1) ... Setting up libjpeg-turbo8 (1.1.90+svn733-0ubuntu4.1) ... Setting up liblcms2-2 (2.2+git20110628-2ubuntu3) ... Setting up libjpeg8 (8c-2ubuntu7) ... Setting up libtiff4 (3.9.5-2ubuntu1.2) ... Setting up libpoppler19 (0.18.4-1ubuntu2) ... Setting up libsm6 (2:1.2.0-2build1) ... Setting up libxt6 (1:1.1.1-2build1) ... Setting up libxmu6 (2:1.1.0-3) ... Setting up libxpm4 (1:3.5.9-4) ... Setting up libxaw7 (2:1.0.9-3ubuntu1) ... Setting up libmagic1 (5.09-2) ... Setting up file (5.09-2) ... Setting up mime-support (3.51-1ubuntu1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode. 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 ed (1.5-3) ... 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 autotools-dev (20120210.1ubuntu1) ... 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 (2.7.102-0ubuntu3.4) ... Setting up debhelper (9.20120115ubuntu3) ... Setting up libkpathsea5 (2009-11ubuntu2) ... Setting up libpaper1 (1.1.24+nmu1build1) ... Creating config file /etc/papersize with new version Setting up libpaper-utils (1.1.24+nmu1build1) ... Setting up luatex (0.70.1-1ubuntu1) ... texlive-base is not ready, cannot create formats Setting up tex-common (2.10) ... Creating config file /etc/texmf/texmf.d/05TeXMF.cnf with new version Creating config file /etc/texmf/texmf.d/15Plain.cnf with new version Creating config file /etc/texmf/texmf.d/45TeXinputs.cnf with new version Creating config file /etc/texmf/texmf.d/55Fonts.cnf with new version Creating config file /etc/texmf/texmf.d/65BibTeX.cnf with new version Creating config file /etc/texmf/texmf.d/75DviPS.cnf with new version Creating config file /etc/texmf/texmf.d/80DVIPDFMx.cnf with new version Creating config file /etc/texmf/texmf.d/85Misc.cnf with new version Creating config file /etc/texmf/texmf.d/90TeXDoc.cnf with new version Creating config file /etc/texmf/texmf.d/95NonPath.cnf with new version Creating config file /etc/texmf/updmap.d/00updmap.cfg with new version Creating config file /etc/texmf/texmf.cnf with new version Running mktexlsr. This may take some time... done. texlive-base is not ready, delaying updmap-sys call texlive-base is not ready, skipping fmtutil-sys --all call Setting up texlive-common (2009-15) ... Setting up texlive-doc-base (2009-2) ... Setting up texlive-binaries (2009-11ubuntu2) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode. update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode. Building format(s) --refresh. This may take some time... done. Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Setting up texlive-base (2009-15) ... Creating config file /etc/texmf/dvips/config/config.ps with new version Creating config file /etc/texmf/tex/generic/config/pdftexconfig.tex with new version Creating config file /etc/texmf/dvipdfmx/dvipdfmx.cfg with new version Creating config file /etc/texmf/xdvi/XDvi with new version Running mktexlsr. This may take some time... done. Building format(s) --all --cnffile /etc/texmf/fmt.d/10texlive-base.cnf. This may take some time... done. Processing triggers for tex-common ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building e-tex based formats --byhyphen /var/lib/texmf/tex/generic/config/language.def. This may take some time... done. Setting up texlive-latex-base (2009-15) ... Running mktexlsr. This may take some time... done. Building format(s) --all --cnffile /etc/texmf/fmt.d/10texlive-latex-base.cnf. This may take some time... done. Processing triggers for libc-bin ... ldconfig deferred processing now taking place Processing triggers for tex-common ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.15-0ubuntu10.3 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 Mon Nov 5 15:28:50 2012 UTC using DSA key ID DA9CD509 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./probabel_0.2.0.99-0ubuntu1~precise1.dsc dpkg-source: info: extracting probabel in probabel-0.2.0.99 dpkg-source: info: unpacking probabel_0.2.0.99.orig.tar.gz dpkg-source: info: unpacking probabel_0.2.0.99-0ubuntu1~precise1.debian.tar.gz 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 probabel dpkg-buildpackage: source version 0.2.0.99-0ubuntu1~precise1 dpkg-source --before-build probabel-0.2.0.99 dpkg-buildpackage: host architecture amd64 /usr/bin/fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean dh_clean debian/rules build dh build dh_testdir dh_auto_configure configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... 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(cached) mawk checking for pdflatex... pdflatex configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating examples/Makefile config.status: creating tests/Makefile config.status: creating src/config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build make[1]: Entering directory `/build/buildd/probabel-0.2.0.99' Making all in src make[2]: Entering directory `/build/buildd/probabel-0.2.0.99/src' make all-am make[3]: Entering directory `/build/buildd/probabel-0.2.0.99/src' g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLINEAR -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palinear-main.o `test -f 'main.cpp' || echo './'`main.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLINEAR -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palinear-AbstractMatrix.o `test -f 'fvlib/AbstractMatrix.cpp' || echo './'`fvlib/AbstractMatrix.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLINEAR -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palinear-CastUtils.o `test -f 'fvlib/CastUtils.cpp' || echo './'`fvlib/CastUtils.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLINEAR -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palinear-convert_util.o `test -f 'fvlib/convert_util.cpp' || echo './'`fvlib/convert_util.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLINEAR -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palinear-FileVector.o `test -f 'fvlib/FileVector.cpp' || echo './'`fvlib/FileVector.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLINEAR -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palinear-FilteredMatrix.o `test -f 'fvlib/FilteredMatrix.cpp' || echo './'`fvlib/FilteredMatrix.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLINEAR -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palinear-frutil.o `test -f 'fvlib/frutil.cpp' || echo './'`fvlib/frutil.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLINEAR -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palinear-Logger.o `test -f 'fvlib/Logger.cpp' || echo './'`fvlib/Logger.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLINEAR -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palinear-RealHandlerWrapper.o `test -f 'fvlib/RealHandlerWrapper.cpp' || echo './'`fvlib/RealHandlerWrapper.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLINEAR -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palinear-ReusableFileHandle.o `test -f 'fvlib/ReusableFileHandle.cpp' || echo './'`fvlib/ReusableFileHandle.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLINEAR -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palinear-Transposer.o `test -f 'fvlib/Transposer.cpp' || echo './'`fvlib/Transposer.cpp g++ -DLINEAR -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o palinear palinear-main.o palinear-AbstractMatrix.o palinear-CastUtils.o palinear-convert_util.o palinear-FileVector.o palinear-FilteredMatrix.o palinear-frutil.o palinear-Logger.o palinear-RealHandlerWrapper.o palinear-ReusableFileHandle.o palinear-Transposer.o g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLOGISTIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palogist-main.o `test -f 'main.cpp' || echo './'`main.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLOGISTIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palogist-AbstractMatrix.o `test -f 'fvlib/AbstractMatrix.cpp' || echo './'`fvlib/AbstractMatrix.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLOGISTIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palogist-CastUtils.o `test -f 'fvlib/CastUtils.cpp' || echo './'`fvlib/CastUtils.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLOGISTIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palogist-convert_util.o `test -f 'fvlib/convert_util.cpp' || echo './'`fvlib/convert_util.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLOGISTIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palogist-FileVector.o `test -f 'fvlib/FileVector.cpp' || echo './'`fvlib/FileVector.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLOGISTIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palogist-FilteredMatrix.o `test -f 'fvlib/FilteredMatrix.cpp' || echo './'`fvlib/FilteredMatrix.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLOGISTIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palogist-frutil.o `test -f 'fvlib/frutil.cpp' || echo './'`fvlib/frutil.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLOGISTIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palogist-Logger.o `test -f 'fvlib/Logger.cpp' || echo './'`fvlib/Logger.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLOGISTIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palogist-RealHandlerWrapper.o `test -f 'fvlib/RealHandlerWrapper.cpp' || echo './'`fvlib/RealHandlerWrapper.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLOGISTIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palogist-ReusableFileHandle.o `test -f 'fvlib/ReusableFileHandle.cpp' || echo './'`fvlib/ReusableFileHandle.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -DLOGISTIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o palogist-Transposer.o `test -f 'fvlib/Transposer.cpp' || echo './'`fvlib/Transposer.cpp g++ -DLOGISTIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o palogist palogist-main.o palogist-AbstractMatrix.o palogist-CastUtils.o palogist-convert_util.o palogist-FileVector.o palogist-FilteredMatrix.o palogist-frutil.o palogist-Logger.o palogist-RealHandlerWrapper.o palogist-ReusableFileHandle.o palogist-Transposer.o g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o extract-snp.o extract-snp.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o AbstractMatrix.o `test -f 'fvlib/AbstractMatrix.cpp' || echo './'`fvlib/AbstractMatrix.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o CastUtils.o `test -f 'fvlib/CastUtils.cpp' || echo './'`fvlib/CastUtils.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o convert_util.o `test -f 'fvlib/convert_util.cpp' || echo './'`fvlib/convert_util.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o FileVector.o `test -f 'fvlib/FileVector.cpp' || echo './'`fvlib/FileVector.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o FilteredMatrix.o `test -f 'fvlib/FilteredMatrix.cpp' || echo './'`fvlib/FilteredMatrix.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o frutil.o `test -f 'fvlib/frutil.cpp' || echo './'`fvlib/frutil.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o Logger.o `test -f 'fvlib/Logger.cpp' || echo './'`fvlib/Logger.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o RealHandlerWrapper.o `test -f 'fvlib/RealHandlerWrapper.cpp' || echo './'`fvlib/RealHandlerWrapper.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o ReusableFileHandle.o `test -f 'fvlib/ReusableFileHandle.cpp' || echo './'`fvlib/ReusableFileHandle.cpp g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -c -o Transposer.o `test -f 'fvlib/Transposer.cpp' || echo './'`fvlib/Transposer.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o extract-snp extract-snp.o AbstractMatrix.o CastUtils.o convert_util.o FileVector.o FilteredMatrix.o frutil.o Logger.o RealHandlerWrapper.o ReusableFileHandle.o Transposer.o make[3]: Leaving directory `/build/buildd/probabel-0.2.0.99/src' make[2]: Leaving directory `/build/buildd/probabel-0.2.0.99/src' Making all in doc make[2]: Entering directory `/build/buildd/probabel-0.2.0.99/doc' === Making ProbABEL_manual.aux file === pdflatex ./ProbABEL_manual.tex This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) entering extended mode (./ProbABEL_manual.tex LaTeX2e <2009/09/24> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, loaded. (/usr/share/texmf-texlive/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/size12.clo)) (/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty) (/usr/share/texmf-texlive/tex/latex/ltxmisc/titleref.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texmf-texlive/tex/latex/amsmath/amstext.sty (/usr/share/texmf-texlive/tex/latex/amsmath/amsgen.sty)) (/usr/share/texmf-texlive/tex/latex/amsmath/amsbsy.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amsopn.sty)) (/usr/share/texmf-texlive/tex/latex/base/makeidx.sty) (/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty (/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty)) (/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty)) (/usr/share/texmf-texlive/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty)) Implicit mode ON; LaTeX internals redefined (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/ifluatex.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ltxcmds.sty)))) (/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty)) *hyperref using driver hpdftex* (/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def) (/usr/share/texmf-texlive/tex/latex/oberdiek/hypcap.sty) Writing index file ProbABEL_manual.idx No file ProbABEL_manual.aux. (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) [1{/var/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] Overfull \hbox (1.47583pt too wide) in paragraph at lines 100--105 \OT1/cmtt/m/n/12 ProbABEL \OT1/cmr/m/n/12 takes three files as in-put: a file c on-tain-ing SNP in-for-ma-tion (e.g. the [2] [3] LaTeX Warning: Reference `sec:runanalysis' on page 4 undefined on input line 17 7. Overfull \hbox (12.66078pt too wide) in paragraph at lines 201--208 []\OT1/cmr/m/n/12 In the case of lin-ear or lo-gis-tic re-gres-sion (pro-grams \OT1/cmtt/m/n/12 palinear \OT1/cmr/m/n/12 and \OT1/cmtt/m/n/12 palogist\OT1/cmr /m/n/12 , [4] [5] [6] Overfull \hbox (5.17282pt too wide) in paragraph at lines 285--290 []\OT1/cmr/m/n/12 There are in to-tal 11 com-mand line op-tions you can spec-if y to the \OT1/cmtt/m/n/12 ProbABEL Overfull \hbox (116.35025pt too wide) in paragraph at lines 292--292 []\OT1/cmtt/m/n/12 ProbABEL v. 0.2.0 (C) Yurii Aulchenko, Lennart C. Karssen, M aksim Struchalin, EMCR[] Overfull \hbox (54.60022pt too wide) in paragraph at lines 302--302 [] \OT1/cmtt/m/n/12 --out : [optional] output file name (default is regress ion.out.txt)[] Overfull \hbox (11.3752pt too wide) in paragraph at lines 303--303 [] \OT1/cmtt/m/n/12 --skipd : [optional] how many columns to skip in the pred ictor[] Overfull \hbox (5.2002pt too wide) in paragraph at lines 305--305 [] \OT1/cmtt/m/n/12 --ntraits : [optional] how many traits are analysed (defaul t 1)[] Overfull \hbox (48.42522pt too wide) in paragraph at lines 308--308 [] \OT1/cmtt/m/n/12 --separat : [optional] character to separate fields (defaul t is space)[] Overfull \hbox (11.3752pt too wide) in paragraph at lines 311--311 [] \OT1/cmtt/m/n/12 --allcov : report estimates for all covariates (large outp uts!)[] Overfull \hbox (246.02531pt too wide) in paragraph at lines 312--312 [] \OT1/cmtt/m/n/12 --interaction: Which covariate to use for interaction with SNP analysis (default is no interaction, 0)[] Overfull \hbox (338.65036pt too wide) in paragraph at lines 313--313 [] \OT1/cmtt/m/n/12 --interaction_only: like previous but without covariate act ing in interaction with SNP (default is no interaction, 0)[] Overfull \hbox (709.15054pt too wide) in paragraph at lines 314--314 [] \OT1/cmtt/m/n/12 --mmscore : score test in samples of related individuals. F ile with inverse of variance-covariance matrix (for palinear) or inverse correl ation (for palogist) as input parameter[] Overfull \hbox (73.12523pt too wide) in paragraph at lines 315--315 [] \OT1/cmtt/m/n/12 --robust : report robust (aka sandwich, aka Hubert-White) standard errors[] [7] LaTeX Warning: Reference `ssec:dosein' on page 8 undefined on input line 329. LaTeX Warning: Reference `ssec:phenoin' on page 8 undefined on input line 331. LaTeX Warning: Reference `ssec:infoin' on page 8 undefined on input line 333. Overfull \hbox (18.38104pt too wide) in paragraph at lines 327--334 []\OT1/cmr/m/n/12 These op-tions are \OT1/cmtt/m/n/12 --dose \OT1/cmr/m/n/12 (o r \OT1/cmtt/m/n/12 -d\OT1/cmr/m/n/12 ), spec-i-fy-ing the ge-nomic pre-dic-tor/ MLDOSE Overfull \hbox (11.3752pt too wide) in paragraph at lines 338--338 []\OT1/cmtt/m/n/12 user@server:~/ProbABEL/examples/$ ../bin/palinear -p height. txt \[] Overfull \hbox (42.25021pt too wide) in paragraph at lines 346--346 []\OT1/cmtt/m/n/12 user@server:~/ProbABEL/examples/$ ../bin/palogist -p logist_ data.txt \[] Overfull \hbox (29.9002pt too wide) in paragraph at lines 357--357 []\OT1/cmtt/m/n/12 user@server:~/ProbABEL/examples/$ ../bin/pacoxph -p coxph_da ta.txt \[] Overfull \hbox (11.3752pt too wide) in paragraph at lines 369--369 []\OT1/cmtt/m/n/12 user@server:~/ProbABEL/examples/$ ../bin/palinear -p height. txt \[] [8] LaTeX Warning: Reference `sec:methodology' on page 9 undefined on input line 38 7. Overfull \hbox (42.25021pt too wide) in paragraph at lines 406--406 [] \OT1/cmtt/m/n/12 h2.obj$InvSigma * h2.obj$h2an$estimate[length(h2.obj$h2an$ estimate)][] Overfull \hbox (43.5931pt too wide) in paragraph at lines 429--447 \OT1/cmr/m/n/12 func-tions. To start us-ing it the con-fig-u-ra-tion file \OT1/ cmtt/m/n/12 etc/probabel[]config.cfg.example [9] [10] [11] [12] Overfull \hbox (8.42549pt too wide) in paragraph at lines 598--600 []\OT1/cmr/m/n/12 Secondly, the Wald test can be used; for that the in-verse va riance-covariance [13] [14] LaTeX Warning: Reference `expectation' on page 15 undefined on input line 694. LaTeX Warning: Reference `kinship' on page 15 undefined on input line 706. [15] [16] [17] No file ProbABEL_manual.ind. [18] (./ProbABEL_manual.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on ProbABEL_manual.pdf (18 pages, 273049 bytes). Transcript written on ProbABEL_manual.log. diff: .btmp: No such file or directory === Making PDF === pdflatex ./ProbABEL_manual.tex This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) entering extended mode (./ProbABEL_manual.tex LaTeX2e <2009/09/24> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, loaded. (/usr/share/texmf-texlive/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/size12.clo)) (/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty) (/usr/share/texmf-texlive/tex/latex/ltxmisc/titleref.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texmf-texlive/tex/latex/amsmath/amstext.sty (/usr/share/texmf-texlive/tex/latex/amsmath/amsgen.sty)) (/usr/share/texmf-texlive/tex/latex/amsmath/amsbsy.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amsopn.sty)) (/usr/share/texmf-texlive/tex/latex/base/makeidx.sty) (/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty (/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty)) (/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty)) (/usr/share/texmf-texlive/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty)) Implicit mode ON; LaTeX internals redefined (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/ifluatex.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ltxcmds.sty)))) (/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty)) *hyperref using driver hpdftex* (/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def) (/usr/share/texmf-texlive/tex/latex/oberdiek/hypcap.sty) Writing index file ProbABEL_manual.idx (./ProbABEL_manual.aux) (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (./ProbABEL_manual.out) (./ProbABEL_manual.out) (./ProbABEL_manual.toc [1{/var/ lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]) [2] Overfull \hbox (1.47583pt too wide) in paragraph at lines 100--105 \OT1/cmtt/m/n/12 ProbABEL \OT1/cmr/m/n/12 takes three files as in-put: a file c on-tain-ing SNP in-for-ma-tion (e.g. the [3] [4] Overfull \hbox (12.66078pt too wide) in paragraph at lines 201--208 []\OT1/cmr/m/n/12 In the case of lin-ear or lo-gis-tic re-gres-sion (pro-grams \OT1/cmtt/m/n/12 palinear \OT1/cmr/m/n/12 and \OT1/cmtt/m/n/12 palogist\OT1/cmr /m/n/12 , [5] [6] Overfull \hbox (5.17282pt too wide) in paragraph at lines 285--290 []\OT1/cmr/m/n/12 There are in to-tal 11 com-mand line op-tions you can spec-if y to the \OT1/cmtt/m/n/12 ProbABEL [7] Overfull \hbox (116.35025pt too wide) in paragraph at lines 292--292 []\OT1/cmtt/m/n/12 ProbABEL v. 0.2.0 (C) Yurii Aulchenko, Lennart C. Karssen, M aksim Struchalin, EMCR[] Overfull \hbox (54.60022pt too wide) in paragraph at lines 302--302 [] \OT1/cmtt/m/n/12 --out : [optional] output file name (default is regress ion.out.txt)[] Overfull \hbox (11.3752pt too wide) in paragraph at lines 303--303 [] \OT1/cmtt/m/n/12 --skipd : [optional] how many columns to skip in the pred ictor[] Overfull \hbox (5.2002pt too wide) in paragraph at lines 305--305 [] \OT1/cmtt/m/n/12 --ntraits : [optional] how many traits are analysed (defaul t 1)[] Overfull \hbox (48.42522pt too wide) in paragraph at lines 308--308 [] \OT1/cmtt/m/n/12 --separat : [optional] character to separate fields (defaul t is space)[] Overfull \hbox (11.3752pt too wide) in paragraph at lines 311--311 [] \OT1/cmtt/m/n/12 --allcov : report estimates for all covariates (large outp uts!)[] Overfull \hbox (246.02531pt too wide) in paragraph at lines 312--312 [] \OT1/cmtt/m/n/12 --interaction: Which covariate to use for interaction with SNP analysis (default is no interaction, 0)[] Overfull \hbox (338.65036pt too wide) in paragraph at lines 313--313 [] \OT1/cmtt/m/n/12 --interaction_only: like previous but without covariate act ing in interaction with SNP (default is no interaction, 0)[] Overfull \hbox (709.15054pt too wide) in paragraph at lines 314--314 [] \OT1/cmtt/m/n/12 --mmscore : score test in samples of related individuals. F ile with inverse of variance-covariance matrix (for palinear) or inverse correl ation (for palogist) as input parameter[] Overfull \hbox (73.12523pt too wide) in paragraph at lines 315--315 [] \OT1/cmtt/m/n/12 --robust : report robust (aka sandwich, aka Hubert-White) standard errors[] Overfull \hbox (18.38104pt too wide) in paragraph at lines 327--334 []\OT1/cmr/m/n/12 These op-tions are \OT1/cmtt/m/n/12 --dose \OT1/cmr/m/n/12 (o r \OT1/cmtt/m/n/12 -d\OT1/cmr/m/n/12 ), spec-i-fy-ing the ge-nomic pre-dic-tor/ MLDOSE [8] Overfull \hbox (11.3752pt too wide) in paragraph at lines 338--338 []\OT1/cmtt/m/n/12 user@server:~/ProbABEL/examples/$ ../bin/palinear -p height. txt \[] Overfull \hbox (42.25021pt too wide) in paragraph at lines 346--346 []\OT1/cmtt/m/n/12 user@server:~/ProbABEL/examples/$ ../bin/palogist -p logist_ data.txt \[] Overfull \hbox (29.9002pt too wide) in paragraph at lines 357--357 []\OT1/cmtt/m/n/12 user@server:~/ProbABEL/examples/$ ../bin/pacoxph -p coxph_da ta.txt \[] Overfull \hbox (11.3752pt too wide) in paragraph at lines 369--369 []\OT1/cmtt/m/n/12 user@server:~/ProbABEL/examples/$ ../bin/palinear -p height. txt \[] [9] Overfull \hbox (42.25021pt too wide) in paragraph at lines 406--406 [] \OT1/cmtt/m/n/12 h2.obj$InvSigma * h2.obj$h2an$estimate[length(h2.obj$h2an$ estimate)][] Overfull \hbox (43.5931pt too wide) in paragraph at lines 429--447 \OT1/cmr/m/n/12 func-tions. To start us-ing it the con-fig-u-ra-tion file \OT1/ cmtt/m/n/12 etc/probabel[]config.cfg.example [10] [11] [12] Overfull \hbox (8.42549pt too wide) in paragraph at lines 598--600 []\OT1/cmr/m/n/12 Secondly, the Wald test can be used; for that the in-verse va riance-covariance [13] [14] [15] [16] [17] No file ProbABEL_manual.ind. [18] (./ProbABEL_manual.aux) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on ProbABEL_manual.pdf (18 pages, 285635 bytes). Transcript written on ProbABEL_manual.log. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ** Re-running LaTeX ** This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) entering extended mode (./ProbABEL_manual.tex LaTeX2e <2009/09/24> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, loaded. (/usr/share/texmf-texlive/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/size12.clo)) (/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty) (/usr/share/texmf-texlive/tex/latex/ltxmisc/titleref.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texmf-texlive/tex/latex/amsmath/amstext.sty (/usr/share/texmf-texlive/tex/latex/amsmath/amsgen.sty)) (/usr/share/texmf-texlive/tex/latex/amsmath/amsbsy.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amsopn.sty)) (/usr/share/texmf-texlive/tex/latex/base/makeidx.sty) (/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty (/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty)) (/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty)) (/usr/share/texmf-texlive/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty)) Implicit mode ON; LaTeX internals redefined (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/ifluatex.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ltxcmds.sty)))) (/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty)) *hyperref using driver hpdftex* (/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def) (/usr/share/texmf-texlive/tex/latex/oberdiek/hypcap.sty) Writing index file ProbABEL_manual.idx (./ProbABEL_manual.aux) (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (./ProbABEL_manual.out) (./ProbABEL_manual.out) (./ProbABEL_manual.toc [1{/var/ lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]) [2] Overfull \hbox (1.47583pt too wide) in paragraph at lines 100--105 \OT1/cmtt/m/n/12 ProbABEL \OT1/cmr/m/n/12 takes three files as in-put: a file c on-tain-ing SNP in-for-ma-tion (e.g. the [3] [4] Overfull \hbox (12.66078pt too wide) in paragraph at lines 201--208 []\OT1/cmr/m/n/12 In the case of lin-ear or lo-gis-tic re-gres-sion (pro-grams \OT1/cmtt/m/n/12 palinear \OT1/cmr/m/n/12 and \OT1/cmtt/m/n/12 palogist\OT1/cmr /m/n/12 , [5] [6] Overfull \hbox (5.17282pt too wide) in paragraph at lines 285--290 []\OT1/cmr/m/n/12 There are in to-tal 11 com-mand line op-tions you can spec-if y to the \OT1/cmtt/m/n/12 ProbABEL [7] Overfull \hbox (116.35025pt too wide) in paragraph at lines 292--292 []\OT1/cmtt/m/n/12 ProbABEL v. 0.2.0 (C) Yurii Aulchenko, Lennart C. Karssen, M aksim Struchalin, EMCR[] Overfull \hbox (54.60022pt too wide) in paragraph at lines 302--302 [] \OT1/cmtt/m/n/12 --out : [optional] output file name (default is regress ion.out.txt)[] Overfull \hbox (11.3752pt too wide) in paragraph at lines 303--303 [] \OT1/cmtt/m/n/12 --skipd : [optional] how many columns to skip in the pred ictor[] Overfull \hbox (5.2002pt too wide) in paragraph at lines 305--305 [] \OT1/cmtt/m/n/12 --ntraits : [optional] how many traits are analysed (defaul t 1)[] Overfull \hbox (48.42522pt too wide) in paragraph at lines 308--308 [] \OT1/cmtt/m/n/12 --separat : [optional] character to separate fields (defaul t is space)[] Overfull \hbox (11.3752pt too wide) in paragraph at lines 311--311 [] \OT1/cmtt/m/n/12 --allcov : report estimates for all covariates (large outp uts!)[] Overfull \hbox (246.02531pt too wide) in paragraph at lines 312--312 [] \OT1/cmtt/m/n/12 --interaction: Which covariate to use for interaction with SNP analysis (default is no interaction, 0)[] Overfull \hbox (338.65036pt too wide) in paragraph at lines 313--313 [] \OT1/cmtt/m/n/12 --interaction_only: like previous but without covariate act ing in interaction with SNP (default is no interaction, 0)[] Overfull \hbox (709.15054pt too wide) in paragraph at lines 314--314 [] \OT1/cmtt/m/n/12 --mmscore : score test in samples of related individuals. F ile with inverse of variance-covariance matrix (for palinear) or inverse correl ation (for palogist) as input parameter[] Overfull \hbox (73.12523pt too wide) in paragraph at lines 315--315 [] \OT1/cmtt/m/n/12 --robust : report robust (aka sandwich, aka Hubert-White) standard errors[] Overfull \hbox (18.38104pt too wide) in paragraph at lines 327--334 []\OT1/cmr/m/n/12 These op-tions are \OT1/cmtt/m/n/12 --dose \OT1/cmr/m/n/12 (o r \OT1/cmtt/m/n/12 -d\OT1/cmr/m/n/12 ), spec-i-fy-ing the ge-nomic pre-dic-tor/ MLDOSE [8] Overfull \hbox (11.3752pt too wide) in paragraph at lines 338--338 []\OT1/cmtt/m/n/12 user@server:~/ProbABEL/examples/$ ../bin/palinear -p height. txt \[] Overfull \hbox (42.25021pt too wide) in paragraph at lines 346--346 []\OT1/cmtt/m/n/12 user@server:~/ProbABEL/examples/$ ../bin/palogist -p logist_ data.txt \[] Overfull \hbox (29.9002pt too wide) in paragraph at lines 357--357 []\OT1/cmtt/m/n/12 user@server:~/ProbABEL/examples/$ ../bin/pacoxph -p coxph_da ta.txt \[] Overfull \hbox (11.3752pt too wide) in paragraph at lines 369--369 []\OT1/cmtt/m/n/12 user@server:~/ProbABEL/examples/$ ../bin/palinear -p height. txt \[] [9] Overfull \hbox (42.25021pt too wide) in paragraph at lines 406--406 [] \OT1/cmtt/m/n/12 h2.obj$InvSigma * h2.obj$h2an$estimate[length(h2.obj$h2an$ estimate)][] Overfull \hbox (43.5931pt too wide) in paragraph at lines 429--447 \OT1/cmr/m/n/12 func-tions. To start us-ing it the con-fig-u-ra-tion file \OT1/ cmtt/m/n/12 etc/probabel[]config.cfg.example [10] [11] [12] Overfull \hbox (8.42549pt too wide) in paragraph at lines 598--600 []\OT1/cmr/m/n/12 Secondly, the Wald test can be used; for that the in-verse va riance-covariance [13] [14] [15] [16] [17] No file ProbABEL_manual.ind. [18] (./ProbABEL_manual.aux) ) (see the transcript file for additional information) Output written on ProbABEL_manual.pdf (18 pages, 285493 bytes). Transcript written on ProbABEL_manual.log. === Making index === makeindex ProbABEL_manual This is makeindex, version 2.15 [TeX Live 2009] (kpathsea + Thai support). Scanning input file ProbABEL_manual.idx....done (3 entries accepted, 0 rejected). Sorting entries....done (4 comparisons). Generating output file ProbABEL_manual.ind....done (14 lines written, 0 warnings). Output written in ProbABEL_manual.ind. Transcript written in ProbABEL_manual.ilg. === Making final PDF === pdflatex ./ProbABEL_manual.tex This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) entering extended mode (./ProbABEL_manual.tex LaTeX2e <2009/09/24> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, loaded. (/usr/share/texmf-texlive/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/size12.clo)) (/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty) (/usr/share/texmf-texlive/tex/latex/ltxmisc/titleref.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texmf-texlive/tex/latex/amsmath/amstext.sty (/usr/share/texmf-texlive/tex/latex/amsmath/amsgen.sty)) (/usr/share/texmf-texlive/tex/latex/amsmath/amsbsy.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amsopn.sty)) (/usr/share/texmf-texlive/tex/latex/base/makeidx.sty) (/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty (/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty)) (/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty)) (/usr/share/texmf-texlive/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty)) Implicit mode ON; LaTeX internals redefined (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/ifluatex.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ltxcmds.sty)))) (/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty)) *hyperref using driver hpdftex* (/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def) (/usr/share/texmf-texlive/tex/latex/oberdiek/hypcap.sty) Writing index file ProbABEL_manual.idx (./ProbABEL_manual.aux) (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (./ProbABEL_manual.out) (./ProbABEL_manual.out) (./ProbABEL_manual.toc [1{/var/ lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]) [2] Overfull \hbox (1.47583pt too wide) in paragraph at lines 100--105 \OT1/cmtt/m/n/12 ProbABEL \OT1/cmr/m/n/12 takes three files as in-put: a file c on-tain-ing SNP in-for-ma-tion (e.g. the [3] [4] Overfull \hbox (12.66078pt too wide) in paragraph at lines 201--208 []\OT1/cmr/m/n/12 In the case of lin-ear or lo-gis-tic re-gres-sion (pro-grams \OT1/cmtt/m/n/12 palinear \OT1/cmr/m/n/12 and \OT1/cmtt/m/n/12 palogist\OT1/cmr /m/n/12 , [5] [6] Overfull \hbox (5.17282pt too wide) in paragraph at lines 285--290 []\OT1/cmr/m/n/12 There are in to-tal 11 com-mand line op-tions you can spec-if y to the \OT1/cmtt/m/n/12 ProbABEL [7] Overfull \hbox (116.35025pt too wide) in paragraph at lines 292--292 []\OT1/cmtt/m/n/12 ProbABEL v. 0.2.0 (C) Yurii Aulchenko, Lennart C. Karssen, M aksim Struchalin, EMCR[] Overfull \hbox (54.60022pt too wide) in paragraph at lines 302--302 [] \OT1/cmtt/m/n/12 --out : [optional] output file name (default is regress ion.out.txt)[] Overfull \hbox (11.3752pt too wide) in paragraph at lines 303--303 [] \OT1/cmtt/m/n/12 --skipd : [optional] how many columns to skip in the pred ictor[] Overfull \hbox (5.2002pt too wide) in paragraph at lines 305--305 [] \OT1/cmtt/m/n/12 --ntraits : [optional] how many traits are analysed (defaul t 1)[] Overfull \hbox (48.42522pt too wide) in paragraph at lines 308--308 [] \OT1/cmtt/m/n/12 --separat : [optional] character to separate fields (defaul t is space)[] Overfull \hbox (11.3752pt too wide) in paragraph at lines 311--311 [] \OT1/cmtt/m/n/12 --allcov : report estimates for all covariates (large outp uts!)[] Overfull \hbox (246.02531pt too wide) in paragraph at lines 312--312 [] \OT1/cmtt/m/n/12 --interaction: Which covariate to use for interaction with SNP analysis (default is no interaction, 0)[] Overfull \hbox (338.65036pt too wide) in paragraph at lines 313--313 [] \OT1/cmtt/m/n/12 --interaction_only: like previous but without covariate act ing in interaction with SNP (default is no interaction, 0)[] Overfull \hbox (709.15054pt too wide) in paragraph at lines 314--314 [] \OT1/cmtt/m/n/12 --mmscore : score test in samples of related individuals. F ile with inverse of variance-covariance matrix (for palinear) or inverse correl ation (for palogist) as input parameter[] Overfull \hbox (73.12523pt too wide) in paragraph at lines 315--315 [] \OT1/cmtt/m/n/12 --robust : report robust (aka sandwich, aka Hubert-White) standard errors[] Overfull \hbox (18.38104pt too wide) in paragraph at lines 327--334 []\OT1/cmr/m/n/12 These op-tions are \OT1/cmtt/m/n/12 --dose \OT1/cmr/m/n/12 (o r \OT1/cmtt/m/n/12 -d\OT1/cmr/m/n/12 ), spec-i-fy-ing the ge-nomic pre-dic-tor/ MLDOSE [8] Overfull \hbox (11.3752pt too wide) in paragraph at lines 338--338 []\OT1/cmtt/m/n/12 user@server:~/ProbABEL/examples/$ ../bin/palinear -p height. txt \[] Overfull \hbox (42.25021pt too wide) in paragraph at lines 346--346 []\OT1/cmtt/m/n/12 user@server:~/ProbABEL/examples/$ ../bin/palogist -p logist_ data.txt \[] Overfull \hbox (29.9002pt too wide) in paragraph at lines 357--357 []\OT1/cmtt/m/n/12 user@server:~/ProbABEL/examples/$ ../bin/pacoxph -p coxph_da ta.txt \[] Overfull \hbox (11.3752pt too wide) in paragraph at lines 369--369 []\OT1/cmtt/m/n/12 user@server:~/ProbABEL/examples/$ ../bin/palinear -p height. txt \[] [9] Overfull \hbox (42.25021pt too wide) in paragraph at lines 406--406 [] \OT1/cmtt/m/n/12 h2.obj$InvSigma * h2.obj$h2an$estimate[length(h2.obj$h2an$ estimate)][] Overfull \hbox (43.5931pt too wide) in paragraph at lines 429--447 \OT1/cmr/m/n/12 func-tions. To start us-ing it the con-fig-u-ra-tion file \OT1/ cmtt/m/n/12 etc/probabel[]config.cfg.example [10] [11] [12] Overfull \hbox (8.42549pt too wide) in paragraph at lines 598--600 []\OT1/cmr/m/n/12 Secondly, the Wald test can be used; for that the in-verse va riance-covariance [13] [14] [15] [16] [17] (./ProbABEL_manual.ind [18] [19]) (./ProbABEL_manual.aux) ) (see the transcript file for additional information) Output written on ProbABEL_manual.pdf (19 pages, 286983 bytes). Transcript written on ProbABEL_manual.log. rm ProbABEL_manual.aux make[2]: Leaving directory `/build/buildd/probabel-0.2.0.99/doc' Making all in examples make[2]: Entering directory `/build/buildd/probabel-0.2.0.99/examples' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/build/buildd/probabel-0.2.0.99/examples' Making all in tests make[2]: Entering directory `/build/buildd/probabel-0.2.0.99/tests' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/build/buildd/probabel-0.2.0.99/tests' make[2]: Entering directory `/build/buildd/probabel-0.2.0.99' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/build/buildd/probabel-0.2.0.99' make[1]: Leaving directory `/build/buildd/probabel-0.2.0.99' dh_auto_test make[1]: Entering directory `/build/buildd/probabel-0.2.0.99' Making check in src make[2]: Entering directory `/build/buildd/probabel-0.2.0.99/src' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/probabel-0.2.0.99/src' Making check in doc make[2]: Entering directory `/build/buildd/probabel-0.2.0.99/doc' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/probabel-0.2.0.99/doc' Making check in examples make[2]: Entering directory `/build/buildd/probabel-0.2.0.99/examples' make example_bt.sh example_qt.sh example_mms.sh make[3]: Entering directory `/build/buildd/probabel-0.2.0.99/examples' make[3]: Nothing to be done for `example_bt.sh'. make[3]: Nothing to be done for `example_qt.sh'. make[3]: Nothing to be done for `example_mms.sh'. make[3]: Leaving directory `/build/buildd/probabel-0.2.0.99/examples' make check-TESTS make[3]: Entering directory `/build/buildd/probabel-0.2.0.99/examples' analysing BT ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./logist_data.txt --info = ./test.mlinfo --dose = ./test.mldose --ntraits = 1 --ngpreds = 1 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = logist --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = OFF Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Logistic model: ( chd ) ~ mu + sex + age + othercov + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./logist_data.txt --info = ./test.mlinfo --dose = ./test.dose.fvi (using FVF data) --ntraits = 1 --ngpreds = 1 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = logist_fv --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = OFF Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Logistic model: ( chd ) ~ mu + sex + age + othercov + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done BT check: dose vs. dose_fv ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./logist_data.txt --info = ./test.mlinfo --dose = ./test.mlprob --ntraits = 1 --ngpreds = 2 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = logist_prob --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = OFF Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Logistic model: ( chd ) ~ mu + sex + age + othercov + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./logist_data.txt --info = ./test.mlinfo --dose = ./test.prob.fvi (using FVF data) --ntraits = 1 --ngpreds = 2 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = logist_prob_fv --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = OFF Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Logistic model: ( chd ) ~ mu + sex + age + othercov + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done BT check: prob vs. prob_fv PASS: example_bt.sh analysing QT base analysis ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./height.txt --info = ./test.mlinfo --dose = ./test.mldose --ntraits = 1 --ngpreds = 1 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = height_base --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = OFF Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./height.txt --info = ./test.mlinfo --dose = ./test.dose.fvi (using FVF data) --ntraits = 1 --ngpreds = 1 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = height_base_fv --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = OFF Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done QT check: dose vs. dose_fv Option --allcov ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./height.txt --info = ./test.mlinfo --dose = ./test.mldose --ntraits = 1 --ngpreds = 1 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = height_allcov --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = ON --robust = OFF Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./height.txt --info = ./test.mlinfo --dose = ./test.dose.fvi (using FVF data) --ntraits = 1 --ngpreds = 1 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = height_allcov_fv --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = ON --robust = OFF Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done QT check: allcov: dose vs. dose_fv Option --interaction=1 ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./height.txt --info = ./test.mlinfo --dose = ./test.mldose --ntraits = 1 --ngpreds = 1 --interaction = 1 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = height_int1 --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = OFF Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 + sex*SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./height.txt --info = ./test.mlinfo --dose = ./test.dose.fvi (using FVF data) --ntraits = 1 --ngpreds = 1 --interaction = 1 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = height_int1_fv --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = OFF Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 + sex*SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done QT check: interactions: dose vs. dose_fv Option --robust ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./height.txt --info = ./test.mlinfo --dose = ./test.mldose --ntraits = 1 --ngpreds = 1 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = height_robust --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = ON Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./height.txt --info = ./test.mlinfo --dose = ./test.dose.fvi (using FVF data) --ntraits = 1 --ngpreds = 1 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = height_robust_fv --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = ON Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done QT check: robust: dose vs. dose_fv Option --robust --interaction=1 ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./height.txt --info = ./test.mlinfo --dose = ./test.mldose --ntraits = 1 --ngpreds = 1 --interaction = 1 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = height_robust_int1 --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = ON Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 + sex*SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./height.txt --info = ./test.mlinfo --dose = ./test.dose.fvi (using FVF data) --ntraits = 1 --ngpreds = 1 --interaction = 1 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = height_robust_int1_fv --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = ON Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 + sex*SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done QT check: robust & interaction: dose vs. dose_fv Option --ngp=2, mlprob file ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./height.txt --info = ./test.mlinfo --dose = ./test.mlprob --ntraits = 1 --ngpreds = 2 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = height_ngp2 --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = OFF Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./height.txt --info = ./test.mlinfo --dose = ./test.prob.fvi (using FVF data) --ntraits = 1 --ngpreds = 2 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = height_ngp2_fv --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = OFF Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done QT check: prob vs. prob_fv Option --ngp=2 --allcov ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./height.txt --info = ./test.mlinfo --dose = ./test.mlprob --ntraits = 1 --ngpreds = 2 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = height_ngp2_allcov --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = ON --robust = OFF Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./height.txt --info = ./test.mlinfo --dose = ./test.prob.fvi (using FVF data) --ntraits = 1 --ngpreds = 2 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = height_ngp2_allcov_fv --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = ON --robust = OFF Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done Option --ngp=2 --interaction=1 ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./height.txt --info = ./test.mlinfo --dose = ./test.mlprob --ntraits = 1 --ngpreds = 2 --interaction = 1 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = height_ngp2_int1 --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = OFF Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 + sex*SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./height.txt --info = ./test.mlinfo --dose = ./test.prob.fvi (using FVF data) --ntraits = 1 --ngpreds = 2 --interaction = 1 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = height_ngp2_int1_fv --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = OFF Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 + sex*SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done Option --ngp=2 --robust ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./height.txt --info = ./test.mlinfo --dose = ./test.mlprob --ntraits = 1 --ngpreds = 2 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = height_ngp2_robust --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = ON Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./height.txt --info = ./test.mlinfo --dose = ./test.prob.fvi (using FVF data) --ntraits = 1 --ngpreds = 2 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = height_ngp2_robust_fv --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = ON Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done Option --ngp=2 --robust --interaction=1 ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./height.txt --info = ./test.mlinfo --dose = ./test.mlprob --ntraits = 1 --ngpreds = 2 --interaction = 1 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = height_ngp2_robust_int1 --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = ON Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 + sex*SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./height.txt --info = ./test.mlinfo --dose = ./test.prob.fvi (using FVF data) --ntraits = 1 --ngpreds = 2 --interaction = 1 --interaction_only = 0 --mmscore = not in output --map = ./test.map --nids = estimated from data --chrom = 19 --out = height_ngp2_robust_int1_fv --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = ON Number of SNPs = 5 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 + sex*SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done PASS: example_qt.sh analysis using MMSCORE ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./mmscore_pheno.PHE --info = ./mmscore_gen.mlinfo --dose = ./mmscore_gen.mldose --ntraits = 1 --ngpreds = 1 --interaction = 0 --interaction_only = 0 --mmscore = ./mmscore_InvSigma_aj.sex.age.dat --map = not in output --nids = estimated from data --chrom = not in output --out = mmscore --skipd = 2 --separat = "," --score = OFF --nohead = OFF --allcov = OFF --robust = OFF Number of SNPs = 5 Actual number of people in phenofile = 500; using all of these Linear model: ( height_residuals ) ~ mu + + SNP_A1 you are running mmscore... Reading data ... loaded InvSigma ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./mmscore_pheno.PHE --info = ./mmscore_gen.mlinfo --dose = ./mmscore_gen.dose.fvi (using FVF data) --ntraits = 1 --ngpreds = 1 --interaction = 0 --interaction_only = 0 --mmscore = ./mmscore_InvSigma_aj.sex.age.dat --map = not in output --nids = estimated from data --chrom = not in output --out = mmscore_fv --skipd = 2 --separat = "," --score = OFF --nohead = OFF --allcov = OFF --robust = OFF Number of SNPs = 5 Actual number of people in phenofile = 500; using all of these Linear model: ( height_residuals ) ~ mu + + SNP_A1 you are running mmscore... Reading data ... loaded InvSigma ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done mmscore check: dose vs. dose_fv ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./mmscore_pheno.PHE --info = ./mmscore_gen.mlinfo --dose = ./mmscore_gen.mlprob --ntraits = 1 --ngpreds = 2 --interaction = 0 --interaction_only = 0 --mmscore = ./mmscore_InvSigma_aj.sex.age.dat --map = not in output --nids = estimated from data --chrom = not in output --out = mmscore_prob --skipd = 2 --separat = "," --score = OFF --nohead = OFF --allcov = OFF --robust = OFF Number of SNPs = 5 Actual number of people in phenofile = 500; using all of these Linear model: ( height_residuals ) ~ mu + + SNP_A1 you are running mmscore... Reading data ... loaded InvSigma ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = ./mmscore_pheno.PHE --info = ./mmscore_gen.mlinfo --dose = ./mmscore_gen.prob.fvi (using FVF data) --ntraits = 1 --ngpreds = 2 --interaction = 0 --interaction_only = 0 --mmscore = ./mmscore_InvSigma_aj.sex.age.dat --map = not in output --nids = estimated from data --chrom = not in output --out = mmscore_prob_fv --skipd = 2 --separat = "," --score = OFF --nohead = OFF --allcov = OFF --robust = OFF Number of SNPs = 5 Actual number of people in phenofile = 500; using all of these Linear model: ( height_residuals ) ~ mu + + SNP_A1 you are running mmscore... Reading data ... loaded InvSigma ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done mmscore check: prob vs. prob_fv PASS: example_mms.sh ================== All 3 tests passed ================== make[3]: Leaving directory `/build/buildd/probabel-0.2.0.99/examples' make[2]: Leaving directory `/build/buildd/probabel-0.2.0.99/examples' Making check in tests make[2]: Entering directory `/build/buildd/probabel-0.2.0.99/tests' make check_probabel.pl_chunk.sh make[3]: Entering directory `/build/buildd/probabel-0.2.0.99/tests' make[3]: Nothing to be done for `check_probabel.pl_chunk.sh'. make[3]: Leaving directory `/build/buildd/probabel-0.2.0.99/tests' make check-TESTS make[3]: Entering directory `/build/buildd/probabel-0.2.0.99/tests' Testing probabel.pl... Checking output using dosages without chunks... Start... Nr. of chunks: 1 ../src/palinear -p height.PHE --ngpreds 1 -i chr1.info -d chr1.dose -m chr1.map --chrom 1 -o height.chunk1.chr1 ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = height.PHE --info = chr1.info --dose = chr1.dose --ntraits = 1 --ngpreds = 1 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = chr1.map --nids = estimated from data --chrom = 1 --out = height.chunk1.chr1 --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = OFF Number of SNPs = 2 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done cat height.chunk1.chr1_add.out.txt >> height.chr1_add.out.txt rm height.chunk1.chr1_add.out.txt cat height.1_add.out.txt >> height_add.out.txt rm height.1_add.out.txt Nr. of chunks: 1 ../src/palinear -p height.PHE --ngpreds 1 -i chr2.info -d chr2.dose -m chr2.map --chrom 2 -o height.chunk1.chr2 --no-head ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = height.PHE --info = chr2.info --dose = chr2.dose --ntraits = 1 --ngpreds = 1 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = chr2.map --nids = estimated from data --chrom = 2 --out = height.chunk1.chr2 --skipd = 2 --separat = " " --score = OFF --nohead = ON --allcov = OFF --robust = OFF Number of SNPs = 3 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done cat height.chunk1.chr2_add.out.txt >> height.chr2_add.out.txt rm height.chunk1.chr2_add.out.txt cat height.2_add.out.txt >> height_add.out.txt rm height.2_add.out.txt Finished all chromosomes ... Verifying height_add.out.txt: -e OK Checking output using probabilities without chunks... Start... Nr. of chunks: 1 ../src/palinear -p height.PHE --ngpreds 2 -i chr1.info -d chr1.prob -m chr1.map --chrom 1 -o height_ngp2.chunk1.chr1 ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = height.PHE --info = chr1.info --dose = chr1.prob --ntraits = 1 --ngpreds = 2 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = chr1.map --nids = estimated from data --chrom = 1 --out = height_ngp2.chunk1.chr1 --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = OFF Number of SNPs = 2 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done Nr. of chunks: 1 ../src/palinear -p height.PHE --ngpreds 2 -i chr2.info -d chr2.prob -m chr2.map --chrom 2 -o height_ngp2.chunk1.chr2 --no-head ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = height.PHE --info = chr2.info --dose = chr2.prob --ntraits = 1 --ngpreds = 2 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = chr2.map --nids = estimated from data --chrom = 2 --out = height_ngp2.chunk1.chr2 --skipd = 2 --separat = " " --score = OFF --nohead = ON --allcov = OFF --robust = OFF Number of SNPs = 3 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done Finished all chromosomes ... Verifying height_ngp2_2df.out.txt: -e OK Verifying height_ngp2_recess.out.txt: -e OK Verifying height_ngp2_over_domin.out.txt: -e OK Verifying height_ngp2_domin.out.txt: -e OK Verifying height_ngp2_add.out.txt: -e OK -------------------- Finished check without chunks -------------------- Checking output using dosages with chunks... Start... Nr. of chunks: 2 ../src/palinear -p height.PHE --ngpreds 1 -i chr1.chunk1.info -d chr1.chunk1.dose -m chr1.chunk1.map --chrom 1 -o height.chunk1.chr1 ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = height.PHE --info = chr1.chunk1.info --dose = chr1.chunk1.dose --ntraits = 1 --ngpreds = 1 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = chr1.chunk1.map --nids = estimated from data --chrom = 1 --out = height.chunk1.chr1 --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = OFF Number of SNPs = 1 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done cat height.chunk1.chr1_add.out.txt >> height.chr1_add.out.txt rm height.chunk1.chr1_add.out.txt ../src/palinear -p height.PHE --ngpreds 1 -i chr1.chunk2.info -d chr1.chunk2.dose -m chr1.chunk2.map --chrom 1 -o height.chunk2.chr1 --no-head ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = height.PHE --info = chr1.chunk2.info --dose = chr1.chunk2.dose --ntraits = 1 --ngpreds = 1 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = chr1.chunk2.map --nids = estimated from data --chrom = 1 --out = height.chunk2.chr1 --skipd = 2 --separat = " " --score = OFF --nohead = ON --allcov = OFF --robust = OFF Number of SNPs = 1 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done cat height.chunk2.chr1_add.out.txt >> height.chr1_add.out.txt rm height.chunk2.chr1_add.out.txt cat height.1_add.out.txt >> height_add.out.txt rm height.1_add.out.txt Nr. of chunks: 2 ../src/palinear -p height.PHE --ngpreds 1 -i chr2.chunk1.info -d chr2.chunk1.dose -m chr2.chunk1.map --chrom 2 -o height.chunk1.chr2 --no-head ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = height.PHE --info = chr2.chunk1.info --dose = chr2.chunk1.dose --ntraits = 1 --ngpreds = 1 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = chr2.chunk1.map --nids = estimated from data --chrom = 2 --out = height.chunk1.chr2 --skipd = 2 --separat = " " --score = OFF --nohead = ON --allcov = OFF --robust = OFF Number of SNPs = 2 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done cat height.chunk1.chr2_add.out.txt >> height.chr2_add.out.txt rm height.chunk1.chr2_add.out.txt ../src/palinear -p height.PHE --ngpreds 1 -i chr2.chunk2.info -d chr2.chunk2.dose -m chr2.chunk2.map --chrom 2 -o height.chunk2.chr2 --no-head ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = height.PHE --info = chr2.chunk2.info --dose = chr2.chunk2.dose --ntraits = 1 --ngpreds = 1 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = chr2.chunk2.map --nids = estimated from data --chrom = 2 --out = height.chunk2.chr2 --skipd = 2 --separat = " " --score = OFF --nohead = ON --allcov = OFF --robust = OFF Number of SNPs = 1 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done cat height.chunk2.chr2_add.out.txt >> height.chr2_add.out.txt rm height.chunk2.chr2_add.out.txt cat height.2_add.out.txt >> height_add.out.txt rm height.2_add.out.txt Finished all chromosomes ... Verifying height_add.out.txt: -e OK Checking output using probabilities with chunks... Start... Nr. of chunks: 2 ../src/palinear -p height.PHE --ngpreds 2 -i chr1.chunk1.info -d chr1.chunk1.prob -m chr1.chunk1.map --chrom 1 -o height_ngp2.chunk1.chr1 ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = height.PHE --info = chr1.chunk1.info --dose = chr1.chunk1.prob --ntraits = 1 --ngpreds = 2 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = chr1.chunk1.map --nids = estimated from data --chrom = 1 --out = height_ngp2.chunk1.chr1 --skipd = 2 --separat = " " --score = OFF --nohead = OFF --allcov = OFF --robust = OFF Number of SNPs = 1 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done ../src/palinear -p height.PHE --ngpreds 2 -i chr1.chunk2.info -d chr1.chunk2.prob -m chr1.chunk2.map --chrom 1 -o height_ngp2.chunk2.chr1 --no-head ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = height.PHE --info = chr1.chunk2.info --dose = chr1.chunk2.prob --ntraits = 1 --ngpreds = 2 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = chr1.chunk2.map --nids = estimated from data --chrom = 1 --out = height_ngp2.chunk2.chr1 --skipd = 2 --separat = " " --score = OFF --nohead = ON --allcov = OFF --robust = OFF Number of SNPs = 1 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done Nr. of chunks: 2 ../src/palinear -p height.PHE --ngpreds 2 -i chr2.chunk1.info -d chr2.chunk1.prob -m chr2.chunk1.map --chrom 2 -o height_ngp2.chunk1.chr2 --no-head ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = height.PHE --info = chr2.chunk1.info --dose = chr2.chunk1.prob --ntraits = 1 --ngpreds = 2 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = chr2.chunk1.map --nids = estimated from data --chrom = 2 --out = height_ngp2.chunk1.chr2 --skipd = 2 --separat = " " --score = OFF --nohead = ON --allcov = OFF --robust = OFF Number of SNPs = 2 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done ../src/palinear -p height.PHE --ngpreds 2 -i chr2.chunk2.info -d chr2.chunk2.prob -m chr2.chunk2.map --chrom 2 -o height_ngp2.chunk2.chr2 --no-head ProbABEL v. 0.2.1-beta1 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR Options in effect: --pheno = height.PHE --info = chr2.chunk2.info --dose = chr2.chunk2.prob --ntraits = 1 --ngpreds = 2 --interaction = 0 --interaction_only = 0 --mmscore = not in output --map = chr2.chunk2.map --nids = estimated from data --chrom = 2 --out = height_ngp2.chunk2.chr2 --skipd = 2 --separat = " " --score = OFF --nohead = ON --allcov = OFF --robust = OFF Number of SNPs = 1 Actual number of people in phenofile = 200; using all of these Linear model: ( height ) ~ mu + sex + age + SNP_A1 Reading data ... loaded genotypic data ... loaded null data ... estimated null model ... formed regression object ... done Analysis: 0.00 ...100.00 ... done Finished all chromosomes ... Verifying height_ngp2_2df.out.txt: -e OK Verifying height_ngp2_recess.out.txt: -e OK Verifying height_ngp2_over_domin.out.txt: -e OK Verifying height_ngp2_domin.out.txt: -e OK Verifying height_ngp2_add.out.txt: -e OK -------------------- Finished check with chunks -------------------- PASS: check_probabel.pl_chunk.sh ============= 1 test passed ============= make[3]: Leaving directory `/build/buildd/probabel-0.2.0.99/tests' make[2]: Leaving directory `/build/buildd/probabel-0.2.0.99/tests' make[2]: Entering directory `/build/buildd/probabel-0.2.0.99' make[2]: Nothing to be done for `check-am'. make[2]: Leaving directory `/build/buildd/probabel-0.2.0.99' make[1]: Leaving directory `/build/buildd/probabel-0.2.0.99' /usr/bin/fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_installdirs -a dh_auto_install -a make[1]: Entering directory `/build/buildd/probabel-0.2.0.99' Making install in src make[2]: Entering directory `/build/buildd/probabel-0.2.0.99/src' make[3]: Entering directory `/build/buildd/probabel-0.2.0.99/src' test -z "/usr/bin" || /bin/mkdir -p "/build/buildd/probabel-0.2.0.99/debian/probabel/usr/bin" /usr/bin/install -c palinear palogist extract-snp '/build/buildd/probabel-0.2.0.99/debian/probabel/usr/bin' test -z "/usr/bin" || /bin/mkdir -p "/build/buildd/probabel-0.2.0.99/debian/probabel/usr/bin" /usr/bin/install -c probabel.pl extIDS.pl '/build/buildd/probabel-0.2.0.99/debian/probabel/usr/bin' test -z "/etc" || /bin/mkdir -p "/build/buildd/probabel-0.2.0.99/debian/probabel/etc" /usr/bin/install -c -m 644 probabel_config.cfg.example '/build/buildd/probabel-0.2.0.99/debian/probabel/etc' make install-exec-hook make[4]: Entering directory `/build/buildd/probabel-0.2.0.99/src' /bin/sed -i "s;probabel_config.cfg;/etc/probabel_config.cfg;" \ /build/buildd/probabel-0.2.0.99/debian/probabel/usr/bin/probabel.pl /bin/sed -i "s;\./;/usr/bin/;" /build/buildd/probabel-0.2.0.99/debian/probabel/usr/bin/probabel.pl /bin/sed -i "s;PROBABEL_VERSION;0.2.1-beta1;" /build/buildd/probabel-0.2.0.99/debian/probabel/usr/bin/probabel.pl make[4]: Leaving directory `/build/buildd/probabel-0.2.0.99/src' make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/build/buildd/probabel-0.2.0.99/src' make[2]: Leaving directory `/build/buildd/probabel-0.2.0.99/src' Making install in doc make[2]: Entering directory `/build/buildd/probabel-0.2.0.99/doc' make[3]: Entering directory `/build/buildd/probabel-0.2.0.99/doc' make[3]: Nothing to be done for `install-exec-am'. test -z "/usr/share/doc/probabel" || /bin/mkdir -p "/build/buildd/probabel-0.2.0.99/debian/probabel/usr/share/doc/probabel" /usr/bin/install -c -m 644 ProbABEL_manual.tex QuickStart.txt short_coxph_data.txt short_height_base_add.out.txt.save short_height.txt short_logist_data.txt short_test.mldose test.map test.mlinfo test_regression.R COPYING LICENSE INSTALL CHANGES.LOG TODO '/build/buildd/probabel-0.2.0.99/debian/probabel/usr/share/doc/probabel' test -z "/usr/share/doc/probabel" || /bin/mkdir -p "/build/buildd/probabel-0.2.0.99/debian/probabel/usr/share/doc/probabel" /usr/bin/install -c -m 644 ProbABEL_manual.pdf '/build/buildd/probabel-0.2.0.99/debian/probabel/usr/share/doc/probabel' test -z "/usr/share/man/man1" || /bin/mkdir -p "/build/buildd/probabel-0.2.0.99/debian/probabel/usr/share/man/man1" /usr/bin/install -c -m 644 palinear.1 palogist.1 pacoxph.1 '/build/buildd/probabel-0.2.0.99/debian/probabel/usr/share/man/man1' make[3]: Leaving directory `/build/buildd/probabel-0.2.0.99/doc' make[2]: Leaving directory `/build/buildd/probabel-0.2.0.99/doc' Making install in examples make[2]: Entering directory `/build/buildd/probabel-0.2.0.99/examples' make[3]: Entering directory `/build/buildd/probabel-0.2.0.99/examples' make[3]: Nothing to be done for `install-exec-am'. test -z "/usr/share/ProbABEL/examples" || /bin/mkdir -p "/build/buildd/probabel-0.2.0.99/debian/probabel/usr/share/ProbABEL/examples" /usr/bin/install -c -m 644 height_ngp2_robust_int1_over_domin.out.txt.save test.prob.fvi mmscore_gen.prob.fvd test.map mldose.IDS impute_with_missing.mlinfo height_ngp2_robust_int1_recess.out.txt.save height_ngp2_2df.out.txt.save mmscore_gen.mlprob mmscore_gen.mlinfo height_ngp2_robust_recess.out.txt.save example_cox.sh test.mlprob test.prob.fvd impute_with_missing_robust_int1_add.out.txt.save test.mlinfo regression_add.out.txt.save height_ngp2_robust_add.out.txt.save mmscore_gen.dose.fvi impute_with_missing_allcov_add.out.txt.save example_bt.sh height_ngp2_int1_recess.out.txt.save example_qt.sh coxph_data.txt height_ngp2_robust_int1_domin.out.txt.save height_ngp2_allcov_2df.out.txt.save impute_with_missing_int1_add.out.txt.save mmscore_gen.mldose example_mms.sh height_ngp2_recess.out.txt.save height_ngp2_over_domin.out.txt.save height_ngp2_int1_domin.out.txt.save height_ngp2_allcov_domin.out.txt.save height_ngp2_robust_over_domin.out.txt.save height_ngp2_robust_int1_add.out.txt.save height_int1_add.out.txt.save height_allcov_add.out.txt.save impute_with_missing_base_add.out.txt.save example_all.sh height_base_add.out.txt.save '/build/buildd/probabel-0.2.0.99/debian/probabel/usr/share/ProbABEL/examples' /usr/bin/install -c -m 644 height_ngp2_int1_over_domin.out.txt.save height_robust_add.out.txt.save test.mldose height_ngp2_allcov_add.out.txt.save mmscore_InvSigma_aj.sex.age.dat height_ngp2_robust_int1_2df.out.txt.save mmscore_gen.dose.fvd mmscore.R test.dose.fvd height_ngp2_domin.out.txt.save test.dose.fvi impute_with_missing_robust_add.out.txt.save allheight.txt mmscore_add.out.txt.save coxph.out.txt_add.out.txt.save mmscore_pheno.PHE height_ngp2_robust_2df.out.txt.save height_ngp2_int1_add.out.txt.save mmscore_gen.prob.fvi height_robust_int1_add.out.txt.save logist.out.txt_add.out.txt.save height_ngp2_allcov_recess.out.txt.save impute_with_missing.PHE height_ngp2_allcov_over_domin.out.txt.save height_ngp2_add.out.txt.save logist_data.txt height_ngp2_int1_2df.out.txt.save impute_with_missing_add.out.txt.save height_ngp2_robust_domin.out.txt.save height.txt '/build/buildd/probabel-0.2.0.99/debian/probabel/usr/share/ProbABEL/examples' make[3]: Leaving directory `/build/buildd/probabel-0.2.0.99/examples' make[2]: Leaving directory `/build/buildd/probabel-0.2.0.99/examples' Making install in tests make[2]: Entering directory `/build/buildd/probabel-0.2.0.99/tests' make[3]: Entering directory `/build/buildd/probabel-0.2.0.99/tests' make[3]: Nothing to be done for `install-exec-am'. test -z "/usr/share/ProbABEL/tests" || /bin/mkdir -p "/build/buildd/probabel-0.2.0.99/debian/probabel/usr/share/ProbABEL/tests" /usr/bin/install -c -m 644 check_probabel.pl_chunk.sh verified_results/height_add.out.txt verified_results/height_ngp2_add.out.txt verified_results/height_ngp2_2df.out.txt verified_results/height_ngp2_domin.out.txt verified_results/height_ngp2_over_domin.out.txt verified_results/height_ngp2_recess.out.txt '/build/buildd/probabel-0.2.0.99/debian/probabel/usr/share/ProbABEL/tests' make[3]: Leaving directory `/build/buildd/probabel-0.2.0.99/tests' make[2]: Leaving directory `/build/buildd/probabel-0.2.0.99/tests' make[2]: Entering directory `/build/buildd/probabel-0.2.0.99' make[3]: Entering directory `/build/buildd/probabel-0.2.0.99' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/build/buildd/probabel-0.2.0.99' make[2]: Leaving directory `/build/buildd/probabel-0.2.0.99' make[1]: Leaving directory `/build/buildd/probabel-0.2.0.99' dh_install -a dh_installdocs -a dh_installchangelogs -a 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: disabling for PPA build dh_strip debug symbol extraction: not doing anything since NO_PKG_MANGLE is given dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a 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 `probabel' in `../probabel_0.2.0.99-0ubuntu1~precise1_amd64.deb'. dpkg-genchanges -B -mUbuntu/amd64 Build Daemon >../probabel_0.2.0.99-0ubuntu1~precise1_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 probabel-0.2.0.99 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20121105-1645 chroot-autobuild/build/buildd/probabel_0.2.0.99-0ubuntu1~precise1_amd64.deb: new debian package, version 2.0. size 2849048 bytes: control archive= 3528 bytes. 33 bytes, 1 lines conffiles 585 bytes, 14 lines control 8743 bytes, 104 lines md5sums Package: probabel Version: 0.2.0.99-0ubuntu1~precise1 Architecture: amd64 Maintainer: L.C. Karssen Installed-Size: 6444 Depends: libc6 (>= 2.14), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0) Recommends: perl Section: science Priority: extra Homepage: http://www.genabel.org Description: Toolset for Genome-Wide Association Analysis The ProbABEL package is part of the GenABEL project for analysis of genome-wide data. ProbABEL is used to run GWAS. Using files in filevector/DatABEL format even allows for running GWAS on computers with only a few GB of RAM. chroot-autobuild/build/buildd/probabel_0.2.0.99-0ubuntu1~precise1_amd64.deb: drwxr-xr-x root/root 0 2012-11-05 16:45 ./ drwxr-xr-x root/root 0 2012-11-05 16:45 ./etc/ -rw-r--r-- root/root 1606 2012-11-05 16:45 ./etc/probabel_config.cfg.example drwxr-xr-x root/root 0 2012-11-05 16:45 ./usr/ drwxr-xr-x root/root 0 2012-11-05 16:45 ./usr/bin/ -rwxr-xr-x root/root 10543 2012-11-05 16:45 ./usr/bin/probabel.pl -rwxr-xr-x root/root 154392 2012-11-05 16:45 ./usr/bin/extract-snp -rwxr-xr-x root/root 228328 2012-11-05 16:45 ./usr/bin/palogist -rwxr-xr-x root/root 118 2012-11-05 16:45 ./usr/bin/extIDS.pl -rwxr-xr-x root/root 224224 2012-11-05 16:45 ./usr/bin/palinear drwxr-xr-x root/root 0 2012-11-05 16:45 ./usr/share/ drwxr-xr-x root/root 0 2012-11-05 16:45 ./usr/share/man/ drwxr-xr-x root/root 0 2012-11-05 16:45 ./usr/share/man/man1/ -rw-r--r-- root/root 1019 2012-11-05 16:45 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./usr/share/ProbABEL/tests/ -rw-r--r-- root/root 554 2012-11-05 16:45 ./usr/share/ProbABEL/tests/height_ngp2_domin.out.txt -rw-r--r-- root/root 558 2012-11-05 16:45 ./usr/share/ProbABEL/tests/height_add.out.txt -rw-r--r-- root/root 555 2012-11-05 16:45 ./usr/share/ProbABEL/tests/height_ngp2_recess.out.txt -rw-r--r-- root/root 665 2012-11-05 16:45 ./usr/share/ProbABEL/tests/height_ngp2_2df.out.txt -rw-r--r-- root/root 4523 2012-11-05 16:45 ./usr/share/ProbABEL/tests/check_probabel.pl_chunk.sh -rw-r--r-- root/root 553 2012-11-05 16:45 ./usr/share/ProbABEL/tests/height_ngp2_add.out.txt -rw-r--r-- root/root 550 2012-11-05 16:45 ./usr/share/ProbABEL/tests/height_ngp2_over_domin.out.txt drwxr-xr-x root/root 0 2012-11-05 16:45 ./usr/share/ProbABEL/examples/ -rw-r--r-- root/root 672 2012-11-05 16:45 ./usr/share/ProbABEL/examples/height_ngp2_robust_2df.out.txt.save -rw-r--r-- root/root 13500 2012-11-05 16:45 ./usr/share/ProbABEL/examples/mmscore_gen.mldose -rw-r--r-- root/root 565 2012-11-05 16:45 ./usr/share/ProbABEL/examples/height_ngp2_domin.out.txt.save -rw-r--r-- root/root 1883 2012-11-05 16:45 ./usr/share/ProbABEL/examples/impute_with_missing.mlinfo -rw-r--r-- root/root 1477 2012-11-05 16:45 ./usr/share/ProbABEL/examples/example_mms.sh -rw-r--r-- root/root 18562 2012-11-05 16:45 ./usr/share/ProbABEL/examples/mmscore_gen.mlprob -rw-r--r-- root/root 4000 2012-11-05 16:45 ./usr/share/ProbABEL/examples/test.dose.fvd -rw-r--r-- root/root 565 2012-11-05 16:45 ./usr/share/ProbABEL/examples/height_base_add.out.txt.save -rw-r--r-- root/root 6608 2012-11-05 16:45 ./usr/share/ProbABEL/examples/test.dose.fvi -rw-r--r-- root/root 9238 2012-11-05 16:45 ./usr/share/ProbABEL/examples/impute_with_missing_allcov_add.out.txt.save -rw-r--r-- root/root 1245 2012-11-05 16:45 ./usr/share/ProbABEL/examples/example_bt.sh -rw-r--r-- root/root 8000 2012-11-05 16:45 ./usr/share/ProbABEL/examples/test.prob.fvd -rw-r--r-- root/root 1782 2012-11-05 16:45 ./usr/share/ProbABEL/examples/mldose.IDS 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./usr/share/ProbABEL/examples/height_ngp2_2df.out.txt.save -rw-r--r-- root/root 885 2012-11-05 16:45 ./usr/share/ProbABEL/examples/height_allcov_add.out.txt.save -rw-r--r-- root/root 731 2012-11-05 16:45 ./usr/share/ProbABEL/examples/height_ngp2_robust_int1_add.out.txt.save -rw-r--r-- root/root 16208 2012-11-05 16:45 ./usr/share/ProbABEL/examples/mmscore_gen.dose.fvi -rw-r--r-- root/root 6624 2012-11-05 16:45 ./usr/share/ProbABEL/examples/example_qt.sh -rw-r--r-- root/root 726 2012-11-05 16:45 ./usr/share/ProbABEL/examples/height_int1_add.out.txt.save -rw-r--r-- root/root 567 2012-11-05 16:45 ./usr/share/ProbABEL/examples/height_ngp2_recess.out.txt.save -rw-r--r-- root/root 564 2012-11-05 16:45 ./usr/share/ProbABEL/examples/height_ngp2_robust_domin.out.txt.save -rw-r--r-- root/root 731 2012-11-05 16:45 ./usr/share/ProbABEL/examples/height_ngp2_int1_over_domin.out.txt.save -rw-r--r-- root/root 6042 2012-11-05 16:45 ./usr/share/ProbABEL/examples/impute_with_missing_add.out.txt.save 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./usr/share/ProbABEL/examples/height_ngp2_allcov_2df.out.txt.save -rw-r--r-- root/root 13020 2012-11-05 16:45 ./usr/share/ProbABEL/examples/allheight.txt -rw-r--r-- root/root 209 2012-11-05 16:45 ./usr/share/ProbABEL/examples/example_all.sh -rw-r--r-- root/root 9852 2012-11-05 16:45 ./usr/share/ProbABEL/examples/coxph_data.txt -rw-r--r-- root/root 806 2012-11-05 16:45 ./usr/share/ProbABEL/examples/example_cox.sh -rw-r--r-- root/root 8698 2012-11-05 16:45 ./usr/share/ProbABEL/examples/height.txt -rw-r--r-- root/root 737 2012-11-05 16:45 ./usr/share/ProbABEL/examples/height_ngp2_int1_recess.out.txt.save -rw-r--r-- root/root 16087 2012-11-05 16:45 ./usr/share/ProbABEL/examples/test.mlprob -rw-r--r-- root/root 500 2012-11-05 16:45 ./usr/share/ProbABEL/examples/regression_add.out.txt.save -rw-r--r-- root/root 731 2012-11-05 16:45 ./usr/share/ProbABEL/examples/height_ngp2_int1_add.out.txt.save -rw-r--r-- root/root 888 2012-11-05 16:45 ./usr/share/ProbABEL/examples/height_ngp2_allcov_add.out.txt.save -rw-r--r-- root/root 572 2012-11-05 16:45 ./usr/share/ProbABEL/examples/coxph.out.txt_add.out.txt.save -rw-r--r-- root/root 893 2012-11-05 16:45 ./usr/share/ProbABEL/examples/height_ngp2_allcov_recess.out.txt.save -rw-r--r-- root/root 444 2012-11-05 16:45 ./usr/share/ProbABEL/examples/mmscore_add.out.txt.save -rw-r--r-- root/root 10000 2012-11-05 16:45 ./usr/share/ProbABEL/examples/mmscore_gen.dose.fvd -rw-r--r-- root/root 741 2012-11-05 16:45 ./usr/share/ProbABEL/examples/height_ngp2_robust_int1_domin.out.txt.save -rw-r--r-- root/root 733 2012-11-05 16:45 ./usr/share/ProbABEL/examples/height_ngp2_robust_int1_recess.out.txt.save -rw-r--r-- root/root 9615 2012-11-05 16:45 ./usr/share/ProbABEL/examples/logist_data.txt -rw-r--r-- root/root 1090 2012-11-05 16:45 ./usr/share/ProbABEL/examples/height_ngp2_robust_int1_2df.out.txt.save probabel_0.2.0.99-0ubuntu1~precise1_amd64.changes: Format: 1.8 Date: Mon, 05 Nov 2012 16:26:53 +0100 Source: probabel Binary: probabel Architecture: amd64 Version: 0.2.0.99-0ubuntu1~precise1 Distribution: precise Urgency: low Maintainer: Ubuntu/amd64 Build Daemon Changed-By: L.C. Karssen Description: probabel - Toolset for Genome-Wide Association Analysis Changes: probabel (0.2.0.99-0ubuntu1~precise1) precise; urgency=low . * Fixed bug #2295: the inverse variance-covariance matrix (used with the --mmscore option) was incorrectly subsetted when NAs are present for one or more SNP dosages. . * Fixed bug #1186: When .map file is missing (but --map option was given), the wrong error message was displayed. . * Fixed bug #2147: The value of the Rsq column in the info file should be > 0, unlike what was mentioned in the documentation. . * Update of the probabel.pl script and probabel_config.cfg. The .cfg file now accepts the chr separator in multiple locations in the path . * probabel.pl can now also run Y chromosome analysis and the help message has been updated. . * probabel.pl and probabel_config.cfg now also accept chunks, where dose, prob, info and map files are split into multiple chunks. Checksums-Sha1: a15ec131726840d989c637b63dee83ddd237d94f 2849048 probabel_0.2.0.99-0ubuntu1~precise1_amd64.deb Checksums-Sha256: 87983b3b79824806a563910c07f7643fe1ad0dddd55345fcf9100711419750e1 2849048 probabel_0.2.0.99-0ubuntu1~precise1_amd64.deb Files: cd64756d45568bed6e4b33c44ac7f568 2849048 science extra probabel_0.2.0.99-0ubuntu1~precise1_amd64.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20121105-1645 Build needed 00:00:49, 40864k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', 'fbed6d25bba59083cf01932877e0382811d31d78'] Scanning for processes to kill in build /home/buildd/build-fbed6d25bba59083cf01932877e0382811d31d78/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'fbed6d25bba59083cf01932877e0382811d31d78'] Unmounting chroot for build fbed6d25bba59083cf01932877e0382811d31d78... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'fbed6d25bba59083cf01932877e0382811d31d78'] Removing build fbed6d25bba59083cf01932877e0382811d31d78