https://launchpad.net/ubuntu/+source/gemma/0.98+dfsg-3/+build/15658639 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-arm64-040 4.4.0-139-generic #165-Ubuntu SMP Wed Oct 24 10:55:47 UTC 2018 aarch64 Buildd toolchain package versions: launchpad-buildd_165 python-lpbuildd_165 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.5 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 13 Nov 23:20:28 ntpdate[1818]: adjust time server 10.211.37.1 offset -0.027798 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=arm64 PACKAGEBUILD-15658639 /home/buildd/filecache-default/bf137a8dadabbe066906202a7cb9d7a8e3a99968 Creating target for build PACKAGEBUILD-15658639 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=arm64 PACKAGEBUILD-15658639 Starting target for build PACKAGEBUILD-15658639 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=arm64 PACKAGEBUILD-15658639 'deb http://ftpmaster.internal/ubuntu disco main universe' 'deb http://ftpmaster.internal/ubuntu disco-security main universe' 'deb http://ftpmaster.internal/ubuntu disco-updates main universe' 'deb http://ftpmaster.internal/ubuntu disco-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-15658639 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=arm64 PACKAGEBUILD-15658639 Updating target for build PACKAGEBUILD-15658639 Get:1 http://ftpmaster.internal/ubuntu disco InRelease [243 kB] Get:2 http://ftpmaster.internal/ubuntu disco-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu disco-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed InRelease [93.2 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main arm64 Packages [977 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [514 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe arm64 Packages [8619 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5106 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 Packages [116 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [70.0 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe arm64 Packages [461 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [263 kB] Fetched 16.6 MB in 6s (2921 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libgdbm6 libperl5.28 perl-modules-5.28 The following packages will be upgraded: apt base-files binutils binutils-aarch64-linux-gnu binutils-common cpp cpp-8 dash dmsetup fakeroot findutils g++ g++-8 gcc gcc-8 gcc-8-base hostname init init-system-helpers libapparmor1 libapt-pkg5.0 libasan5 libatomic1 libaudit-common libaudit1 libbinutils libcap-ng0 libcc1-0 libdb5.3 libdevmapper1.02.1 libfakeroot libgcc-8-dev libgcc1 libgcrypt20 libgdbm-compat4 libgnutls30 libgomp1 libgpg-error0 libitm1 libkmod2 liblsan0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsqlite3-0 libstdc++-8-dev libstdc++6 libsystemd0 libtsan0 libubsan1 libudev1 linux-libc-dev lockfile-progs perl perl-base sed systemd systemd-sysv tzdata 60 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 43.0 MB of archives. After this operation, 48.5 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main arm64 base-files arm64 10.1ubuntu8 [60.1 kB] Get:2 http://ftpmaster.internal/ubuntu disco/main arm64 dash arm64 0.5.10.2-1 [88.0 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main arm64 findutils arm64 4.6.0+git+20181018-1 [290 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main arm64 hostname arm64 3.21 [10.9 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main arm64 perl-modules-5.28 all 5.28.0-3 [2818 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main arm64 libgdbm6 arm64 1.18.1-1 [26.8 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main arm64 libgdbm-compat4 arm64 1.18.1-1 [6016 B] Get:8 http://ftpmaster.internal/ubuntu disco/main arm64 libperl5.28 arm64 5.28.0-3 [3667 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main arm64 perl arm64 5.28.0-3 [204 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main arm64 perl-base arm64 5.28.0-3 [1398 kB] Get:11 http://ftpmaster.internal/ubuntu disco/main arm64 libdb5.3 arm64 5.3.28+dfsg1-0.2 [616 kB] Get:12 http://ftpmaster.internal/ubuntu disco/main arm64 sed arm64 4.5-2 [182 kB] Get:13 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 init-system-helpers all 1.55 [38.5 kB] Get:14 http://ftpmaster.internal/ubuntu disco/main arm64 libcc1-0 arm64 8.2.0-9ubuntu1 [36.3 kB] Get:15 http://ftpmaster.internal/ubuntu disco/main arm64 gcc-8-base arm64 8.2.0-9ubuntu1 [18.6 kB] Get:16 http://ftpmaster.internal/ubuntu disco/main arm64 libgcc1 arm64 1:8.2.0-9ubuntu1 [34.3 kB] Get:17 http://ftpmaster.internal/ubuntu disco/main arm64 libgomp1 arm64 8.2.0-9ubuntu1 [69.6 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main arm64 libitm1 arm64 8.2.0-9ubuntu1 [24.4 kB] Get:19 http://ftpmaster.internal/ubuntu disco/main arm64 libatomic1 arm64 8.2.0-9ubuntu1 [9124 B] Get:20 http://ftpmaster.internal/ubuntu disco/main arm64 libasan5 arm64 8.2.0-9ubuntu1 [336 kB] Get:21 http://ftpmaster.internal/ubuntu disco/main arm64 liblsan0 arm64 8.2.0-9ubuntu1 [121 kB] Get:22 http://ftpmaster.internal/ubuntu disco/main arm64 libtsan0 arm64 8.2.0-9ubuntu1 [269 kB] Get:23 http://ftpmaster.internal/ubuntu disco/main arm64 libubsan1 arm64 8.2.0-9ubuntu1 [113 kB] Get:24 http://ftpmaster.internal/ubuntu disco/main arm64 g++-8 arm64 8.2.0-9ubuntu1 [6548 kB] Get:25 http://ftpmaster.internal/ubuntu disco/main arm64 libstdc++-8-dev arm64 8.2.0-9ubuntu1 [1513 kB] Get:26 http://ftpmaster.internal/ubuntu disco/main arm64 libgcc-8-dev arm64 8.2.0-9ubuntu1 [857 kB] Get:27 http://ftpmaster.internal/ubuntu disco/main arm64 gcc-8 arm64 8.2.0-9ubuntu1 [6470 kB] Get:28 http://ftpmaster.internal/ubuntu disco/main arm64 cpp-8 arm64 8.2.0-9ubuntu1 [5713 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main arm64 libstdc++6 arm64 8.2.0-9ubuntu1 [372 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main arm64 libbinutils arm64 2.31.1-7ubuntu1 [462 kB] Get:31 http://ftpmaster.internal/ubuntu disco/main arm64 binutils-common arm64 2.31.1-7ubuntu1 [194 kB] Get:32 http://ftpmaster.internal/ubuntu disco/main arm64 binutils arm64 2.31.1-7ubuntu1 [3364 B] Get:33 http://ftpmaster.internal/ubuntu disco/main arm64 binutils-aarch64-linux-gnu arm64 2.31.1-7ubuntu1 [2173 kB] Get:34 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libudev1 arm64 239-7ubuntu10.3 [50.1 kB] Get:35 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libapt-pkg5.0 arm64 1.8.0~alpha2 [750 kB] Get:36 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libgnutls30 arm64 3.6.4-2ubuntu2 [686 kB] Get:37 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libseccomp2 arm64 2.3.3-3ubuntu2 [38.6 kB] Get:38 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 apt arm64 1.8.0~alpha2 [1133 kB] Get:39 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 systemd-sysv arm64 239-7ubuntu10.3 [9404 B] Get:40 http://ftpmaster.internal/ubuntu disco/main arm64 libapparmor1 arm64 2.12-4ubuntu10 [29.1 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main arm64 libaudit-common all 1:2.8.3-1ubuntu3 [4068 B] Get:42 http://ftpmaster.internal/ubuntu disco/main arm64 libcap-ng0 arm64 0.7.9-1build1 [10.5 kB] Get:43 http://ftpmaster.internal/ubuntu disco/main arm64 libaudit1 arm64 1:2.8.3-1ubuntu3 [38.1 kB] Get:44 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libgpg-error0 arm64 1.32-3 [53.4 kB] Get:45 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libkmod2 arm64 25-1ubuntu2 [38.6 kB] Get:46 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 systemd arm64 239-7ubuntu10.3 [2755 kB] Get:47 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libsystemd0 arm64 239-7ubuntu10.3 [195 kB] Get:48 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 init arm64 1.55 [6476 B] Get:49 http://ftpmaster.internal/ubuntu disco/main arm64 libgcrypt20 arm64 1.8.4-3ubuntu1 [350 kB] Get:50 http://ftpmaster.internal/ubuntu disco/main arm64 libselinux1 arm64 2.8-1build2 [64.9 kB] Get:51 http://ftpmaster.internal/ubuntu disco/main arm64 libsemanage-common all 2.8-1build2 [6892 B] Get:52 http://ftpmaster.internal/ubuntu disco/main arm64 libsemanage1 arm64 2.8-1build2 [79.7 kB] Get:53 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libdevmapper1.02.1 arm64 2:1.02.145-4.1ubuntu4 [109 kB] Get:54 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 dmsetup arm64 2:1.02.145-4.1ubuntu4 [67.6 kB] Get:55 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libsqlite3-0 arm64 3.25.3-1 [490 kB] Get:56 http://ftpmaster.internal/ubuntu disco/main arm64 tzdata all 2018g-1 [188 kB] Get:57 http://ftpmaster.internal/ubuntu disco/main arm64 g++ arm64 4:8.2.0-2ubuntu2 [1592 B] Get:58 http://ftpmaster.internal/ubuntu disco/main arm64 gcc arm64 4:8.2.0-2ubuntu2 [5232 B] Get:59 http://ftpmaster.internal/ubuntu disco/main arm64 cpp arm64 4:8.2.0-2ubuntu2 [27.6 kB] Get:60 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libfakeroot arm64 1.23-1 [25.2 kB] Get:61 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 fakeroot arm64 1.23-1 [62.0 kB] Get:62 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 linux-libc-dev arm64 4.18.0-11.12 [1019 kB] Get:63 http://ftpmaster.internal/ubuntu disco/main arm64 lockfile-progs arm64 0.1.18 [9748 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 43.0 MB in 1s (32.3 MB/s) (Reading database ... 12627 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu8_arm64.deb ... Unpacking base-files (10.1ubuntu8) over (10.1ubuntu7) ... Setting up base-files (10.1ubuntu8) ... 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 ... 12627 files and directories currently installed.) Preparing to unpack .../dash_0.5.10.2-1_arm64.deb ... Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' Unpacking dash (0.5.10.2-1) over (0.5.8-2.10) ... Setting up dash (0.5.10.2-1) ... Removing 'diversion of /bin/sh to /bin/sh.distrib by bash' Adding 'diversion of /bin/sh to /bin/sh.distrib by dash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' (Reading database ... 12627 files and directories currently installed.) Preparing to unpack .../findutils_4.6.0+git+20181018-1_arm64.deb ... Unpacking findutils (4.6.0+git+20181018-1) over (4.6.0+git+20180808-2) ... Setting up findutils (4.6.0+git+20181018-1) ... (Reading database ... 12627 files and directories currently installed.) Preparing to unpack .../hostname_3.21_arm64.deb ... Unpacking hostname (3.21) over (3.20) ... Setting up hostname (3.21) ... (Reading database ... 12627 files and directories currently installed.) Preparing to unpack .../0-perl_5.28.0-3_arm64.deb ... Unpacking perl (5.28.0-3) over (5.26.2-7) ... 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Setting up init (1.55) ... Setting up libtsan0:arm64 (8.2.0-9ubuntu1) ... Setting up linux-libc-dev:arm64 (4.18.0-11.12) ... Setting up libdevmapper1.02.1:arm64 (2:1.02.145-4.1ubuntu4) ... Setting up liblsan0:arm64 (8.2.0-9ubuntu1) ... Setting up libgdbm6:arm64 (1.18.1-1) ... Setting up binutils-common:arm64 (2.31.1-7ubuntu1) ... Setting up perl-modules-5.28 (5.28.0-3) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up libfakeroot:arm64 (1.23-1) ... Setting up libsqlite3-0:arm64 (3.25.3-1) ... Setting up dmsetup (2:1.02.145-4.1ubuntu4) ... Setting up libgdbm-compat4:arm64 (1.18.1-1) ... Setting up lockfile-progs (0.1.18) ... Setting up libasan5:arm64 (8.2.0-9ubuntu1) ... Setting up libitm1:arm64 (8.2.0-9ubuntu1) ... Setting up libubsan1:arm64 (8.2.0-9ubuntu1) ... Setting up libbinutils:arm64 (2.31.1-7ubuntu1) ... Setting up libperl5.28:arm64 (5.28.0-3) ... Setting up fakeroot (1.23-1) ... Setting up perl (5.28.0-3) ... Setting up binutils-aarch64-linux-gnu (2.31.1-7ubuntu1) ... Setting up libgcc-8-dev:arm64 (8.2.0-9ubuntu1) ... Setting up binutils (2.31.1-7ubuntu1) ... Setting up libstdc++-8-dev:arm64 (8.2.0-9ubuntu1) ... Setting up gcc-8 (8.2.0-9ubuntu1) ... Setting up g++-8 (8.2.0-9ubuntu1) ... Setting up gcc (4:8.2.0-2ubuntu2) ... Setting up g++ (4:8.2.0-2ubuntu2) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-15658639 arm64 disco-proposed -c chroot:build-PACKAGEBUILD-15658639 --arch=arm64 --dist=disco-proposed --nolog gemma_0.98+dfsg-3.dsc Initiating build PACKAGEBUILD-15658639 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-139-generic #165-Ubuntu SMP Wed Oct 24 10:55:47 UTC 2018 aarch64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-040.buildd +==============================================================================+ | gemma 0.98+dfsg-3 (arm64) 13 Nov 2018 23:21 | +==============================================================================+ Package: gemma Version: 0.98+dfsg-3 Source Version: 0.98+dfsg-3 Distribution: disco-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 I: NOTICE: Log filtering will replace 'build/gemma-1BH6Qi/gemma-0.98+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/gemma-1BH6Qi' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15658639/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- gemma_0.98+dfsg-3.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-eb65RM/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-eb65RM/apt_archive ./ InRelease Get:2 copy:/<>/resolver-eb65RM/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-eb65RM/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-eb65RM/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-eb65RM/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (134 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-eb65RM/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14518 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11~), gfortran, libopenblas-dev, libeigen3-dev, libgsl-dev, zlib1g-dev, catch, shunit2 Filtered Build-Depends: debhelper (>= 11~), gfortran, libopenblas-dev, libeigen3-dev, libgsl-dev, zlib1g-dev, catch, shunit2 dpkg-deb: building package 'sbuild-build-depends-gemma-dummy' in '/<>/resolver-oDWKDQ/apt_archive/sbuild-build-depends-gemma-dummy.deb'. Ign:1 copy:/<>/resolver-oDWKDQ/apt_archive ./ InRelease Get:2 copy:/<>/resolver-oDWKDQ/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-oDWKDQ/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-oDWKDQ/apt_archive ./ Sources [254 B] Get:5 copy:/<>/resolver-oDWKDQ/apt_archive ./ Packages [572 B] Fetched 2945 B in 0s (142 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install gemma build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils catch debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran gfortran-8 groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libeigen3-dev libelf1 libfile-stripnondeterminism-perl libgfortran-8-dev libgfortran5 libglib2.0-0 libgsl-dev libgsl23 libgslcblas0 libicu63 libmagic-mgc libmagic1 libopenblas-base libopenblas-dev libpipeline1 libsigsegv2 libtool libxml2 m4 man-db pkg-config po-debconf shunit2 zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc gfortran-8-doc libgfortran5-dbg libcoarrays-dev groff libeigen3-doc libmpfrc++-dev gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libtool-doc gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils catch debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran gfortran-8 groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libeigen3-dev libelf1 libfile-stripnondeterminism-perl libgfortran-8-dev libgfortran5 libglib2.0-0 libgsl-dev libgsl23 libgslcblas0 libicu63 libmagic-mgc libmagic1 libopenblas-base libopenblas-dev libpipeline1 libsigsegv2 libtool libxml2 m4 man-db pkg-config po-debconf sbuild-build-depends-gemma-dummy shunit2 zlib1g-dev 0 upgraded, 45 newly installed, 0 to remove and 0 not upgraded. Need to get 30.0 MB of archives. After this operation, 133 MB of additional disk space will be used. 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(Reading database ... 14518 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-1_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2ubuntu2_arm64.deb ... Unpacking bsdmainutils (11.1.2ubuntu2) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.3-10_arm64.deb ... Unpacking groff-base (1.22.3-10) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../03-libpipeline1_1.5.0-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.0-2) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.8.4-3_arm64.deb ... Unpacking man-db (2.8.4-3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.34-2_arm64.deb ... Unpacking libmagic-mgc (1:5.34-2) ... Selecting previously unselected package libmagic1:arm64. 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Unpacking zlib1g-dev:arm64 (1:1.2.11.dfsg-0ubuntu2) ... Selecting previously unselected package libeigen3-dev. Preparing to unpack .../43-libeigen3-dev_3.3.5-2_all.deb ... Unpacking libeigen3-dev (3.3.5-2) ... Selecting previously unselected package sbuild-build-depends-gemma-dummy. Preparing to unpack .../44-sbuild-build-depends-gemma-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-gemma-dummy (0.invalid.0) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libicu63:arm64 (63.1-4) ... Setting up libsigsegv2:arm64 (2.12-2) ... Setting up libelf1:arm64 (0.170-0.5.0ubuntu1) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:arm64 (2.58.1-2) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-9) ... Setting up libpipeline1:arm64 (1.5.0-2) ... Setting up m4 (1.4.18-1ubuntu1) ... Setting up libbsd0:arm64 (0.9.1-1) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7ubuntu3) ... Setting up libmagic-mgc (1:5.34-2) ... Setting up libmagic1:arm64 (1:5.34-2) ... Setting up libcroco3:arm64 (0.6.12-2) ... Setting up pkg-config (0.29.1-0ubuntu2) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up dwz (0.12-2) ... Setting up autotools-dev (20180224.1) ... Setting up shunit2 (2.1.6-1.1ubuntu1) ... Setting up bsdmainutils (11.1.2ubuntu2) ... 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 libgslcblas0:arm64 (2.5+dfsg-5) ... Setting up libgfortran5:arm64 (8.2.0-9ubuntu1) ... Setting up catch (1.12.1-1) ... Setting up autopoint (0.19.8.1-9) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.45.0-1) ... Setting up libopenblas-base:arm64 (0.3.3+ds-1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libgsl23:arm64 (2.5+dfsg-5) ... Setting up gettext (0.19.8.1-9) ... Setting up libgsl-dev (2.5+dfsg-5) ... Setting up libeigen3-dev (3.3.5-2) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.34-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.4-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libopenblas-dev:arm64 (0.3.3+ds-1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up libgfortran-8-dev:arm64 (8.2.0-9ubuntu1) ... Setting up libtool (2.4.6-6) ... Setting up po-debconf (1.0.20) ... Setting up gfortran-8 (8.2.0-9ubuntu1) ... Setting up gfortran (4:8.2.0-2ubuntu2) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up debhelper (11.3.2ubuntu1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (0.45.0-1) ... Setting up sbuild-build-depends-gemma-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-139-generic arm64 (aarch64) Toolchain package versions: binutils_2.31.1-7ubuntu1 dpkg-dev_1.19.0.5ubuntu5 g++-8_8.2.0-9ubuntu1 gcc-8_8.2.0-9ubuntu1 libc6-dev_2.28-0ubuntu1 libstdc++-8-dev_8.2.0-9ubuntu1 libstdc++6_8.2.0-9ubuntu1 linux-libc-dev_4.18.0-11.12 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.8.0~alpha2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1ubuntu8 base-passwd_3.5.45 bash_4.4.18-2ubuntu3 binutils_2.31.1-7ubuntu1 binutils-aarch64-linux-gnu_2.31.1-7ubuntu1 binutils-common_2.31.1-7ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.32-0.1ubuntu2 build-essential_12.5ubuntu2 bzip2_1.0.6-9 ca-certificates_20180409 catch_1.12.1-1 coreutils_8.28-1ubuntu2 cpp_4:8.2.0-2ubuntu2 cpp-8_8.2.0-9ubuntu1 dash_0.5.10.2-1 debconf_1.5.69 debhelper_11.3.2ubuntu1 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.45.0-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu4 dpkg_1.19.0.5ubuntu5 dpkg-dev_1.19.0.5ubuntu5 dwz_0.12-2 e2fslibs_1.44.4-2 e2fsprogs_1.44.4-2 fakeroot_1.23-1 fdisk_2.32-0.1ubuntu2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 g++_4:8.2.0-2ubuntu2 g++-8_8.2.0-9ubuntu1 gcc_4:8.2.0-2ubuntu2 gcc-8_8.2.0-9ubuntu1 gcc-8-base_8.2.0-9ubuntu1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gfortran_4:8.2.0-2ubuntu2 gfortran-8_8.2.0-9ubuntu1 gpg_2.2.8-3ubuntu1 gpg-agent_2.2.8-3ubuntu1 gpgconf_2.2.8-3ubuntu1 gpgv_2.2.8-3ubuntu1 grep_3.1-2ubuntu1 groff-base_1.22.3-10 gzip_1.6-5ubuntu2 hostname_3.21 init_1.55 init-system-helpers_1.55 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu10 libapt-pkg5.0_1.8.0~alpha2 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-9ubuntu1 libassuan0_2.5.1-2 libatomic1_8.2.0-9ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.3-1ubuntu3 libaudit1_1:2.8.3-1ubuntu3 libbinutils_2.31.1-7ubuntu1 libblkid1_2.32-0.1ubuntu2 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-0ubuntu1 libc-dev-bin_2.28-0ubuntu1 libc6_2.28-0ubuntu1 libc6-dev_2.28-0ubuntu1 libcap-ng0_0.7.9-1build1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-9ubuntu1 libcom-err2_1.44.4-2 libcomerr2_1.44.4-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2ubuntu2 libdb5.3_5.3.28+dfsg1-0.2 libdebconfclient0_0.244ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu4 libdpkg-perl_1.19.0.5ubuntu5 libeigen3-dev_3.3.5-2 libelf1_0.170-0.5.0ubuntu1 libext2fs2_1.44.4-2 libfakeroot_1.23-1 libfdisk1_2.32-0.1ubuntu2 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.45.0-1 libgcc-8-dev_8.2.0-9ubuntu1 libgcc1_1:8.2.0-9ubuntu1 libgcrypt20_1.8.4-3ubuntu1 libgdbm-compat4_1.18.1-1 libgdbm5_1.14.1-6 libgdbm6_1.18.1-1 libgfortran-8-dev_8.2.0-9ubuntu1 libgfortran5_8.2.0-9ubuntu1 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.6.4-2ubuntu2 libgomp1_8.2.0-9ubuntu1 libgpg-error0_1.32-3 libgsl-dev_2.5+dfsg-5 libgsl23_2.5+dfsg-5 libgslcblas0_2.5+dfsg-5 libhogweed4_3.4-1 libicu63_63.1-4 libidn11_1.33-2.2ubuntu1 libidn2-0_2.0.5-1 libip4tc0_1.6.1-2ubuntu2 libisl19_0.20-2 libitm1_8.2.0-9ubuntu1 libjson-c3_0.12.1-1.3 libkmod2_25-1ubuntu2 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblsan0_8.2.0-9ubuntu1 liblz4-1_1.8.2-1ubuntu1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32-0.1ubuntu2 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses6_6.1+20180210-4ubuntu1 libncursesw6_6.1+20180210-4ubuntu1 libnettle6_3.4-1 libnpth0_1.6-1 libopenblas-base_0.3.3+ds-1 libopenblas-dev_0.3.3+ds-1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpcre3_2:8.39-11 libperl5.26_5.26.2-7 libperl5.28_5.28.0-3 libpipeline1_1.5.0-2 libpng16-16_1.6.34-2 libprocps7_2:3.3.15-2ubuntu1 libreadline7_7.0-5 libseccomp2_2.3.3-3ubuntu2 libselinux1_2.8-1build2 libsemanage-common_2.8-1build2 libsemanage1_2.8-1build2 libsepol1_2.8-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsmartcols1_2.32-0.1ubuntu2 libsqlite3-0_3.25.3-1 libss2_1.44.4-2 libssl1.1_1.1.1-1ubuntu2 libstdc++-8-dev_8.2.0-9ubuntu1 libstdc++6_8.2.0-9ubuntu1 libsystemd0_239-7ubuntu10.3 libtasn1-6_4.13-3 libtinfo6_6.1+20180210-4ubuntu1 libtool_2.4.6-6 libtsan0_8.2.0-9ubuntu1 libubsan1_8.2.0-9ubuntu1 libudev1_239-7ubuntu10.3 libunistring2_0.9.10-1ubuntu1 libusb-0.1-4_2:0.1.12-32 libustr-1.0-1_1.0.4-6 libuuid1_2.32-0.1ubuntu2 libxml2_2.9.4+dfsg1-7ubuntu3 libzstd1_1.3.5+dfsg-1ubuntu1 linux-libc-dev_4.18.0-11.12 lockfile-progs_0.1.18 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1ubuntu1 make_4.2.1-1.2 man-db_2.8.4-3 mawk_1.3.3-17ubuntu3 mount_2.32-0.1ubuntu2 multiarch-support_2.28-0ubuntu1 ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 openssl_1.1.1-1ubuntu2 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-3 perl_5.28.0-3 perl-base_5.28.0-3 perl-modules-5.26_5.26.2-7 perl-modules-5.28_5.28.0-3 pinentry-curses_1.1.0-1build2 pkg-config_0.29.1-0ubuntu2 pkgbinarymangler_143 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu1 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gemma-dummy_0.invalid.0 sed_4.5-2 sensible-utils_0.0.12 shunit2_2.1.6-1.1ubuntu1 systemd_239-7ubuntu10.3 systemd-sysv_239-7ubuntu10.3 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu2 tar_1.30+dfsg-2 tzdata_2018g-1 ubuntu-keyring_2018.09.18.1 util-linux_2.32-0.1ubuntu2 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Nov 13 13:59:46 2018 UTC gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gemma_0.98+dfsg-3.dsc dpkg-source: info: extracting gemma in gemma-0.98+dfsg dpkg-source: info: unpacking gemma_0.98+dfsg.orig.tar.gz dpkg-source: info: unpacking gemma_0.98+dfsg-3.debian.tar.xz dpkg-source: info: applying Reproducible_builds.patch dpkg-source: info: applying no-lquadmath.patch dpkg-source: info: applying Makefile.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-15658639 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15658639 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15658639 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package gemma dpkg-buildpackage: info: source version 0.98+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build gemma-0.98+dfsg dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean dh_auto_clean make -j4 clean make[1]: Entering directory '/<>/gemma-0.98+dfsg' rm -vf ./src/*.o rm -vf ./src/*~ rm -vf ./test/src/*.o rm -vf ./bin/gemma rm -vf ./bin/unittests-gemma make[1]: Leaving directory '/<>/gemma-0.98+dfsg' debian/rules override_dh_clean make[1]: Entering directory '/<>/gemma-0.98+dfsg' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/gemma.substvars debian/gemma-doc.substvars debian/files rm -fr -- debian/gemma/ debian/tmp/ debian/gemma-doc/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) rm -f *.log rm -rf test/output/ rm -f bin/gemma make[1]: Leaving directory '/<>/gemma-0.98+dfsg' debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/gemma-0.98+dfsg' g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/bslmm.o src/bslmm.cpp g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/bslmmdap.o src/bslmmdap.cpp g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/debug.o src/debug.cpp g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/eigenlib.o src/eigenlib.cpp src/debug.cpp:60:44: warning: extra ‘;’ [-Wpedantic] bool is_debug_mode() { return debug_mode; }; ^ src/debug.cpp:61:54: warning: extra ‘;’ [-Wpedantic] bool is_debug_data_mode() { return debug_data_mode; }; ^ src/debug.cpp:62:49: warning: extra ‘;’ [-Wpedantic] bool is_no_check_mode() { return !debug_check; }; ^ src/debug.cpp:63:45: warning: extra ‘;’ [-Wpedantic] bool is_check_mode() { return debug_check; }; ^ src/debug.cpp:64:53: warning: extra ‘;’ [-Wpedantic] bool is_fpe_check_mode() { return debug_fpe_check; }; ^ src/debug.cpp:65:47: warning: extra ‘;’ [-Wpedantic] bool is_strict_mode() { return debug_strict; }; ^ src/debug.cpp:66:45: warning: extra ‘;’ [-Wpedantic] bool is_quiet_mode() { return debug_quiet; }; ^ src/debug.cpp:67:59: warning: extra ‘;’ [-Wpedantic] bool is_issue(uint issue) { return issue == debug_issue; }; ^ src/debug.cpp:68:47: warning: extra ‘;’ [-Wpedantic] bool is_legacy_mode() { return debug_legacy; }; ^ g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/fastblas.o src/fastblas.cpp g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/gemma.o src/gemma.cpp g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/gemma_io.o src/gemma_io.cpp g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/gzstream.o src/gzstream.cpp g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/lapack.o src/lapack.cpp g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/ldr.o src/ldr.cpp g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/lm.o src/lm.cpp g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/lmm.o src/lmm.cpp g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/logistic.o src/logistic.cpp g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/main.o src/main.cpp g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/mathfunc.o src/mathfunc.cpp g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/mvlmm.o src/mvlmm.cpp g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/param.o src/param.cpp g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/prdt.o src/prdt.cpp g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/varcov.o src/varcov.cpp g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/vc.o src/vc.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc src/bslmm.o src/bslmmdap.o src/debug.o src/eigenlib.o src/fastblas.o src/gemma.o src/gemma_io.o src/gzstream.o src/lapack.o src/ldr.o src/lm.o src/lmm.o src/logistic.o src/main.o src/mathfunc.o src/mvlmm.o src/param.o src/prdt.o src/varcov.o src/vc.o -lgsl -lz -lopenblas -lgfortran -o ./bin/gemma make[1]: Leaving directory '/<>/gemma-0.98+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/gemma-0.98+dfsg' dh_auto_test --no-parallel make -j1 check make[2]: Entering directory '/<>/gemma-0.98+dfsg' g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o test/src/unittests-main.o test/src/unittests-main.cpp g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o test/src/unittests-math.o test/src/unittests-math.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc ./test/src/unittests-main.o ./test/src/unittests-math.o src/bslmm.o src/bslmmdap.o src/debug.o src/eigenlib.o src/fastblas.o src/gemma.o src/gemma_io.o src/gzstream.o src/lapack.o src/ldr.o src/lm.o src/lmm.o src/logistic.o src/mathfunc.o src/mvlmm.o src/param.o src/prdt.o src/varcov.o src/vc.o -lgsl -lz -lopenblas -lgfortran -o ./bin/unittests-gemma ./bin/unittests-gemma Mismatch coordinates (1,0)0:3! This example computes real matrix C=alpha*A*B+beta*C using Intel(R) MKL function dgemm, where A, B, and C are matrices and alpha and beta are double precision scalars Initializing data for matrix multiplication C=A*B for matrix A(2000x200) and matrix B(200x1000) Allocating memory for matrices aligned on 64-byte boundary for better performance Intializing matrix data Computing matrix product using Intel(R) MKL dgemm function via CBLAS interface * RowMajor 101 transA 111 transB 111 m 2000 n 1000 k 200 * lda 200 ldb 1000 ldc 1000 alpha 1.000e+00 beta 0.000e+00 * A03 4.000e+00 B03 -4.000e+00 C03 0.000e+00 Asum 8.000e+10 Bsum -2.000e+10 Csum 0.000e+00 This example computes real matrix C=alpha*A*B+beta*C using Intel(R) MKL function dgemm, where A, B, and C are matrices and alpha and beta are double precision scalars Initializing data for matrix multiplication C=A*B for matrix A(2000x200) and matrix B(200x1000) Allocating memory for matrices aligned on 64-byte boundary for better performance Intializing matrix data Computing matrix product using Intel(R) MKL dgemm function via CBLAS interface Computations completed. =============================================================================== All tests passed (24 assertions in 4 test cases) rm -vf test/output/* cd test && ./dev_test_suite.sh | tee ../dev_test.log run system shunit2 testLinearModel GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno **** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno **** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno ## number of total individuals = 1940 ## number of analyzed individuals = 1410 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10768 **** DEBUG: entering in src/lm.cpp at line 383 in AnalyzeBimbam 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. ## total computation time = 0.151165 min testBXDStandardRelatednessMatrixKSingularError GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** DEBUG: entered in src/gemma_io.cpp at line 444 in ReadFile_cvt **** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno **** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno **** INFO: no intercept term is found in the cvt file: a column of 1s is added. **** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno GSL ERROR: matrix is singular in lu.c at line 266 errno 1 testBXDStandardRelatednessMatrixK GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** DEBUG: entered in src/gemma_io.cpp at line 444 in ReadFile_cvt **** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno **** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno **** INFO: no intercept term is found in the cvt file: a column of 1s is added. **** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno ## number of total individuals = 198 ## number of analyzed individuals = 67 ## number of covariates = 3 ## number of phenotypes = 1 ## number of total SNPs/var = 7320 ## number of analyzed SNPs = 7317 Calculating Relatedness Matrix ... **** DEBUG: entered in src/gemma_io.cpp at line 1397 in BimbamKin 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% **** INFO: Done. testBXDLMLikelihoodRatio GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** DEBUG: entered in src/gemma_io.cpp at line 444 in ReadFile_cvt **** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno **** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno **** INFO: no intercept term is found in the cvt file: a column of 1s is added. **** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno ## number of total individuals = 198 ## number of analyzed individuals = 67 ## number of covariates = 3 ## number of phenotypes = 1 ## number of total SNPs/var = 7320 ## number of analyzed SNPs = 7317 **** DEBUG: entering in src/lm.cpp at line 383 in AnalyzeBimbam 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% **** INFO: Done. testBXDLMMLikelihoodRatio GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** DEBUG: entered in src/gemma_io.cpp at line 444 in ReadFile_cvt **** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno **** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno **** INFO: no intercept term is found in the cvt file: a column of 1s is added. **** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno ## number of total individuals = 198 ## number of analyzed individuals = 67 ## number of covariates = 3 ## number of phenotypes = 1 ## number of total SNPs/var = 7320 ## number of analyzed SNPs = 7317 **** DEBUG: entered in src/gemma_io.cpp at line 1164 in ReadFile_kin Start Eigen-Decomposition... pve estimate =0.00100086 se(pve) =0.204166 **** DEBUG: ../example/BXD_geno.txt.gz in src/lmm.cpp at line 1649 in AnalyzeBimbam 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% ================================================== 100% **** DEBUG: LMM::WriteFiles in src/lmm.cpp at line 100 in WriteFiles **** INFO: Done. testCenteredRelatednessMatrixKLOCO1 GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** DEBUG: entered in src/gemma_io.cpp at line 153 in ReadFile_snps **** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno **** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno **** TEST MODE: trim individuals from 1940 to 400 **** TEST MODE: trim individuals from 1940 to 400 **** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno ## number of total individuals = 400 ## number of analyzed individuals = 247 ## number of covariates = 1 ## number of phenotypes = 1 ## leave one chromosome out (LOCO) = 1 ## number of total SNPs/var = 12226 ## number of considered SNPS = 1000 ## number of SNPS for K = 11182 ## number of SNPS for GWAS = 1044 ## number of analyzed SNPs = 889 Calculating Relatedness Matrix ... **** DEBUG: entered in src/gemma_io.cpp at line 1397 in BimbamKin 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. ## total computation time = 0.11529 min testUnivariateLinearMixedModelLOCO1 GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018 **** DEBUG: Reading Files ... entered in src/gemma_io.cpp at line 153 in ReadFile_snps **** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno **** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno **** TEST MODE: trim individuals from 1940 to 400 **** TEST MODE: trim individuals from 1940 to 400 **** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno ## number of total individuals = 400 ## number of analyzed individuals = 247 ## number of covariates = 1 ## number of phenotypes = 1 ## leave one chromosome out (LOCO) = 1 ## number of total SNPs/var = 12226 ## number of considered SNPS = 1000 ## number of SNPS for K = 11182 ## number of SNPS for GWAS = 1044 ## number of analyzed SNPs = 889 **** DEBUG: entered in src/gemma_io.cpp at line 1164 in ReadFile_kin Start Eigen-Decomposition... pve estimate =0.678775 se(pve) =0.0717914 **** DEBUG: ../example/mouse_hs1940.geno.txt.gz in src/lmm.cpp at line 1649 in AnalyzeBimbam **** DEBUG: Analyze subset of SNPs (LOCO) in src/lmm.cpp at line 1471 in Analyze 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% **** DEBUG: LMM::WriteFiles in src/lmm.cpp at line 100 in WriteFiles **** INFO: Done. ## total computation time = 0.0593842 min testPlinkCenteredRelatednessMatrixKLOCO1 testPlinkUnivariateLinearMixedModelLOCO1 testCorrelatedPhenotypesMvLLM GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno **** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno **** DEBUG: Can't figure out position for 1-10583-rs58108140 in src/gemma_io.cpp at line 719 in ReadFile_geno **** DEBUG: Can't figure out position for 1-10611-rs189107123 in src/gemma_io.cpp at line 719 in ReadFile_geno **** DEBUG: Can't figure out position for 1-13302-rs180734498 in src/gemma_io.cpp at line 719 in ReadFile_geno **** DEBUG: Can't figure out position for 1-13327-rs144762171 in src/gemma_io.cpp at line 719 in ReadFile_geno **** DEBUG: Can't figure out position for 1-13980-rs151276478 in src/gemma_io.cpp at line 719 in ReadFile_geno **** DEBUG: Can't figure out position for 1-30923-rs140337953 in src/gemma_io.cpp at line 719 in ReadFile_geno **** DEBUG: Can't figure out position for 1-51479-rs116400033 in src/gemma_io.cpp at line 719 in ReadFile_geno **** DEBUG: Can't figure out position for 1-52058-rs62637813 in src/gemma_io.cpp at line 719 in ReadFile_geno **** DEBUG: Can't figure out position for 1-52238-rs150021059 in src/gemma_io.cpp at line 719 in ReadFile_geno **** DEBUG: Can't figure out position for 1-54421-rs146477069 in src/gemma_io.cpp at line 719 in ReadFile_geno **** DEBUG: Skipping similar warnings in src/gemma_io.cpp at line 721 in ReadFile_geno ## number of total individuals = 1000 ## number of analyzed individuals = 1000 ## number of covariates = 1 ## number of phenotypes = 5 ## number of total SNPs/var = 100 ## number of analyzed SNPs = 100 **** DEBUG: entered in src/gemma_io.cpp at line 1299 in ReadFile_eigenU **** DEBUG: entered in src/gemma_io.cpp at line 1348 in ReadFile_eigenD **** DEBUG: entering in src/mvlmm.cpp at line 2973 in AnalyzeBimbam **** DEBUG: MphInitial in src/mvlmm.cpp at line 2770 in MphInitial REMLE estimate for Vg in the null model: 0.8091 0.1435 0.0660 -0.1456 -0.0664 0.1165 0.0907 0.0362 -0.0830 0.0639 -0.5533 -0.0985 0.1171 -0.0765 0.4131 se(Vg): 0.0736 0.0355 0.0299 0.0421 0.0264 0.0422 0.0444 0.0279 0.0430 0.0479 0.0516 0.0254 0.0295 0.0313 0.0389 REMLE estimate for Ve in the null model: 0.0334 0.0267 0.4502 -0.0529 -0.0883 0.6004 0.0683 0.1413 -0.6502 0.8400 -0.0128 -0.0041 -0.0706 0.0880 0.0419 se(Ve): 0.0378 0.0252 0.0329 0.0299 0.0281 0.0456 0.0332 0.0319 0.0494 0.0583 0.0266 0.0186 0.0215 0.0242 0.0208 REMLE likelihood = -3813.3258 MLE estimate for Vg in the null model: 0.8082 0.1434 0.0660 -0.1455 -0.0664 0.1165 0.0906 0.0362 -0.0830 0.0639 -0.5528 -0.0984 0.1170 -0.0764 0.4127 se(Vg): 0.0735 0.0355 0.0298 0.0420 0.0264 0.0421 0.0443 0.0278 0.0430 0.0478 0.0515 0.0254 0.0295 0.0313 0.0388 MLE estimate for Ve in the null model: 0.0334 0.0267 0.4497 -0.0529 -0.0882 0.5997 0.0682 0.1412 -0.6495 0.8391 -0.0128 -0.0040 -0.0705 0.0879 0.0418 se(Ve): 0.0378 0.0252 0.0329 0.0298 0.0281 0.0455 0.0331 0.0318 0.0493 0.0582 0.0265 0.0185 0.0215 0.0242 0.0207 MLE likelihood = -3814.3913 0% ================================================== 100% **** INFO: Done. Ran 10 tests. OK tail -n 1 dev_test.log | grep -q 'OK' rm -vf test/output/* removed 'test/output/BXD.cXX.txt' removed 'test/output/BXD.log.txt' removed 'test/output/BXD_LMM_LR.assoc.txt' removed 'test/output/BXD_LMM_LR.log.txt' removed 'test/output/BXD_LM_LR.assoc.txt' removed 'test/output/BXD_LM_LR.log.txt' removed 'test/output/corrpheno.assoc.txt' removed 'test/output/corrpheno.log.txt' removed 'test/output/mouse_hs1940_CD8_LOCO1_lmm.assoc.txt' removed 'test/output/mouse_hs1940_CD8_LOCO1_lmm.log.txt' removed 'test/output/mouse_hs1940_CD8_lm.assoc.txt' removed 'test/output/mouse_hs1940_CD8_lm.log.txt' removed 'test/output/mouse_hs1940_LOCO1.cXX.txt' removed 'test/output/mouse_hs1940_LOCO1.log.txt' cd test && ./test_suite.sh | tee ../test.log run system shunit2 testBslmm1 GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno **** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno **** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno ## number of total individuals = 1940 ## number of analyzed individuals = 757 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10775 **** DEBUG: entered in src/gemma_io.cpp at line 1689 in ReadFile_geno Start Eigen-Decomposition... pve estimate =0.590431 se(pve) =0.0480392 Calculating UtX... initial value of h = 0.590431 initial value of rho = 0.41375 initial value of pi = 0.00269142 initial value of |gamma| = 29 0% 0.00 ==== 9% 0.16 ========= 18% 0.17 ============= 27% 0.17 ================== 36% 0.17 ====================== 45% 0.17 =========================== 55% 0.16 =============================== 64% 0.16 ==================================== 73% 0.16 ======================================== 82% 0.16 ============================================= 91% 0.16 ================================================== 100% 0.16 **** INFO: Done. testBslmm2 GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno **** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno **** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno ## number of total individuals = 1940 ## number of analyzed individuals = 757 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10775 Calculating Relatedness Matrix ... **** DEBUG: entered in src/gemma_io.cpp at line 1397 in BimbamKin 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testBslmm3 GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno **** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno **** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno ## number of total individuals = 1940 ## number of analyzed individuals = 757 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10775 **** DEBUG: entered in src/gemma_io.cpp at line 1689 in ReadFile_geno Start Eigen-Decomposition... pve estimate =0.372151 se(pve) =0.0522377 Calculating UtX... initial value of h = 0.372151 initial value of rho = 0.393216 initial value of pi = 0.00194896 initial value of |gamma| = 21 0% 0.00 ==== 9% 0.26 ========= 18% 0.25 ============= 27% 0.24 ================== 36% 0.23 ====================== 45% 0.23 =========================== 55% 0.23 =============================== 64% 0.23 ==================================== 73% 0.23 ======================================== 82% 0.22 ============================================= 91% 0.22 ================================================== 100% 0.22 **** INFO: Done. testBslmm4 GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** DEBUG: entered in src/gemma_io.cpp at line 2170 in ReadFile_est **** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno **** DEBUG: entered in src/gemma_io.cpp at line 2236 in CountFileLines **** DEBUG: entered in src/gemma_io.cpp at line 342 in ReadFile_column **** DEBUG: ReadFile_log in src/gemma_io.cpp at line 239 in ReadFile_log ## number of total individuals = 1940 ## number of analyzed individuals = 757 ## number of covariates = 1 ## number of phenotypes = 1 Adding Breeding Values ... **** DEBUG: entered in src/gemma_io.cpp at line 1164 in ReadFile_kin Start Eigen-Decomposition... **** DEBUG: entering in src/prdt.cpp at line 208 in AnalyzeBimbam 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testBslmm5 GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** DEBUG: entered in src/gemma_io.cpp at line 2170 in ReadFile_est **** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno **** DEBUG: entered in src/gemma_io.cpp at line 2236 in CountFileLines **** DEBUG: ReadFile_log in src/gemma_io.cpp at line 239 in ReadFile_log ## number of total individuals = 1940 ## number of analyzed individuals = 757 ## number of covariates = 1 ## number of phenotypes = 1 **** DEBUG: entering in src/prdt.cpp at line 208 in AnalyzeBimbam 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testCenteredRelatednessMatrixKFullLOCO1 GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno **** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno **** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno ## number of total individuals = 1940 ## number of analyzed individuals = 1410 ## number of covariates = 1 ## number of phenotypes = 1 ## leave one chromosome out (LOCO) = 1 ## number of total SNPs/var = 12226 ## number of SNPS for K = 11182 ## number of SNPS for GWAS = 1044 ## number of analyzed SNPs = 10768 Calculating Relatedness Matrix ... **** DEBUG: entered in src/gemma_io.cpp at line 1397 in BimbamKin 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testUnivariateLinearMixedModelFullLOCO1 GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018 **** DEBUG: ReadFile_annoReading Files ... in src/gemma_io.cpp at line 282 in ReadFile_anno **** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno **** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno ## number of total individuals = 1940 ## number of analyzed individuals = 1410 ## number of covariates = 1 ## number of phenotypes = 1 ## leave one chromosome out (LOCO) = 1 ## number of total SNPs/var = 12226 ## number of SNPS for K = 11182 ## number of SNPS for GWAS = 1044 ## number of analyzed SNPs = 10768 **** DEBUG: entered in src/gemma_io.cpp at line 1164 in ReadFile_kin Start Eigen-Decomposition... pve estimate =0.593114 se(pve) =0.0332587 **** DEBUG: ../example/mouse_hs1940.geno.txt.gz in src/lmm.cpp at line 1649 in AnalyzeBimbam **** DEBUG: Analyze subset of SNPs (LOCO) in src/lmm.cpp at line 1471 in Analyze 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% **** DEBUG: LMM::WriteFiles in src/lmm.cpp at line 100 in WriteFiles **** INFO: Done. ## total computation time = 0.443344 min testCenteredRelatednessMatrixK GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno **** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno **** DEBUG: Can't figure out position for rs3683945 in src/gemma_io.cpp at line 719 in ReadFile_geno **** DEBUG: Can't figure out position for rs3707673 in src/gemma_io.cpp at line 719 in ReadFile_geno **** DEBUG: Can't figure out position for rs6269442 in src/gemma_io.cpp at line 719 in ReadFile_geno **** DEBUG: Can't figure out position for rs6336442 in src/gemma_io.cpp at line 719 in ReadFile_geno **** DEBUG: Can't figure out position for rs13475699 in src/gemma_io.cpp at line 719 in ReadFile_geno **** DEBUG: Can't figure out position for rs13475700 in src/gemma_io.cpp at line 719 in ReadFile_geno **** DEBUG: Can't figure out position for rs3658242 in src/gemma_io.cpp at line 719 in ReadFile_geno **** DEBUG: Can't figure out position for rs6243160 in src/gemma_io.cpp at line 719 in ReadFile_geno **** DEBUG: Can't figure out position for rs13475701 in src/gemma_io.cpp at line 719 in ReadFile_geno **** DEBUG: Can't figure out position for rs6198069 in src/gemma_io.cpp at line 719 in ReadFile_geno **** DEBUG: Skipping similar warnings in src/gemma_io.cpp at line 721 in ReadFile_geno ## number of total individuals = 1940 ## number of analyzed individuals = 1410 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10768 Calculating Relatedness Matrix ... **** DEBUG: entered in src/gemma_io.cpp at line 1397 in BimbamKin 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testUnivariateLinearMixedModel GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno **** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno **** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno ## number of total individuals = 1940 ## number of analyzed individuals = 1410 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10768 **** DEBUG: entered in src/gemma_io.cpp at line 1164 in ReadFile_kin Start Eigen-Decomposition... pve estimate =0.608801 se(pve) =0.032774 **** DEBUG: ../example/mouse_hs1940.geno.txt.gz in src/lmm.cpp at line 1649 in AnalyzeBimbam 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% **** DEBUG: LMM::WriteFiles in src/lmm.cpp at line 100 in WriteFiles **** INFO: Done. ## total computation time = 1.29899 min testLinearMixedModelPhenotypes GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno **** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno **** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno ## number of total individuals = 1940 ## number of analyzed individuals = 1197 ## number of covariates = 1 ## number of phenotypes = 2 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10758 **** DEBUG: entered in src/gemma_io.cpp at line 1164 in ReadFile_kin Start Eigen-Decomposition... **** DEBUG: entering in src/mvlmm.cpp at line 2973 in AnalyzeBimbam **** DEBUG: MphInitial in src/mvlmm.cpp at line 2770 in MphInitial REMLE estimate for Vg in the null model: 1.3940 -0.2267 2.0817 se(Vg): 0.1567 0.1363 0.2359 REMLE estimate for Ve in the null model: 0.3489 0.0491 0.4144 se(Ve): 0.0206 0.0166 0.0267 REMLE likelihood = -2855.1664 MLE estimate for Vg in the null model: 1.3959 -0.2267 2.0854 se(Vg): 0.1568 0.1365 0.2361 MLE estimate for Ve in the null model: 0.3483 0.0490 0.4136 se(Ve): 0.0206 0.0166 0.0266 MLE likelihood = -2856.0280 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testPlinkStandardRelatednessMatrixK GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** DEBUG: entered in src/gemma_io.cpp at line 511 in ReadFile_bim **** DEBUG: entered in src/gemma_io.cpp at line 558 in ReadFile_fam **** DEBUG: entered in src/gemma_io.cpp at line 857 in ReadFile_bed ## number of total individuals = 427 ## number of analyzed individuals = 427 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 358499 ## number of analyzed SNPs = 273349 Calculating Relatedness Matrix ... **** DEBUG: entered in src/gemma_io.cpp at line 1546 in PlinkKin 0% 0% 1% 1% 1% 1% 2% 2% = 2% = 3% = 3% = 3% = 3% = 4% = 4% == 4% == 4% == 5% == 5% == 5% == 6% == 6% === 6% === 6% === 7% === 7% === 7% === 8% === 8% ==== 8% ==== 8% ==== 9% ==== 9% ==== 9% ==== 9% ==== 10% ===== 10% ===== 10% ===== 11% ===== 11% ===== 11% ===== 11% ===== 12% ===== 12% ====== 12% ====== 13% ====== 13% ====== 13% ====== 13% ====== 14% ====== 14% ======= 14% ======= 15% ======= 15% ======= 15% ======= 15% ======= 16% ======= 16% ======== 16% ======== 16% ======== 17% ======== 17% ======== 17% ======== 18% ======== 18% ========= 18% ========= 18% ========= 19% ========= 19% ========= 19% ========= 20% ========= 20% ========== 20% ========== 20% ========== 21% ========== 21% ========== 21% ========== 21% ========== 22% =========== 22% =========== 22% =========== 23% =========== 23% =========== 23% =========== 23% =========== 24% =========== 24% ============ 24% ============ 25% 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ReadFile_cvt **** DEBUG: entered in src/gemma_io.cpp at line 511 in ReadFile_bim **** DEBUG: entered in src/gemma_io.cpp at line 558 in ReadFile_fam **** INFO: no intercept term is found in the cvt file: a column of 1s is added. **** DEBUG: entered in src/gemma_io.cpp at line 857 in ReadFile_bed ## number of total individuals = 427 ## number of analyzed individuals = 427 ## number of covariates = 2 ## number of phenotypes = 1 ## number of total SNPs/var = 358499 ## number of analyzed SNPs = 223242 **** DEBUG: entered in src/gemma_io.cpp at line 1164 in ReadFile_kin Start Eigen-Decomposition... pve estimate =0.365545 se(pve) =0.47481 **** DEBUG: ../example/HLC.bed in src/lmm.cpp at line 1698 in AnalyzePlink 0% 2% = 4% == 6% === 8% ==== 10% ===== 12% ====== 14% ======= 16% ======== 18% ========= 20% ========== 22% =========== 24% ============ 26% ============= 28% ============== 30% =============== 32% ================ 34% ================= 36% ================== 38% =================== 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Ran 12 tests. OK tail -n 1 test.log | grep -q 'OK' test.log make[2]: Leaving directory '/<>/gemma-0.98+dfsg' make[1]: Leaving directory '/<>/gemma-0.98+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a rm -f -- debian/gemma.substvars rm -fr -- debian/.debhelper/generated/gemma/ debian/gemma/ debian/tmp/ dh_auto_install -a install -d /<>/gemma-0.98\+dfsg/debian/tmp dh_install -a install -d debian/gemma/usr/bin cp --reflink=auto -a ./bin/gemma debian/gemma/usr/bin/ install -d debian/.debhelper/generated/gemma install -d debian/.debhelper/generated/gemma-doc dh_installdocs -a install -d debian/gemma/usr/share/doc/gemma cp --reflink=auto -a ./RELEASE-NOTES.md debian/gemma/usr/share/doc/gemma cp --reflink=auto -a ./README.md debian/gemma/usr/share/doc/gemma chown -R 0:0 debian/gemma/usr/share/doc chmod -R u\+rw,go=rX debian/gemma/usr/share/doc install -p -m0644 debian/copyright debian/gemma/usr/share/doc/gemma/copyright dh_installchangelogs -a install -p -m0644 debian/changelog debian/gemma/usr/share/doc/gemma/changelog.Debian dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a cd debian/gemma chmod a-x usr/share/doc/gemma/README.md usr/share/doc/gemma/RELEASE-NOTES.md usr/share/doc/gemma/changelog.Debian gzip -9nf usr/share/doc/gemma/README.md usr/share/doc/gemma/RELEASE-NOTES.md usr/share/doc/gemma/changelog.Debian cd '/<>/gemma-0.98+dfsg' dh_fixperms -a find debian/gemma -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/gemma ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/gemma/usr/share/doc -type f -a -true -a ! -regex 'debian/gemma/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/gemma/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/gemma -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/gemma/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing -a dh_strip -a install -d debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/3e objcopy --only-keep-debug --compress-debug-sections debian/gemma/usr/bin/gemma debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/3e/f659c36fe5f489abeb3099c617f46cfe40b07f.debug chmod 0644 -- debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/3e/f659c36fe5f489abeb3099c617f46cfe40b07f.debug chown 0:0 -- debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/3e/f659c36fe5f489abeb3099c617f46cfe40b07f.debug strip --remove-section=.comment --remove-section=.note debian/gemma/usr/bin/gemma objcopy --add-gnu-debuglink debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/3e/f659c36fe5f489abeb3099c617f46cfe40b07f.debug debian/gemma/usr/bin/gemma install -d debian/.debhelper/gemma/dbgsym-root/usr/share/doc ln -s gemma debian/.debhelper/gemma/dbgsym-root/usr/share/doc/gemma-dbgsym dh_makeshlibs -a rm -f debian/gemma/DEBIAN/shlibs dh_shlibdeps -a install -d debian/gemma/DEBIAN dpkg-shlibdeps -Tdebian/gemma.substvars debian/gemma/usr/bin/gemma dh_installdeb -a dh_gencontrol -a echo misc:Depends= >> debian/gemma.substvars echo misc:Pre-Depends= >> debian/gemma.substvars install -d debian/.debhelper/gemma/dbgsym-root/DEBIAN dpkg-gencontrol -pgemma -ldebian/changelog -Tdebian/gemma.substvars -Pdebian/.debhelper/gemma/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=gemma-dbgsym "-DDepends=gemma (= \${binary:Version})" "-DDescription=debug symbols for gemma" -DBuild-Ids=3ef659c36fe5f489abeb3099c617f46cfe40b07f -DSection=debug -DPackage-Type=ddeb -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/gemma/dbgsym-root/DEBIAN/control chown 0:0 -- debian/.debhelper/gemma/dbgsym-root/DEBIAN/control dpkg-gencontrol -pgemma -ldebian/changelog -Tdebian/gemma.substvars -Pdebian/gemma -UMulti-Arch chmod 0644 -- debian/gemma/DEBIAN/control chown 0:0 -- debian/gemma/DEBIAN/control dh_md5sums -a (cd debian/gemma >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null chmod 0644 -- debian/gemma/DEBIAN/md5sums chown 0:0 -- debian/gemma/DEBIAN/md5sums (cd debian/.debhelper/gemma/dbgsym-root >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null chmod 0644 -- debian/.debhelper/gemma/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/gemma/dbgsym-root/DEBIAN/md5sums dh_builddeb -a dpkg-deb --build debian/gemma .. install -d debian/.debhelper/scratch-space/build-gemma dpkg-deb --build debian/.debhelper/gemma/dbgsym-root debian/.debhelper/scratch-space/build-gemma INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 pkgstriptranslations: processing gemma (in debian/gemma); do_strip: , oemstrip: pkgstriptranslations: processing gemma-dbgsym (in debian/.debhelper/gemma/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/gemma/DEBIAN/control, package gemma, directory debian/gemma pkgstripfiles: processing control file: debian/.debhelper/gemma/dbgsym-root/DEBIAN/control, package gemma-dbgsym, directory debian/.debhelper/gemma/dbgsym-root dpkg-deb: building package 'gemma-dbgsym' in 'debian/.debhelper/scratch-space/build-gemma/gemma-dbgsym_0.98+dfsg-3_arm64.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package gemma ... pkgstripfiles: No PNG files. dpkg-deb: building package 'gemma' in '../gemma_0.98+dfsg-3_arm64.deb'. Renaming gemma-dbgsym_0.98+dfsg-3_arm64.deb to gemma-dbgsym_0.98+dfsg-3_arm64.ddeb mv debian/.debhelper/scratch-space/build-gemma/gemma-dbgsym_0.98\+dfsg-3_arm64.deb ../gemma-dbgsym_0.98\+dfsg-3_arm64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../gemma_0.98+dfsg-3_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build gemma-0.98+dfsg dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20181113-2337 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ gemma_0.98+dfsg-3_arm64.changes: -------------------------------- Format: 1.8 Date: Tue, 13 Nov 2018 13:33:54 +0000 Source: gemma Binary: gemma gemma-doc Architecture: arm64 Version: 0.98+dfsg-3 Distribution: disco-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Graham Inggs Description: gemma - Genome-wide Efficient Mixed Model Association gemma-doc - Example folder for GEMMA Changes: gemma (0.98+dfsg-3) unstable; urgency=medium . * Team upload * Allow output to stderr in autopkgtests Checksums-Sha1: ad8ad1e949c9aa7043fe36a97f3bbdd1fcf74759 7876000 gemma-dbgsym_0.98+dfsg-3_arm64.ddeb a2409a87595b76b5152c7b59cf5faf84fdd35fb2 5248 gemma_0.98+dfsg-3_arm64.buildinfo 1f9e2714cbe35f470aec14cfcf969060bcacaa28 285448 gemma_0.98+dfsg-3_arm64.deb Checksums-Sha256: 284d13e37071977d374aa1b9e5975f4518959480271476a61010e18d1affeb2b 7876000 gemma-dbgsym_0.98+dfsg-3_arm64.ddeb 708635e089b95237ed34e38aa827d68d0c61ec23bdbd3a2933481ecc32513a0a 5248 gemma_0.98+dfsg-3_arm64.buildinfo db81d893045e4c0c18c44fe445c051c2d5b547e36b682fb791e69521118ac449 285448 gemma_0.98+dfsg-3_arm64.deb Files: 63a257475d7d7b2cc4463bbac86e11b7 7876000 debug optional gemma-dbgsym_0.98+dfsg-3_arm64.ddeb 089378c31c9869b1bb6314efb47f4087 5248 science optional gemma_0.98+dfsg-3_arm64.buildinfo c7bcd22df4503b536f224794da68b179 285448 science optional gemma_0.98+dfsg-3_arm64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ gemma_0.98+dfsg-3_arm64.deb --------------------------- new debian package, version 2.0. size 285448 bytes: control archive=1404 bytes. 2018 bytes, 35 lines control 327 bytes, 5 lines md5sums Package: gemma Version: 0.98+dfsg-3 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1091 Depends: libc6 (>= 2.17), libgcc1 (>= 1:3.0), libgsl23 (>= 2.5), libopenblas-base, libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4) Section: science Priority: optional Homepage: http://www.xzlab.org/software.html Description: Genome-wide Efficient Mixed Model Association GEMMA is the software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model and some of its close relatives for genome-wide association studies (GWAS): . * It fits a univariate linear mixed model (LMM) for marker association tests with a single phenotype to account for population stratification and sample structure, and for estimating the proportion of variance in phenotypes explained (PVE) by typed genotypes (i.e. "chip heritability"). * It fits a multivariate linear mixed model (mvLMM) for testing marker associations with multiple phenotypes simultaneously while controlling for population stratification, and for estimating genetic correlations among complex phenotypes. * It fits a Bayesian sparse linear mixed model (BSLMM) using Markov chain Monte Carlo (MCMC) for estimating PVE by typed genotypes, predicting phenotypes, and identifying associated markers by jointly modeling all markers while controlling for population structure. * It estimates variance component/chip heritability, and partitions it by different SNP functional categories. In particular, it uses HE regression or REML AI algorithm to estimate variance components when individual-level data are available. It uses MQS to estimate variance components when only summary statisics are available. . GEMMA is computationally efficient for large scale GWAS and uses freely available open-source numerical libraries. drwxr-xr-x root/root 0 2018-11-13 13:33 ./ drwxr-xr-x root/root 0 2018-11-13 13:33 ./usr/ drwxr-xr-x root/root 0 2018-11-13 13:33 ./usr/bin/ -rwxr-xr-x root/root 1096824 2018-11-13 13:33 ./usr/bin/gemma drwxr-xr-x root/root 0 2018-11-13 13:33 ./usr/share/ drwxr-xr-x root/root 0 2018-11-13 13:33 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-11-13 13:33 ./usr/share/doc/gemma/ -rw-r--r-- root/root 4498 2018-09-28 16:23 ./usr/share/doc/gemma/README.md.gz -rw-r--r-- root/root 2164 2018-09-28 16:23 ./usr/share/doc/gemma/RELEASE-NOTES.md.gz -rw-r--r-- root/root 721 2018-11-13 13:33 ./usr/share/doc/gemma/changelog.Debian.gz -rw-r--r-- root/root 2231 2018-10-22 05:32 ./usr/share/doc/gemma/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build-Space: 475640 Build-Time: 967 Distribution: disco-proposed Host Architecture: arm64 Install-Time: 20 Job: gemma_0.98+dfsg-3.dsc Machine Architecture: arm64 Package: gemma Package-Time: 992 Source-Version: 0.98+dfsg-3 Space: 475640 Status: successful Version: 0.98+dfsg-3 -------------------------------------------------------------------------------- Finished at 20181113-2337 Build needed 00:16:32, 475640k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=disco --arch=arm64 PACKAGEBUILD-15658639 Scanning for processes to kill in build PACKAGEBUILD-15658639