https://launchpad.net/ubuntu/+source/gemma/0.98.1+dfsg-1/+build/15793601 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-arm64-028 4.4.0-141-generic #167-Ubuntu SMP Wed Dec 5 10:50:27 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_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 30 Jan 08:50:38 ntpdate[1813]: adjust time server 10.211.37.1 offset 0.005314 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=arm64 PACKAGEBUILD-15793601 /home/buildd/filecache-default/12198815be27835f4527655ec2ee7fabeb41ea11 Creating target for build PACKAGEBUILD-15793601 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=arm64 PACKAGEBUILD-15793601 Starting target for build PACKAGEBUILD-15793601 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=arm64 PACKAGEBUILD-15793601 '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-15793601 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=arm64 PACKAGEBUILD-15793601 Updating target for build PACKAGEBUILD-15793601 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 [971 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe arm64 Packages [8738 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5213 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 Packages [50.3 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [22.4 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe arm64 Packages [159 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [98.2 kB] Fetched 16.2 MB in 6s (2654 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libreadline7 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: libreadline8 The following packages will be upgraded: apt bash binutils binutils-aarch64-linux-gnu binutils-common bsdutils ca-certificates coreutils cpp-8 dash debconf debianutils dpkg dpkg-dev e2fslibs e2fsprogs fdisk findutils g++-8 gcc-8 gcc-8-base gpg gpg-agent gpgconf gpgv grep gzip init init-system-helpers libapt-pkg5.0 libargon2-1 libasan5 libassuan0 libatomic1 libbinutils libblkid1 libcap-ng0 libcc1-0 libcom-err2 libcomerr2 libdpkg-perl libext2fs2 libfdisk1 libgcc-8-dev libgcc1 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error0 libhogweed4 libitm1 libjson-c3 liblsan0 liblz4-1 liblzma5 libmount1 libmpfr6 libnettle6 libpng16-16 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libss2 libstdc++-8-dev libstdc++6 libtsan0 libubsan1 libuuid1 libzstd1 linux-libc-dev login mount passwd readline-common sed tar tzdata util-linux xz-utils zlib1g 82 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 46.2 MB of archives. After this operation, 5744 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main arm64 debianutils arm64 4.8.6.1 [85.4 kB] Get:2 http://ftpmaster.internal/ubuntu disco/main arm64 bash arm64 5.0-2ubuntu1 [611 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main arm64 bsdutils arm64 1:2.33.1-0.1ubuntu1 [61.4 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main arm64 coreutils arm64 8.30-1ubuntu1 [1173 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main arm64 tar arm64 1.30+dfsg-4 [231 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main arm64 dpkg arm64 1.19.2ubuntu2 [1088 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main arm64 debconf all 1.5.70 [122 kB] Get:8 http://ftpmaster.internal/ubuntu disco/main arm64 dash arm64 0.5.10.2-4ubuntu1 [84.1 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main arm64 findutils arm64 4.6.0+git+20190105-2 [322 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main arm64 grep arm64 3.3-1 [143 kB] Get:11 http://ftpmaster.internal/ubuntu disco/main arm64 gzip arm64 1.9-3 [91.6 kB] Get:12 http://ftpmaster.internal/ubuntu disco/main arm64 libsmartcols1 arm64 2.33.1-0.1ubuntu1 [86.5 kB] Get:13 http://ftpmaster.internal/ubuntu disco/main arm64 libuuid1 arm64 2.33.1-0.1ubuntu1 [20.4 kB] Get:14 http://ftpmaster.internal/ubuntu disco/main arm64 libblkid1 arm64 2.33.1-0.1ubuntu1 [126 kB] Get:15 http://ftpmaster.internal/ubuntu disco/main arm64 libfdisk1 arm64 2.33.1-0.1ubuntu1 [160 kB] Get:16 http://ftpmaster.internal/ubuntu disco/main arm64 libmount1 arm64 2.33.1-0.1ubuntu1 [137 kB] Get:17 http://ftpmaster.internal/ubuntu disco/main arm64 fdisk arm64 2.33.1-0.1ubuntu1 [113 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main arm64 login arm64 1:4.5-1.1ubuntu1 [262 kB] Get:19 http://ftpmaster.internal/ubuntu disco/main arm64 util-linux arm64 2.33.1-0.1ubuntu1 [965 kB] Get:20 http://ftpmaster.internal/ubuntu disco/main arm64 sed arm64 4.7-1 [186 kB] Get:21 http://ftpmaster.internal/ubuntu disco/main arm64 init-system-helpers all 1.56+nmu1 [38.2 kB] Get:22 http://ftpmaster.internal/ubuntu disco/main arm64 libnettle6 arm64 3.4.1-1 [122 kB] Get:23 http://ftpmaster.internal/ubuntu disco/main arm64 libhogweed4 arm64 3.4.1-1 [137 kB] Get:24 http://ftpmaster.internal/ubuntu disco/main arm64 libgnutls30 arm64 3.6.5-2ubuntu1 [699 kB] Get:25 http://ftpmaster.internal/ubuntu disco/main arm64 libcc1-0 arm64 8.2.0-15ubuntu1 [46.0 kB] Get:26 http://ftpmaster.internal/ubuntu disco/main arm64 gcc-8-base arm64 8.2.0-15ubuntu1 [18.6 kB] Get:27 http://ftpmaster.internal/ubuntu disco/main arm64 libgcc1 arm64 1:8.2.0-15ubuntu1 [34.3 kB] Get:28 http://ftpmaster.internal/ubuntu disco/main arm64 libgomp1 arm64 8.2.0-15ubuntu1 [69.6 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main arm64 libitm1 arm64 8.2.0-15ubuntu1 [24.4 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main arm64 libatomic1 arm64 8.2.0-15ubuntu1 [9136 B] Get:31 http://ftpmaster.internal/ubuntu disco/main arm64 libasan5 arm64 8.2.0-15ubuntu1 [337 kB] Get:32 http://ftpmaster.internal/ubuntu disco/main arm64 liblsan0 arm64 8.2.0-15ubuntu1 [121 kB] Get:33 http://ftpmaster.internal/ubuntu disco/main arm64 libtsan0 arm64 8.2.0-15ubuntu1 [268 kB] Get:34 http://ftpmaster.internal/ubuntu disco/main arm64 libubsan1 arm64 8.2.0-15ubuntu1 [113 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main arm64 g++-8 arm64 8.2.0-15ubuntu1 [8495 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main arm64 libstdc++-8-dev arm64 8.2.0-15ubuntu1 [1515 kB] Get:37 http://ftpmaster.internal/ubuntu disco/main arm64 libgcc-8-dev arm64 8.2.0-15ubuntu1 [851 kB] Get:38 http://ftpmaster.internal/ubuntu disco/main arm64 gcc-8 arm64 8.2.0-15ubuntu1 [8222 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main arm64 cpp-8 arm64 8.2.0-15ubuntu1 [7408 kB] Get:40 http://ftpmaster.internal/ubuntu disco/main arm64 libstdc++6 arm64 8.2.0-15ubuntu1 [371 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main arm64 libmpfr6 arm64 4.0.2~rc1-1 [212 kB] Get:42 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 zlib1g arm64 1:1.2.11.dfsg-1ubuntu2 [51.6 kB] Get:43 http://ftpmaster.internal/ubuntu disco/main arm64 libbinutils arm64 2.31.1-11ubuntu1 [461 kB] Get:44 http://ftpmaster.internal/ubuntu disco/main arm64 binutils-common arm64 2.31.1-11ubuntu1 [194 kB] Get:45 http://ftpmaster.internal/ubuntu disco/main arm64 binutils arm64 2.31.1-11ubuntu1 [3364 B] Get:46 http://ftpmaster.internal/ubuntu disco/main arm64 binutils-aarch64-linux-gnu arm64 2.31.1-11ubuntu1 [2177 kB] Get:47 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 liblz4-1 arm64 1.8.3-1ubuntu1 [64.6 kB] Get:48 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 liblzma5 arm64 5.2.4-1 [89.1 kB] Get:49 http://ftpmaster.internal/ubuntu disco/main arm64 libzstd1 arm64 1.3.8+dfsg-3 [204 kB] Get:50 http://ftpmaster.internal/ubuntu disco/main arm64 libapt-pkg5.0 arm64 1.8.0~beta1 [749 kB] Get:51 http://ftpmaster.internal/ubuntu disco/main arm64 libgpg-error0 arm64 1.33-3 [54.8 kB] Get:52 http://ftpmaster.internal/ubuntu disco/main arm64 gpgv arm64 2.2.12-1ubuntu2 [182 kB] Get:53 http://ftpmaster.internal/ubuntu disco/main arm64 apt arm64 1.8.0~beta1 [1121 kB] Get:54 http://ftpmaster.internal/ubuntu disco/main arm64 libext2fs2 arm64 1.44.5-1 [153 kB] Get:55 http://ftpmaster.internal/ubuntu disco/main arm64 e2fsprogs arm64 1.44.5-1 [491 kB] Get:56 http://ftpmaster.internal/ubuntu disco/main arm64 mount arm64 2.33.1-0.1ubuntu1 [110 kB] Get:57 http://ftpmaster.internal/ubuntu disco/main arm64 init arm64 1.56+nmu1 [6080 B] Get:58 http://ftpmaster.internal/ubuntu disco/main arm64 libcap-ng0 arm64 0.7.9-2 [10.5 kB] Get:59 http://ftpmaster.internal/ubuntu disco/main arm64 libsemanage-common all 2.8-2 [7016 B] Get:60 http://ftpmaster.internal/ubuntu disco/main arm64 libsemanage1 arm64 2.8-2 [79.7 kB] Get:61 http://ftpmaster.internal/ubuntu disco/main arm64 passwd arm64 1:4.5-1.1ubuntu1 [790 kB] Get:62 http://ftpmaster.internal/ubuntu disco/main arm64 libcom-err2 arm64 1.44.5-1 [9216 B] Get:63 http://ftpmaster.internal/ubuntu disco/main arm64 libss2 arm64 1.44.5-1 [10.6 kB] Get:64 http://ftpmaster.internal/ubuntu disco/main arm64 ca-certificates all 20190110 [146 kB] Get:65 http://ftpmaster.internal/ubuntu disco/main arm64 libargon2-1 arm64 0~20171227-0.2 [18.4 kB] Get:66 http://ftpmaster.internal/ubuntu disco/main arm64 libjson-c3 arm64 0.12.1+ds-2 [21.8 kB] Get:67 http://ftpmaster.internal/ubuntu disco/main arm64 readline-common all 8.0-1 [53.4 kB] Get:68 http://ftpmaster.internal/ubuntu disco/main arm64 libreadline8 arm64 8.0-1 [123 kB] Get:69 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libsqlite3-0 arm64 3.26.0+fossilbc891ac6b-2 [492 kB] Get:70 http://ftpmaster.internal/ubuntu disco/main arm64 tzdata all 2018i-1 [189 kB] Get:71 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 xz-utils arm64 5.2.4-1 [81.5 kB] Get:72 http://ftpmaster.internal/ubuntu disco/main arm64 libgdbm6 arm64 1.18.1-2build1 [26.6 kB] Get:73 http://ftpmaster.internal/ubuntu disco/main arm64 libpng16-16 arm64 1.6.36-3 [174 kB] Get:74 http://ftpmaster.internal/ubuntu disco/main arm64 dpkg-dev all 1.19.2ubuntu2 [549 kB] Get:75 http://ftpmaster.internal/ubuntu disco/main arm64 libdpkg-perl all 1.19.2ubuntu2 [227 kB] Get:76 http://ftpmaster.internal/ubuntu disco/main arm64 e2fslibs arm64 1.44.5-1 [2704 B] Get:77 http://ftpmaster.internal/ubuntu disco/main arm64 libassuan0 arm64 2.5.2-1 [32.9 kB] Get:78 http://ftpmaster.internal/ubuntu disco/main arm64 gpg arm64 2.2.12-1ubuntu2 [437 kB] Get:79 http://ftpmaster.internal/ubuntu disco/main arm64 gpgconf arm64 2.2.12-1ubuntu2 [116 kB] Get:80 http://ftpmaster.internal/ubuntu disco/main arm64 gpg-agent arm64 2.2.12-1ubuntu2 [213 kB] Get:81 http://ftpmaster.internal/ubuntu disco/main arm64 libcomerr2 arm64 1.44.5-1 [2700 B] Get:82 http://ftpmaster.internal/ubuntu disco/main arm64 libgdbm-compat4 arm64 1.18.1-2build1 [6020 B] Get:83 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 linux-libc-dev arm64 4.19.0-12.13 [1049 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 46.2 MB in 2s (23.5 MB/s) (Reading database ... 12642 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.6.1_arm64.deb ... Unpacking debianutils (4.8.6.1) over (4.8.6) ... Setting up debianutils (4.8.6.1) ... (Reading database ... 12642 files and directories currently installed.) Preparing to unpack .../bash_5.0-2ubuntu1_arm64.deb ... Unpacking bash (5.0-2ubuntu1) over (4.4.18-2ubuntu3) ... Setting up bash (5.0-2ubuntu1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 12642 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.33.1-0.1ubuntu1_arm64.deb ... Unpacking bsdutils (1:2.33.1-0.1ubuntu1) over (1:2.32-0.1ubuntu2) ... Setting up bsdutils (1:2.33.1-0.1ubuntu1) ... (Reading database ... 12642 files and directories currently installed.) Preparing to unpack .../coreutils_8.30-1ubuntu1_arm64.deb ... Unpacking coreutils (8.30-1ubuntu1) over (8.28-1ubuntu2) ... Setting up coreutils (8.30-1ubuntu1) ... (Reading database ... 12642 files and directories currently installed.) Preparing to unpack .../tar_1.30+dfsg-4_arm64.deb ... Unpacking tar (1.30+dfsg-4) over (1.30+dfsg-3) ... Setting up tar (1.30+dfsg-4) ... (Reading database ... 12642 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.2ubuntu2_arm64.deb ... Unpacking dpkg (1.19.2ubuntu2) over (1.19.2ubuntu1) ... Setting up dpkg (1.19.2ubuntu2) ... (Reading database ... 12642 files and directories currently installed.) Preparing to unpack .../debconf_1.5.70_all.deb ... Unpacking debconf (1.5.70) over (1.5.69) ... Setting up debconf (1.5.70) ... (Reading database ... 12642 files and directories currently installed.) Preparing to unpack .../dash_0.5.10.2-4ubuntu1_arm64.deb ... Unpacking dash (0.5.10.2-4ubuntu1) over (0.5.10.2-2) ... Setting up dash (0.5.10.2-4ubuntu1) ... (Reading database ... 12642 files and directories currently installed.) Preparing to unpack .../findutils_4.6.0+git+20190105-2_arm64.deb ... Unpacking findutils (4.6.0+git+20190105-2) over (4.6.0+git+20181018-1) ... Setting up findutils (4.6.0+git+20190105-2) ... (Reading database ... 12642 files and directories currently installed.) Preparing to unpack .../archives/grep_3.3-1_arm64.deb ... Unpacking grep (3.3-1) over (3.1-3) ... Setting up grep (3.3-1) ... (Reading database ... 12642 files and directories currently installed.) Preparing to unpack .../archives/gzip_1.9-3_arm64.deb ... Unpacking gzip (1.9-3) over (1.6-5ubuntu2) ... Setting up gzip (1.9-3) ... (Reading database ... 12642 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.33.1-0.1ubuntu1_arm64.deb ... Unpacking libsmartcols1:arm64 (2.33.1-0.1ubuntu1) over (2.32-0.1ubuntu2) ... Setting up libsmartcols1:arm64 (2.33.1-0.1ubuntu1) ... (Reading database ... 12642 files and directories currently installed.) Preparing to unpack .../libuuid1_2.33.1-0.1ubuntu1_arm64.deb ... Unpacking libuuid1:arm64 (2.33.1-0.1ubuntu1) over (2.32-0.1ubuntu2) ... Setting up libuuid1:arm64 (2.33.1-0.1ubuntu1) ... (Reading database ... 12642 files and directories currently installed.) Preparing to unpack .../libblkid1_2.33.1-0.1ubuntu1_arm64.deb ... Unpacking libblkid1:arm64 (2.33.1-0.1ubuntu1) over (2.32-0.1ubuntu2) ... Setting up libblkid1:arm64 (2.33.1-0.1ubuntu1) ... (Reading database ... 12642 files and directories currently installed.) Preparing to unpack .../libfdisk1_2.33.1-0.1ubuntu1_arm64.deb ... Unpacking libfdisk1:arm64 (2.33.1-0.1ubuntu1) over (2.32-0.1ubuntu2) ... Setting up libfdisk1:arm64 (2.33.1-0.1ubuntu1) ... (Reading database ... 12642 files and directories currently installed.) Preparing to unpack .../libmount1_2.33.1-0.1ubuntu1_arm64.deb ... Unpacking libmount1:arm64 (2.33.1-0.1ubuntu1) over (2.32-0.1ubuntu2) ... Setting up libmount1:arm64 (2.33.1-0.1ubuntu1) ... (Reading database ... 12642 files and directories currently installed.) Preparing to unpack .../fdisk_2.33.1-0.1ubuntu1_arm64.deb ... Unpacking fdisk (2.33.1-0.1ubuntu1) over (2.32-0.1ubuntu2) ... Setting up fdisk (2.33.1-0.1ubuntu1) ... (Reading database ... 12645 files and directories currently installed.) Preparing to unpack .../util-linux_2.33.1-0.1ubuntu1_arm64.deb ... Unpacking util-linux (2.33.1-0.1ubuntu1) over (2.32-0.1ubuntu2) ... Replacing files in old package login (1:4.5-1ubuntu1) ... Preparing to unpack .../login_1%3a4.5-1.1ubuntu1_arm64.deb ... Unpacking login (1:4.5-1.1ubuntu1) over (1:4.5-1ubuntu1) ... Setting up login (1:4.5-1.1ubuntu1) ... (Reading database ... 12649 files and directories currently installed.) Preparing to unpack .../archives/sed_4.7-1_arm64.deb ... Unpacking sed (4.7-1) over (4.5-2) ... Setting up sed (4.7-1) ... (Reading database ... 12649 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.56+nmu1_all.deb ... Unpacking init-system-helpers (1.56+nmu1) over (1.56) ... Setting up init-system-helpers (1.56+nmu1) ... (Reading database ... 12649 files and directories currently installed.) Preparing to unpack .../libnettle6_3.4.1-1_arm64.deb ... Unpacking libnettle6:arm64 (3.4.1-1) over (3.4.1~rc1-1) ... Setting up libnettle6:arm64 (3.4.1-1) ... (Reading database ... 12649 files and directories currently installed.) Preparing to unpack .../libhogweed4_3.4.1-1_arm64.deb ... Unpacking libhogweed4:arm64 (3.4.1-1) over (3.4.1~rc1-1) ... Setting up libhogweed4:arm64 (3.4.1-1) ... (Reading database ... 12649 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.6.5-2ubuntu1_arm64.deb ... Unpacking libgnutls30:arm64 (3.6.5-2ubuntu1) over (3.6.4-2ubuntu2) ... Setting up libgnutls30:arm64 (3.6.5-2ubuntu1) ... (Reading database ... 12649 files and directories currently installed.) Preparing to unpack .../libcc1-0_8.2.0-15ubuntu1_arm64.deb ... Unpacking libcc1-0:arm64 (8.2.0-15ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../gcc-8-base_8.2.0-15ubuntu1_arm64.deb ... Unpacking gcc-8-base:arm64 (8.2.0-15ubuntu1) over (8.2.0-12ubuntu1) ... Setting up gcc-8-base:arm64 (8.2.0-15ubuntu1) ... (Reading database ... 12649 files and directories currently installed.) Preparing to unpack .../libgcc1_1%3a8.2.0-15ubuntu1_arm64.deb ... Unpacking libgcc1:arm64 (1:8.2.0-15ubuntu1) over (1:8.2.0-12ubuntu1) ... Setting up libgcc1:arm64 (1:8.2.0-15ubuntu1) ... (Reading database ... 12649 files and directories currently installed.) Preparing to unpack .../00-libgomp1_8.2.0-15ubuntu1_arm64.deb ... Unpacking libgomp1:arm64 (8.2.0-15ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../01-libitm1_8.2.0-15ubuntu1_arm64.deb ... Unpacking libitm1:arm64 (8.2.0-15ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../02-libatomic1_8.2.0-15ubuntu1_arm64.deb ... Unpacking libatomic1:arm64 (8.2.0-15ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../03-libasan5_8.2.0-15ubuntu1_arm64.deb ... Unpacking libasan5:arm64 (8.2.0-15ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../04-liblsan0_8.2.0-15ubuntu1_arm64.deb ... Unpacking liblsan0:arm64 (8.2.0-15ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../05-libtsan0_8.2.0-15ubuntu1_arm64.deb ... Unpacking libtsan0:arm64 (8.2.0-15ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../06-libubsan1_8.2.0-15ubuntu1_arm64.deb ... Unpacking libubsan1:arm64 (8.2.0-15ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../07-g++-8_8.2.0-15ubuntu1_arm64.deb ... Unpacking g++-8 (8.2.0-15ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../08-libstdc++-8-dev_8.2.0-15ubuntu1_arm64.deb ... Unpacking libstdc++-8-dev:arm64 (8.2.0-15ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../09-libgcc-8-dev_8.2.0-15ubuntu1_arm64.deb ... Unpacking libgcc-8-dev:arm64 (8.2.0-15ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../10-gcc-8_8.2.0-15ubuntu1_arm64.deb ... Unpacking gcc-8 (8.2.0-15ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../11-cpp-8_8.2.0-15ubuntu1_arm64.deb ... Unpacking cpp-8 (8.2.0-15ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../12-libstdc++6_8.2.0-15ubuntu1_arm64.deb ... Unpacking libstdc++6:arm64 (8.2.0-15ubuntu1) over (8.2.0-12ubuntu1) ... Setting up libstdc++6:arm64 (8.2.0-15ubuntu1) ... (Reading database ... 12649 files and directories currently installed.) Preparing to unpack .../libmpfr6_4.0.2~rc1-1_arm64.deb ... Unpacking libmpfr6:arm64 (4.0.2~rc1-1) over (4.0.1-2) ... Preparing to unpack .../zlib1g_1%3a1.2.11.dfsg-1ubuntu2_arm64.deb ... Unpacking zlib1g:arm64 (1:1.2.11.dfsg-1ubuntu2) over (1:1.2.11.dfsg-0ubuntu2) ... Setting up zlib1g:arm64 (1:1.2.11.dfsg-1ubuntu2) ... (Reading database ... 12649 files and directories currently installed.) Preparing to unpack .../libbinutils_2.31.1-11ubuntu1_arm64.deb ... Unpacking libbinutils:arm64 (2.31.1-11ubuntu1) over (2.31.1-10ubuntu1) ... Preparing to unpack .../binutils-common_2.31.1-11ubuntu1_arm64.deb ... Unpacking binutils-common:arm64 (2.31.1-11ubuntu1) over (2.31.1-10ubuntu1) ... Preparing to unpack .../binutils_2.31.1-11ubuntu1_arm64.deb ... Unpacking binutils (2.31.1-11ubuntu1) over (2.31.1-10ubuntu1) ... Preparing to unpack .../binutils-aarch64-linux-gnu_2.31.1-11ubuntu1_arm64.deb ... Unpacking binutils-aarch64-linux-gnu (2.31.1-11ubuntu1) over (2.31.1-10ubuntu1) ... Preparing to unpack .../liblz4-1_1.8.3-1ubuntu1_arm64.deb ... Unpacking liblz4-1:arm64 (1.8.3-1ubuntu1) over (1.8.2-1ubuntu1) ... Setting up liblz4-1:arm64 (1.8.3-1ubuntu1) ... (Reading database ... 12649 files and directories currently installed.) Preparing to unpack .../liblzma5_5.2.4-1_arm64.deb ... Unpacking liblzma5:arm64 (5.2.4-1) over (5.2.2-1.3) ... Setting up liblzma5:arm64 (5.2.4-1) ... (Reading database ... 12649 files and directories currently installed.) Preparing to unpack .../libzstd1_1.3.8+dfsg-3_arm64.deb ... Unpacking libzstd1:arm64 (1.3.8+dfsg-3) over (1.3.5+dfsg-1ubuntu1) ... Setting up libzstd1:arm64 (1.3.8+dfsg-3) ... (Reading database ... 12649 files and directories currently installed.) Preparing to unpack .../libapt-pkg5.0_1.8.0~beta1_arm64.deb ... Unpacking libapt-pkg5.0:arm64 (1.8.0~beta1) over (1.8.0~alpha2ubuntu1) ... Setting up libapt-pkg5.0:arm64 (1.8.0~beta1) ... (Reading database ... 12649 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.33-3_arm64.deb ... Unpacking libgpg-error0:arm64 (1.33-3) over (1.32-3) ... Setting up libgpg-error0:arm64 (1.33-3) ... (Reading database ... 12649 files and directories currently installed.) Preparing to unpack .../gpgv_2.2.12-1ubuntu2_arm64.deb ... Unpacking gpgv (2.2.12-1ubuntu2) over (2.2.8-3ubuntu1) ... Setting up gpgv (2.2.12-1ubuntu2) ... (Reading database ... 12649 files and directories currently installed.) Preparing to unpack .../apt_1.8.0~beta1_arm64.deb ... Unpacking apt (1.8.0~beta1) over (1.8.0~alpha2ubuntu1) ... Setting up apt (1.8.0~beta1) ... (Reading database ... 12648 files and directories currently installed.) Preparing to unpack .../libext2fs2_1.44.5-1_arm64.deb ... Unpacking libext2fs2:arm64 (1.44.5-1) over (1.44.4-2ubuntu1) ... Setting up libext2fs2:arm64 (1.44.5-1) ... (Reading database ... 12647 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.44.5-1_arm64.deb ... Unpacking e2fsprogs (1.44.5-1) over (1.44.4-2ubuntu1) ... Preparing to unpack .../mount_2.33.1-0.1ubuntu1_arm64.deb ... Unpacking mount (2.33.1-0.1ubuntu1) over (2.32-0.1ubuntu2) ... Preparing to unpack .../init_1.56+nmu1_arm64.deb ... Unpacking init (1.56+nmu1) over (1.56) ... Preparing to unpack .../libcap-ng0_0.7.9-2_arm64.deb ... Unpacking libcap-ng0:arm64 (0.7.9-2) over (0.7.9-1build1) ... Setting up libcap-ng0:arm64 (0.7.9-2) ... (Reading database ... 12647 files and directories currently installed.) Preparing to unpack .../libsemanage-common_2.8-2_all.deb ... Unpacking libsemanage-common (2.8-2) over (2.8-1build2) ... Setting up libsemanage-common (2.8-2) ... (Reading database ... 12647 files and directories currently installed.) Preparing to unpack .../libsemanage1_2.8-2_arm64.deb ... Unpacking libsemanage1:arm64 (2.8-2) over (2.8-1build2) ... Setting up libsemanage1:arm64 (2.8-2) ... (Reading database ... 12647 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.5-1.1ubuntu1_arm64.deb ... Unpacking passwd (1:4.5-1.1ubuntu1) over (1:4.5-1ubuntu1) ... Setting up passwd (1:4.5-1.1ubuntu1) ... (Reading database ... 12647 files and directories currently installed.) Preparing to unpack .../00-libcom-err2_1.44.5-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.44.5-1) over (1.44.4-2ubuntu1) ... Preparing to unpack .../01-libss2_1.44.5-1_arm64.deb ... Unpacking libss2:arm64 (1.44.5-1) over (1.44.4-2ubuntu1) ... Preparing to unpack .../02-ca-certificates_20190110_all.deb ... Unpacking ca-certificates (20190110) over (20180409) ... Preparing to unpack .../03-libargon2-1_0~20171227-0.2_arm64.deb ... Unpacking libargon2-1:arm64 (0~20171227-0.2) over (0~20171227-0.1) ... Preparing to unpack .../04-libjson-c3_0.12.1+ds-2_arm64.deb ... Unpacking libjson-c3:arm64 (0.12.1+ds-2) over (0.12.1-1.3) ... Preparing to unpack .../05-readline-common_8.0-1_all.deb ... Unpacking readline-common (8.0-1) over (7.0-5) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../06-libreadline8_8.0-1_arm64.deb ... Unpacking libreadline8:arm64 (8.0-1) ... Preparing to unpack .../07-libsqlite3-0_3.26.0+fossilbc891ac6b-2_arm64.deb ... Unpacking libsqlite3-0:arm64 (3.26.0+fossilbc891ac6b-2) over (3.26.0-2) ... Preparing to unpack .../08-tzdata_2018i-1_all.deb ... Unpacking tzdata (2018i-1) over (2018g-1) ... Preparing to unpack .../09-xz-utils_5.2.4-1_arm64.deb ... Unpacking xz-utils (5.2.4-1) over (5.2.2-1.3) ... Preparing to unpack .../10-libgdbm6_1.18.1-2build1_arm64.deb ... Unpacking libgdbm6:arm64 (1.18.1-2build1) over (1.18.1-2) ... Preparing to unpack .../11-libpng16-16_1.6.36-3_arm64.deb ... Unpacking libpng16-16:arm64 (1.6.36-3) over (1.6.34-2) ... Preparing to unpack .../12-dpkg-dev_1.19.2ubuntu2_all.deb ... Unpacking dpkg-dev (1.19.2ubuntu2) over (1.19.2ubuntu1) ... Preparing to unpack .../13-libdpkg-perl_1.19.2ubuntu2_all.deb ... Unpacking libdpkg-perl (1.19.2ubuntu2) over (1.19.2ubuntu1) ... Preparing to unpack .../14-e2fslibs_1.44.5-1_arm64.deb ... Unpacking e2fslibs:arm64 (1.44.5-1) over (1.44.4-2ubuntu1) ... Preparing to unpack .../15-libassuan0_2.5.2-1_arm64.deb ... Unpacking libassuan0:arm64 (2.5.2-1) over (2.5.1-2) ... Preparing to unpack .../16-gpg_2.2.12-1ubuntu2_arm64.deb ... Unpacking gpg (2.2.12-1ubuntu2) over (2.2.8-3ubuntu1) ... Preparing to unpack .../17-gpgconf_2.2.12-1ubuntu2_arm64.deb ... Unpacking gpgconf (2.2.12-1ubuntu2) over (2.2.8-3ubuntu1) ... Preparing to unpack .../18-gpg-agent_2.2.12-1ubuntu2_arm64.deb ... Unpacking gpg-agent (2.2.12-1ubuntu2) over (2.2.8-3ubuntu1) ... Preparing to unpack .../19-libcomerr2_1.44.5-1_arm64.deb ... Unpacking libcomerr2:arm64 (1.44.5-1) over (1.44.4-2ubuntu1) ... Preparing to unpack .../20-libgdbm-compat4_1.18.1-2build1_arm64.deb ... Unpacking libgdbm-compat4:arm64 (1.18.1-2build1) over (1.18.1-2) ... Preparing to unpack .../21-linux-libc-dev_4.19.0-12.13_arm64.deb ... Unpacking linux-libc-dev:arm64 (4.19.0-12.13) over (4.18.0-11.12) ... Setting up libcom-err2:arm64 (1.44.5-1) ... Setting up libgomp1:arm64 (8.2.0-15ubuntu1) ... Setting up libatomic1:arm64 (8.2.0-15ubuntu1) ... Setting up readline-common (8.0-1) ... Setting up libss2:arm64 (1.44.5-1) ... Setting up libcc1-0:arm64 (8.2.0-15ubuntu1) ... Setting up e2fslibs:arm64 (1.44.5-1) ... Setting up libpng16-16:arm64 (1.6.36-3) ... Setting up libjson-c3:arm64 (0.12.1+ds-2) ... Setting up tzdata (2018i-1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Jan 30 08:51:16 UTC 2019. Universal Time is now: Wed Jan 30 08:51:16 UTC 2019. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up init (1.56+nmu1) ... Setting up libtsan0:arm64 (8.2.0-15ubuntu1) ... Setting up linux-libc-dev:arm64 (4.19.0-12.13) ... Setting up libmpfr6:arm64 (4.0.2~rc1-1) ... Setting up libdpkg-perl (1.19.2ubuntu2) ... Setting up e2fsprogs (1.44.5-1) ... Setting up liblsan0:arm64 (8.2.0-15ubuntu1) ... Setting up libgdbm6:arm64 (1.18.1-2build1) ... Setting up binutils-common:arm64 (2.31.1-11ubuntu1) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up xz-utils (5.2.4-1) ... Setting up libsqlite3-0:arm64 (3.26.0+fossilbc891ac6b-2) ... Setting up libcomerr2:arm64 (1.44.5-1) ... Setting up libgdbm-compat4:arm64 (1.18.1-2build1) ... Setting up libargon2-1:arm64 (0~20171227-0.2) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 2 added, 7 removed; done. Setting up libasan5:arm64 (8.2.0-15ubuntu1) ... Setting up libassuan0:arm64 (2.5.2-1) ... Setting up libitm1:arm64 (8.2.0-15ubuntu1) ... Setting up util-linux (2.33.1-0.1ubuntu1) ... Setting up libreadline8:arm64 (8.0-1) ... Setting up libubsan1:arm64 (8.2.0-15ubuntu1) ... Setting up cpp-8 (8.2.0-15ubuntu1) ... Setting up libbinutils:arm64 (2.31.1-11ubuntu1) ... Setting up gpgconf (2.2.12-1ubuntu2) ... Setting up mount (2.33.1-0.1ubuntu1) ... Setting up gpg-agent (2.2.12-1ubuntu2) ... Setting up binutils-aarch64-linux-gnu (2.31.1-11ubuntu1) ... Processing triggers for systemd (239-7ubuntu15) ... Setting up libgcc-8-dev:arm64 (8.2.0-15ubuntu1) ... Setting up binutils (2.31.1-11ubuntu1) ... Setting up gpg (2.2.12-1ubuntu2) ... Setting up libstdc++-8-dev:arm64 (8.2.0-15ubuntu1) ... Setting up gcc-8 (8.2.0-15ubuntu1) ... Setting up g++-8 (8.2.0-15ubuntu1) ... Setting up dpkg-dev (1.19.2ubuntu2) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-15793601 arm64 disco-proposed -c chroot:build-PACKAGEBUILD-15793601 --arch=arm64 --dist=disco-proposed --nolog gemma_0.98.1+dfsg-1.dsc Initiating build PACKAGEBUILD-15793601 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-141-generic #167-Ubuntu SMP Wed Dec 5 10:50:27 UTC 2018 aarch64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-028.buildd +==============================================================================+ | gemma 0.98.1+dfsg-1 (arm64) 30 Jan 2019 08:51 | +==============================================================================+ Package: gemma Version: 0.98.1+dfsg-1 Source Version: 0.98.1+dfsg-1 Distribution: disco-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 I: NOTICE: Log filtering will replace 'build/gemma-q585fO/gemma-0.98.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/gemma-q585fO' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15793601/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- gemma_0.98.1+dfsg-1.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-LiLgPA/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-LiLgPA/apt_archive ./ InRelease Get:2 copy:/<>/resolver-LiLgPA/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-LiLgPA/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-LiLgPA/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-LiLgPA/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (146 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 package was automatically installed and is no longer required: libreadline7 Use 'apt autoremove' to remove it. 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-LiLgPA/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 ... 12659 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-CGI5ir/apt_archive/sbuild-build-depends-gemma-dummy.deb'. Ign:1 copy:/<>/resolver-CGI5ir/apt_archive ./ InRelease Get:2 copy:/<>/resolver-CGI5ir/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-CGI5ir/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-CGI5ir/apt_archive ./ Sources [254 B] Get:5 copy:/<>/resolver-CGI5ir/apt_archive ./ Packages [570 B] Fetched 2943 B in 0s (156 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 package was automatically installed and is no longer required: libreadline7 Use 'apt autoremove' to remove it. 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 libuchardet0 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 libuchardet0 libxml2 m4 man-db pkg-config po-debconf sbuild-build-depends-gemma-dummy shunit2 zlib1g-dev 0 upgraded, 46 newly installed, 0 to remove and 0 not upgraded. Need to get 32.2 MB of archives. After this operation, 143 MB of additional disk space will be used. Get:1 copy:/<>/resolver-CGI5ir/apt_archive ./ sbuild-build-depends-gemma-dummy 0.invalid.0 [900 B] Get:2 http://ftpmaster.internal/ubuntu disco/main arm64 libbsd0 arm64 0.9.1-1 [39.4 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main arm64 bsdmainutils arm64 11.1.2ubuntu2 [175 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main arm64 groff-base arm64 1.22.4-2 [813 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main arm64 libpipeline1 arm64 1.5.1-1 [24.5 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main arm64 man-db arm64 2.8.5-1 [1086 kB] Get:8 http://ftpmaster.internal/ubuntu disco/main arm64 libmagic-mgc arm64 1:5.35-2 [200 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main arm64 libmagic1 arm64 1:5.35-2 [70.5 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main arm64 file arm64 1:5.35-2 [23.0 kB] Get:11 http://ftpmaster.internal/ubuntu disco/main arm64 libelf1 arm64 0.175-2 [43.6 kB] Get:12 http://ftpmaster.internal/ubuntu disco/main arm64 libglib2.0-0 arm64 2.58.1-2 [1106 kB] Get:13 http://ftpmaster.internal/ubuntu disco/main arm64 libicu63 arm64 63.1-6 [8144 kB] Get:14 http://ftpmaster.internal/ubuntu disco/main arm64 libxml2 arm64 2.9.4+dfsg1-7ubuntu3 [562 kB] Get:15 http://ftpmaster.internal/ubuntu disco/main arm64 gettext-base arm64 0.19.8.1-9 [48.0 kB] Get:16 http://ftpmaster.internal/ubuntu disco/main arm64 libsigsegv2 arm64 2.12-2 [13.3 kB] Get:17 http://ftpmaster.internal/ubuntu disco/main arm64 m4 arm64 1.4.18-2 [194 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main arm64 autoconf all 2.69-11 [322 kB] Get:19 http://ftpmaster.internal/ubuntu disco/main arm64 autotools-dev all 20180224.1 [39.6 kB] Get:20 http://ftpmaster.internal/ubuntu disco/main arm64 automake all 1:1.16.1-4ubuntu3 [522 kB] Get:21 http://ftpmaster.internal/ubuntu disco/main arm64 autopoint all 0.19.8.1-9 [412 kB] Get:22 http://ftpmaster.internal/ubuntu disco/universe arm64 catch arm64 1.12.1-1 [114 kB] Get:23 http://ftpmaster.internal/ubuntu disco/main arm64 libtool all 2.4.6-9 [194 kB] Get:24 http://ftpmaster.internal/ubuntu disco/main arm64 dh-autoreconf all 19 [16.1 kB] Get:25 http://ftpmaster.internal/ubuntu disco/main arm64 libarchive-zip-perl all 1.64-1 [84.9 kB] Get:26 http://ftpmaster.internal/ubuntu disco/main arm64 libfile-stripnondeterminism-perl all 1.1.0-1 [13.6 kB] Get:27 http://ftpmaster.internal/ubuntu disco/main arm64 dh-strip-nondeterminism all 1.1.0-1 [5100 B] Get:28 http://ftpmaster.internal/ubuntu disco/main arm64 dwz arm64 0.12-3 [71.8 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main arm64 libcroco3 arm64 0.6.12-3 [76.8 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main arm64 gettext arm64 0.19.8.1-9 [853 kB] Get:31 http://ftpmaster.internal/ubuntu disco/main arm64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:32 http://ftpmaster.internal/ubuntu disco/main arm64 po-debconf all 1.0.21 [233 kB] Get:33 http://ftpmaster.internal/ubuntu disco/main arm64 debhelper all 12ubuntu1 [887 kB] Get:34 http://ftpmaster.internal/ubuntu disco/main arm64 libgfortran5 arm64 8.2.0-15ubuntu1 [308 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main arm64 libgfortran-8-dev arm64 8.2.0-15ubuntu1 [356 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main arm64 gfortran-8 arm64 8.2.0-15ubuntu1 [7884 kB] Get:37 http://ftpmaster.internal/ubuntu disco/main arm64 gfortran arm64 4:8.2.0-2ubuntu2 [1364 B] Get:38 http://ftpmaster.internal/ubuntu disco/universe arm64 libgslcblas0 arm64 2.5+dfsg-6 [52.4 kB] Get:39 http://ftpmaster.internal/ubuntu disco/universe arm64 libgsl23 arm64 2.5+dfsg-6 [737 kB] Get:40 http://ftpmaster.internal/ubuntu disco/universe arm64 libgsl-dev arm64 2.5+dfsg-6 [939 kB] Get:41 http://ftpmaster.internal/ubuntu disco/universe arm64 libopenblas-base arm64 0.3.5+ds-1 [2291 kB] Get:42 http://ftpmaster.internal/ubuntu disco/universe arm64 libopenblas-dev arm64 0.3.5+ds-1 [2134 kB] Get:43 http://ftpmaster.internal/ubuntu disco/main arm64 pkg-config arm64 0.29.1-0ubuntu2 [42.8 kB] Get:44 http://ftpmaster.internal/ubuntu disco/universe arm64 shunit2 all 2.1.6-1.1ubuntu1 [38.6 kB] Get:45 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-1ubuntu2 [170 kB] Get:46 http://ftpmaster.internal/ubuntu disco/universe arm64 libeigen3-dev all 3.3.7-1 [814 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 32.2 MB in 2s (15.5 MB/s) Selecting previously unselected package libbsd0:arm64. (Reading database ... 12659 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 libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-2_arm64.deb ... Unpacking groff-base (1.22.4-2) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-1) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-1_arm64.deb ... Unpacking man-db (2.8.5-1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.35-2_arm64.deb ... Unpacking libmagic-mgc (1:5.35-2) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../07-libmagic1_1%3a5.35-2_arm64.deb ... Unpacking libmagic1:arm64 (1:5.35-2) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.35-2_arm64.deb ... Unpacking file (1:5.35-2) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../09-libelf1_0.175-2_arm64.deb ... Unpacking libelf1:arm64 (0.175-2) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../10-libglib2.0-0_2.58.1-2_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.58.1-2) ... Selecting previously unselected package libicu63:arm64. Preparing to unpack .../11-libicu63_63.1-6_arm64.deb ... Unpacking libicu63:arm64 (63.1-6) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../12-libxml2_2.9.4+dfsg1-7ubuntu3_arm64.deb ... Unpacking libxml2:arm64 (2.9.4+dfsg1-7ubuntu3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../13-gettext-base_0.19.8.1-9_arm64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../14-libsigsegv2_2.12-2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../15-m4_1.4.18-2_arm64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../16-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../17-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../18-automake_1%3a1.16.1-4ubuntu3_all.deb ... Unpacking automake (1:1.16.1-4ubuntu3) ... Selecting previously unselected package autopoint. Preparing to unpack .../19-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package catch. Preparing to unpack .../20-catch_1.12.1-1_arm64.deb ... Unpacking catch (1.12.1-1) ... Selecting previously unselected package libtool. Preparing to unpack .../21-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../22-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../23-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../24-libfile-stripnondeterminism-perl_1.1.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../25-dh-strip-nondeterminism_1.1.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.0-1) ... Selecting previously unselected package dwz. Preparing to unpack .../26-dwz_0.12-3_arm64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libcroco3:arm64. Preparing to unpack .../27-libcroco3_0.6.12-3_arm64.deb ... Unpacking libcroco3:arm64 (0.6.12-3) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.19.8.1-9_arm64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_12ubuntu1_all.deb ... Unpacking debhelper (12ubuntu1) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../32-libgfortran5_8.2.0-15ubuntu1_arm64.deb ... Unpacking libgfortran5:arm64 (8.2.0-15ubuntu1) ... Selecting previously unselected package libgfortran-8-dev:arm64. Preparing to unpack .../33-libgfortran-8-dev_8.2.0-15ubuntu1_arm64.deb ... Unpacking libgfortran-8-dev:arm64 (8.2.0-15ubuntu1) ... Selecting previously unselected package gfortran-8. Preparing to unpack .../34-gfortran-8_8.2.0-15ubuntu1_arm64.deb ... Unpacking gfortran-8 (8.2.0-15ubuntu1) ... Selecting previously unselected package gfortran. Preparing to unpack .../35-gfortran_4%3a8.2.0-2ubuntu2_arm64.deb ... Unpacking gfortran (4:8.2.0-2ubuntu2) ... Selecting previously unselected package libgslcblas0:arm64. Preparing to unpack .../36-libgslcblas0_2.5+dfsg-6_arm64.deb ... Unpacking libgslcblas0:arm64 (2.5+dfsg-6) ... Selecting previously unselected package libgsl23:arm64. Preparing to unpack .../37-libgsl23_2.5+dfsg-6_arm64.deb ... Unpacking libgsl23:arm64 (2.5+dfsg-6) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../38-libgsl-dev_2.5+dfsg-6_arm64.deb ... Unpacking libgsl-dev (2.5+dfsg-6) ... Selecting previously unselected package libopenblas-base:arm64. Preparing to unpack .../39-libopenblas-base_0.3.5+ds-1_arm64.deb ... Unpacking libopenblas-base:arm64 (0.3.5+ds-1) ... Selecting previously unselected package libopenblas-dev:arm64. Preparing to unpack .../40-libopenblas-dev_0.3.5+ds-1_arm64.deb ... Unpacking libopenblas-dev:arm64 (0.3.5+ds-1) ... Selecting previously unselected package pkg-config. Preparing to unpack .../41-pkg-config_0.29.1-0ubuntu2_arm64.deb ... Unpacking pkg-config (0.29.1-0ubuntu2) ... Selecting previously unselected package shunit2. Preparing to unpack .../42-shunit2_2.1.6-1.1ubuntu1_all.deb ... Unpacking shunit2 (2.1.6-1.1ubuntu1) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../43-zlib1g-dev_1%3a1.2.11.dfsg-1ubuntu2_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.2.11.dfsg-1ubuntu2) ... Selecting previously unselected package libeigen3-dev. Preparing to unpack .../44-libeigen3-dev_3.3.7-1_all.deb ... Unpacking libeigen3-dev (3.3.7-1) ... Selecting previously unselected package sbuild-build-depends-gemma-dummy. Preparing to unpack .../45-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 (63.1-6) ... Setting up libsigsegv2:arm64 (2.12-2) ... Setting up libelf1:arm64 (0.175-2) ... 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 (1.5.1-1) ... Setting up m4 (1.4.18-2) ... Setting up libbsd0:arm64 (0.9.1-1) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7ubuntu3) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up libmagic-mgc (1:5.35-2) ... Setting up libmagic1:arm64 (1:5.35-2) ... Setting up libcroco3:arm64 (0.6.12-3) ... Setting up pkg-config (0.29.1-0ubuntu2) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up dwz (0.12-3) ... 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-6) ... Setting up libgfortran5:arm64 (8.2.0-15ubuntu1) ... 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-1ubuntu2) ... Setting up libfile-stripnondeterminism-perl (1.1.0-1) ... Setting up libopenblas-base:arm64 (0.3.5+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-6) ... Setting up gettext (0.19.8.1-9) ... Setting up libgsl-dev (2.5+dfsg-6) ... Setting up libeigen3-dev (3.3.7-1) ... Setting up groff-base (1.22.4-2) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.35-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up automake (1:1.16.1-4ubuntu3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.5-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libopenblas-dev:arm64 (0.3.5+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 (8.2.0-15ubuntu1) ... Setting up libtool (2.4.6-9) ... Setting up po-debconf (1.0.21) ... Setting up gfortran-8 (8.2.0-15ubuntu1) ... 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 (12ubuntu1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.0-1) ... Setting up sbuild-build-depends-gemma-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-141-generic arm64 (aarch64) Toolchain package versions: binutils_2.31.1-11ubuntu1 dpkg-dev_1.19.2ubuntu2 g++-8_8.2.0-15ubuntu1 gcc-8_8.2.0-15ubuntu1 libc6-dev_2.28-0ubuntu1 libstdc++-8-dev_8.2.0-15ubuntu1 libstdc++6_8.2.0-15ubuntu1 linux-libc-dev_4.19.0-12.13 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.8.0~beta1 autoconf_2.69-11 automake_1:1.16.1-4ubuntu3 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1ubuntu8 base-passwd_3.5.45 bash_5.0-2ubuntu1 binutils_2.31.1-11ubuntu1 binutils-aarch64-linux-gnu_2.31.1-11ubuntu1 binutils-common_2.31.1-11ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.33.1-0.1ubuntu1 build-essential_12.5ubuntu2 bzip2_1.0.6-9 ca-certificates_20190110 catch_1.12.1-1 coreutils_8.30-1ubuntu1 cpp_4:8.2.0-2ubuntu2 cpp-8_8.2.0-15ubuntu1 dash_0.5.10.2-4ubuntu1 debconf_1.5.70 debhelper_12ubuntu1 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.0-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu4 dpkg_1.19.2ubuntu2 dpkg-dev_1.19.2ubuntu2 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1ubuntu1 file_1:5.35-2 findutils_4.6.0+git+20190105-2 g++_4:8.2.0-2ubuntu2 g++-8_8.2.0-15ubuntu1 gcc_4:8.2.0-2ubuntu2 gcc-8_8.2.0-15ubuntu1 gcc-8-base_8.2.0-15ubuntu1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gfortran_4:8.2.0-2ubuntu2 gfortran-8_8.2.0-15ubuntu1 gpg_2.2.12-1ubuntu2 gpg-agent_2.2.12-1ubuntu2 gpgconf_2.2.12-1ubuntu2 gpgv_2.2.12-1ubuntu2 grep_3.3-1 groff-base_1.22.4-2 gzip_1.9-3 hostname_3.21 init_1.56+nmu1 init-system-helpers_1.56+nmu1 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.5 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu10 libapt-pkg5.0_1.8.0~beta1 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.2 libasan5_8.2.0-15ubuntu1 libassuan0_2.5.2-1 libatomic1_8.2.0-15ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.3-1ubuntu3 libaudit1_1:2.8.3-1ubuntu3 libbinutils_2.31.1-11ubuntu1 libblkid1_2.33.1-0.1ubuntu1 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_0.7.9-2 libcap2_1:2.25-1.2 libcc1-0_8.2.0-15ubuntu1 libcom-err2_1.44.5-1 libcomerr2_1.44.5-1 libcroco3_0.6.12-3 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_1.19.2ubuntu2 libeigen3-dev_3.3.7-1 libelf1_0.175-2 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1ubuntu1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.0-1 libgcc-8-dev_8.2.0-15ubuntu1 libgcc1_1:8.2.0-15ubuntu1 libgcrypt20_1.8.4-3ubuntu1 libgdbm-compat4_1.18.1-2build1 libgdbm6_1.18.1-2build1 libgfortran-8-dev_8.2.0-15ubuntu1 libgfortran5_8.2.0-15ubuntu1 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.5-2ubuntu1 libgomp1_8.2.0-15ubuntu1 libgpg-error0_1.33-3 libgsl-dev_2.5+dfsg-6 libgsl23_2.5+dfsg-6 libgslcblas0_2.5+dfsg-6 libhogweed4_3.4.1-1 libicu63_63.1-6 libidn11_1.33-2.2ubuntu1 libidn2-0_2.0.5-1 libip4tc0_1.6.1-2ubuntu3 libisl19_0.20-2 libitm1_8.2.0-15ubuntu1 libjson-c3_0.12.1+ds-2 libkmod2_25-1ubuntu2 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblsan0_8.2.0-15ubuntu1 liblz4-1_1.8.3-1ubuntu1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-2 libmagic1_1:5.35-2 libmount1_2.33.1-0.1ubuntu1 libmpc3_1.1.0-1 libmpfr6_4.0.2~rc1-1 libncurses6_6.1+20180210-4ubuntu1 libncursesw6_6.1+20180210-4ubuntu1 libnettle6_3.4.1-1 libnpth0_1.6-1 libopenblas-base_0.3.5+ds-1 libopenblas-dev_0.3.5+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 libperl5.28_5.28.1-3 libpipeline1_1.5.1-1 libpng16-16_1.6.36-3 libprocps7_2:3.3.15-2ubuntu1 libreadline7_7.0-5 libreadline8_8.0-1 libseccomp2_2.3.3-3ubuntu2 libselinux1_2.8-1build2 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsmartcols1_2.33.1-0.1ubuntu1 libsqlite3-0_3.26.0+fossilbc891ac6b-2 libss2_1.44.5-1 libssl1.1_1.1.1a-1ubuntu2 libstdc++-8-dev_8.2.0-15ubuntu1 libstdc++6_8.2.0-15ubuntu1 libsystemd0_239-7ubuntu15 libtasn1-6_4.13-3 libtinfo6_6.1+20180210-4ubuntu1 libtool_2.4.6-9 libtsan0_8.2.0-15ubuntu1 libubsan1_8.2.0-15ubuntu1 libuchardet0_0.0.6-3 libudev1_239-7ubuntu15 libunistring2_0.9.10-1ubuntu1 libusb-0.1-4_2:0.1.12-32 libustr-1.0-1_1.0.4-6 libuuid1_2.33.1-0.1ubuntu1 libxml2_2.9.4+dfsg1-7ubuntu3 libzstd1_1.3.8+dfsg-3 linux-libc-dev_4.19.0-12.13 lockfile-progs_0.1.18 login_1:4.5-1.1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-1 mawk_1.3.3-17ubuntu3 mount_2.33.1-0.1ubuntu1 multiarch-support_2.28-0ubuntu1 ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 openssl_1.1.1a-1ubuntu2 optipng_0.7.6-1.1 passwd_1:4.5-1.1ubuntu1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1build2 pkg-config_0.29.1-0ubuntu2 pkgbinarymangler_143 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu1 readline-common_8.0-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gemma-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 shunit2_2.1.6-1.1ubuntu1 systemd_239-7ubuntu15 systemd-sysv_239-7ubuntu15 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu2 tar_1.30+dfsg-4 tzdata_2018i-1 ubuntu-keyring_2018.09.18.1 util-linux_2.33.1-0.1ubuntu1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu2 zlib1g-dev_1:1.2.11.dfsg-1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Dec 18 15:38:49 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gemma_0.98.1+dfsg-1.dsc dpkg-source: info: extracting gemma in gemma-0.98.1+dfsg dpkg-source: info: unpacking gemma_0.98.1+dfsg.orig.tar.xz dpkg-source: info: unpacking gemma_0.98.1+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series 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-15793601 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15793601 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15793601 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 0.98.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean dh_auto_clean make -j4 clean make[1]: Entering directory '/<>/gemma-0.98.1+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-0.98.1+dfsg' debian/rules override_dh_clean make[1]: Entering directory '/<>/gemma-0.98.1+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-0.98.1+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-0.98.1+dfsg' g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98.1+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 -DNDEBUG -O3 -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-0.98.1+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 -DNDEBUG -O3 -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-0.98.1+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 -DNDEBUG -O3 -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-0.98.1+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 -DNDEBUG -O3 -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-0.98.1+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 -DNDEBUG -O3 -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-0.98.1+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 -DNDEBUG -O3 -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-0.98.1+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 -DNDEBUG -O3 -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-0.98.1+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 -DNDEBUG -O3 -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-0.98.1+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 -DNDEBUG -O3 -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-0.98.1+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 -DNDEBUG -O3 -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-0.98.1+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 -DNDEBUG -O3 -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-0.98.1+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 -DNDEBUG -O3 -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-0.98.1+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 -DNDEBUG -O3 -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 src/lmm.cpp: In function ‘void CalcPab(size_t, size_t, const gsl_vector*, const gsl_matrix*, const gsl_vector*, gsl_matrix*)’: src/lmm.cpp:281:10: warning: unused variable ‘n_index’ [-Wunused-variable] size_t n_index = (n_cvt + 2 + 1) * (n_cvt + 2) / 2; // result size ^~~~~~~ src/lmm.cpp:282:8: warning: unused variable ‘ni_test’ [-Wunused-variable] auto ni_test = Uab->size1; // inds ^~~~~~~ src/lmm.cpp: In function ‘double LogL_dev1(double, void*)’: src/lmm.cpp:596:8: warning: unused variable ‘Uab’ [-Wunused-variable] auto Uab = p->Uab; ^~~ src/lmm.cpp:597:8: warning: unused variable ‘ab’ [-Wunused-variable] auto ab = p->ab; ^~ g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98.1+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 -DNDEBUG -O3 -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-0.98.1+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 -DNDEBUG -O3 -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 src/mathfunc.cpp: In function ‘bool isMatrixIllConditioned(const gsl_vector*, double)’: src/mathfunc.cpp:390:8: warning: unused variable ‘absmin’ [-Wunused-variable] auto absmin = get<0>(t); ^~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98.1+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 -DNDEBUG -O3 -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-0.98.1+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 -DNDEBUG -O3 -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-0.98.1+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 -DNDEBUG -O3 -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-0.98.1+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 -DNDEBUG -O3 -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-0.98.1+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 -DNDEBUG -O3 -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 -DNDEBUG -O3 -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 -o ./bin/gemma make[1]: Leaving directory '/<>/gemma-0.98.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/gemma-0.98.1+dfsg' dh_auto_test --no-parallel make -j1 check make[2]: Entering directory '/<>/gemma-0.98.1+dfsg' g++ -g -O2 -fdebug-prefix-map=/<>/gemma-0.98.1+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 -Og -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -Og -g -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-0.98.1+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 -Og -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -Og -g -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 -Og -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -Og -g -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 -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 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 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... ## 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 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. ## total computation time = 0.147627 min testBXDStandardRelatednessMatrixKSingularError GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** INFO: no intercept term is found in the cvt file: a column of 1s is added. GSL ERROR: matrix is singular in lu.c at line 266 errno 1 testBXDStandardRelatednessMatrixK GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** INFO: no intercept term is found in the cvt file: a column of 1s is added. ## 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 ... 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% **** INFO: Done. testBXDLMLikelihoodRatio GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** INFO: no intercept term is found in the cvt file: a column of 1s is added. ## 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 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% **** INFO: Done. testBXDLMMLikelihoodRatio GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** INFO: no intercept term is found in the cvt file: a column of 1s is added. ## 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 Start Eigen-Decomposition... pve estimate =0.00100086 se(pve) =0.204166 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% ================================================== 100% **** INFO: Done. testCenteredRelatednessMatrixissue188 GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... ## number of total individuals = 1008 ## number of analyzed individuals = 876 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 2000 ## number of analyzed SNPs = 1850 Calculating Relatedness Matrix ... 0% ========================= 50% ================================================== 100% **** WARNING: K has 75 eigenvalues close to zero in src/gemma.cpp at line 1912 **** WARNING: K is ill conditioned! in src/gemma.cpp at line 1912 **** INFO: Done. testLMMissue188 GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... ## number of total individuals = 1008 ## number of analyzed individuals = 876 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 2000 ## number of analyzed SNPs = 1850 **** WARNING: K has 3 eigenvalues close to zero in src/gemma.cpp at line 2588 **** WARNING: K is ill conditioned! in src/gemma.cpp at line 2588 Start Eigen-Decomposition... **** WARNING: Matrix G has 3 eigenvalues close to zero pve estimate =0.631857 se(pve) =0.0548406 0% ========================= 50% ================================================== 100% **** INFO: Done. testCenteredRelatednessMatrixKLOCO1 GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** TEST MODE: trim individuals from 1940 to 400 **** TEST MODE: trim individuals from 1940 to 400 ## 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 ... 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. ## total computation time = 0.0910134 min testUnivariateLinearMixedModelLOCO1 GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** TEST MODE: trim individuals from 1940 to 400 **** TEST MODE: trim individuals from 1940 to 400 ## 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 Start Eigen-Decomposition... pve estimate =0.678775 se(pve) =0.0717914 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% **** INFO: Done. ## total computation time = 0.0568309 min testPlinkCenteredRelatednessMatrixKLOCO1 testPlinkUnivariateLinearMixedModelLOCO1 testCorrelatedPhenotypesMvLLM GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... ## 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 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 0.8392 -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 12 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/issue188.assoc.txt' removed 'test/output/issue188.cXX.txt' removed 'test/output/issue188.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 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... ## 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 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 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... ## 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 ... 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testBslmm3 GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... ## 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 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 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 757 ## number of covariates = 1 ## number of phenotypes = 1 Adding Breeding Values ... Start Eigen-Decomposition... 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testBslmm5 GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 757 ## number of covariates = 1 ## number of phenotypes = 1 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testCenteredRelatednessMatrixKFullLOCO1 GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... ## 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 ... 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testUnivariateLinearMixedModelFullLOCO1 GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... ## 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 Start Eigen-Decomposition... pve estimate =0.593114 se(pve) =0.0332587 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% **** INFO: Done. ## total computation time = 0.396713 min testCenteredRelatednessMatrixK GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... ## 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 ... 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testUnivariateLinearMixedModel GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... ## 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 Start Eigen-Decomposition... pve estimate =0.608801 se(pve) =0.032774 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% **** INFO: Done. ## total computation time = 1.10167 min testLinearMixedModelPhenotypes GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... ## 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 Start Eigen-Decomposition... 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 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... ## 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 ... 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% ============ 25% ============ 25% ============ 25% ============ 26% ============ 26% ============= 26% ============= 26% ============= 27% ============= 27% ============= 27% ============= 28% ============= 28% ============== 28% ============== 28% ============== 29% ============== 29% ============== 29% ============== 30% ============== 30% =============== 30% =============== 30% =============== 31% =============== 31% =============== 31% =============== 32% =============== 32% ================ 32% ================ 32% ================ 33% ================ 33% ================ 33% ================ 33% ================ 34% ================= 34% ================= 34% ================= 35% ================= 35% ================= 35% ================= 35% ================= 36% ================= 36% ================== 36% ================== 37% ================== 37% ================== 37% ================== 37% ================== 38% ================== 38% =================== 38% =================== 38% =================== 39% =================== 39% =================== 39% =================== 40% =================== 40% ==================== 40% ==================== 40% ==================== 41% ==================== 41% ==================== 41% ==================== 42% ==================== 42% ===================== 42% ===================== 42% ===================== 43% ===================== 43% ===================== 43% ===================== 44% ===================== 44% ====================== 44% ====================== 44% ====================== 45% ====================== 45% ====================== 45% ====================== 45% ====================== 46% ======================= 46% ======================= 46% ======================= 47% ======================= 47% ======================= 47% ======================= 47% ======================= 48% ======================= 48% ======================== 48% ======================== 49% ======================== 49% ======================== 49% ======================== 49% ======================== 50% ======================== 50% ========================= 50% ========================= 50% ========================= 51% ========================= 51% ========================= 51% ========================= 52% ========================= 52% ========================== 52% ========================== 52% ========================== 53% ========================== 53% ========================== 53% ========================== 54% ========================== 54% =========================== 54% =========================== 54% =========================== 55% =========================== 55% =========================== 55% =========================== 56% =========================== 56% ============================ 56% ============================ 56% ============================ 57% ============================ 57% ============================ 57% ============================ 57% ============================ 58% ============================= 58% ============================= 58% ============================= 59% ============================= 59% ============================= 59% ============================= 59% ============================= 60% ============================= 60% ============================== 60% ============================== 61% ============================== 61% ============================== 61% ============================== 61% ============================== 62% ============================== 62% =============================== 62% =============================== 62% =============================== 63% =============================== 63% =============================== 63% =============================== 64% =============================== 64% ================================ 64% ================================ 64% ================================ 65% ================================ 65% ================================ 65% ================================ 66% ================================ 66% ================================= 66% ================================= 66% ================================= 67% ================================= 67% ================================= 67% ================================= 68% ================================= 68% ================================== 68% ================================== 68% ================================== 69% ================================== 69% ================================== 69% ================================== 69% ================================== 70% =================================== 70% =================================== 70% =================================== 71% =================================== 71% =================================== 71% =================================== 71% =================================== 72% =================================== 72% ==================================== 72% ==================================== 73% ==================================== 73% ==================================== 73% ==================================== 73% ==================================== 74% ==================================== 74% ===================================== 74% ===================================== 74% ===================================== 75% ===================================== 75% ===================================== 75% ===================================== 76% ===================================== 76% ====================================== 76% ====================================== 76% ====================================== 77% ====================================== 77% ====================================== 77% ====================================== 78% ====================================== 78% ======================================= 78% ======================================= 78% ======================================= 79% ======================================= 79% ======================================= 79% ======================================= 79% ======================================= 80% ======================================== 80% ======================================== 80% ======================================== 81% ======================================== 81% ======================================== 81% ======================================== 81% ======================================== 82% ========================================= 82% ========================================= 82% ========================================= 83% ========================================= 83% ========================================= 83% ========================================= 83% ========================================= 84% ========================================= 84% ========================================== 84% ========================================== 85% ========================================== 85% ========================================== 85% ========================================== 85% ========================================== 86% ========================================== 86% =========================================== 86% =========================================== 86% =========================================== 87% =========================================== 87% =========================================== 87% =========================================== 88% =========================================== 88% ============================================ 88% ============================================ 88% ============================================ 89% ============================================ 89% ============================================ 89% ============================================ 90% ============================================ 90% ============================================= 90% ============================================= 90% ============================================= 91% ============================================= 91% ============================================= 91% ============================================= 91% ============================================= 92% ============================================== 92% ============================================== 92% ============================================== 93% ============================================== 93% ============================================== 93% ============================================== 93% ============================================== 94% =============================================== 94% =============================================== 94% =============================================== 95% =============================================== 95% =============================================== 95% =============================================== 95% =============================================== 96% =============================================== 96% ================================================ 96% ================================================ 97% ================================================ 97% ================================================ 97% ================================================ 97% ================================================ 98% ================================================ 98% ================================================= 98% ================================================= 98% ================================================= 99% ================================================= 99% ================================================= 99% ================================================= 100% ================================================= 100% ================================================== 100% **** INFO: Done. testPlinkLinearMixedModelCovariates GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ... **** INFO: no intercept term is found in the cvt file: a column of 1s is added. ## 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 Start Eigen-Decomposition... pve estimate =0.365545 se(pve) =0.47481 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% ============ 25% ============ 25% ============ 25% ============ 26% ============ 26% ============= 26% ============= 26% ============= 27% ============= 27% ============= 27% ============= 28% ============= 28% ============== 28% ============== 28% ============== 29% ============== 29% ============== 29% ============== 30% ============== 30% =============== 30% =============== 30% =============== 31% =============== 31% =============== 31% =============== 32% =============== 32% ================ 32% ================ 32% ================ 33% ================ 33% ================ 33% ================ 33% ================ 34% ================= 34% ================= 34% ================= 35% ================= 35% ================= 35% ================= 35% ================= 36% ================= 36% ================== 36% ================== 37% ================== 37% ================== 37% ================== 37% ================== 38% ================== 38% =================== 38% =================== 38% =================== 39% =================== 39% =================== 39% =================== 40% =================== 40% ==================== 40% ==================== 40% ==================== 41% ==================== 41% ==================== 41% ==================== 42% ==================== 42% ===================== 42% ===================== 42% ===================== 43% ===================== 43% ===================== 43% ===================== 44% ===================== 44% ====================== 44% ====================== 44% ====================== 45% ====================== 45% ====================== 45% ====================== 45% ====================== 46% ======================= 46% ======================= 46% ======================= 47% ======================= 47% ======================= 47% ======================= 47% ======================= 48% ======================= 48% ======================== 48% ======================== 49% ======================== 49% ======================== 49% ======================== 49% ======================== 50% ======================== 50% ========================= 50% ========================= 50% ========================= 51% ========================= 51% ========================= 51% ========================= 52% ========================= 52% ========================== 52% ========================== 52% ========================== 53% ========================== 53% ========================== 53% ========================== 54% ========================== 54% =========================== 54% =========================== 54% =========================== 55% =========================== 55% =========================== 55% =========================== 56% =========================== 56% ============================ 56% ============================ 56% ============================ 57% ============================ 57% ============================ 57% ============================ 57% ============================ 58% ============================= 58% ============================= 58% ============================= 59% ============================= 59% ============================= 59% ============================= 59% ============================= 60% ============================= 60% ============================== 60% ============================== 61% ============================== 61% ============================== 61% ============================== 61% ============================== 62% ============================== 62% =============================== 62% =============================== 62% =============================== 63% =============================== 63% =============================== 63% =============================== 64% =============================== 64% ================================ 64% ================================ 64% ================================ 65% ================================ 65% ================================ 65% ================================ 66% ================================ 66% ================================= 66% ================================= 66% ================================= 67% ================================= 67% ================================= 67% ================================= 68% ================================= 68% ================================== 68% ================================== 68% ================================== 69% ================================== 69% ================================== 69% ================================== 69% ================================== 70% =================================== 70% =================================== 70% =================================== 71% =================================== 71% =================================== 71% =================================== 71% =================================== 72% =================================== 72% ==================================== 72% ==================================== 73% ==================================== 73% ==================================== 73% ==================================== 73% ==================================== 74% ==================================== 74% ===================================== 74% ===================================== 74% ===================================== 75% ===================================== 75% ===================================== 75% ===================================== 76% ===================================== 76% ====================================== 76% ====================================== 76% ====================================== 77% ====================================== 77% ====================================== 77% ====================================== 78% ====================================== 78% ======================================= 78% ======================================= 78% ======================================= 79% ======================================= 79% ======================================= 79% ======================================= 79% ======================================= 80% ======================================== 80% ======================================== 80% ======================================== 81% ======================================== 81% ======================================== 81% ======================================== 81% ======================================== 82% ========================================= 82% ========================================= 82% ========================================= 83% ========================================= 83% ========================================= 83% ========================================= 83% ========================================= 84% ========================================= 84% ========================================== 84% ========================================== 85% ========================================== 85% ========================================== 85% ========================================== 85% ========================================== 86% ========================================== 86% =========================================== 86% =========================================== 86% =========================================== 87% =========================================== 87% =========================================== 87% =========================================== 88% =========================================== 88% ============================================ 88% ============================================ 88% ============================================ 89% ============================================ 89% ============================================ 89% ============================================ 90% ============================================ 90% ============================================= 90% ============================================= 90% ============================================= 91% ============================================= 91% ============================================= 91% ============================================= 91% ============================================= 92% ============================================== 92% ============================================== 92% ============================================== 93% ============================================== 93% ============================================== 93% ============================================== 93% ============================================== 94% =============================================== 94% =============================================== 94% =============================================== 95% =============================================== 95% =============================================== 95% =============================================== 95% =============================================== 96% =============================================== 96% ================================================ 96% ================================================ 97% ================================================ 97% ================================================ 97% ================================================ 97% ================================================ 98% ================================================ 98% ================================================= 98% ================================================= 98% ================================================= 99% ================================================= 99% ================================================= 99% ================================================= 100% ================================================= 100% ================================================== 100% **** INFO: Done. Ran 12 tests. OK tail -n 1 test.log | grep -q 'OK' test.log make[2]: Leaving directory '/<>/gemma-0.98.1+dfsg' make[1]: Leaving directory '/<>/gemma-0.98.1+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-0.98.1\+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-0.98.1+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/97 objcopy --only-keep-debug --compress-debug-sections debian/gemma/usr/bin/gemma debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/97/5266dbdcf791ce220f862add1e82dc5e966e41.debug chmod 0644 -- debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/97/5266dbdcf791ce220f862add1e82dc5e966e41.debug chown 0:0 -- debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/97/5266dbdcf791ce220f862add1e82dc5e966e41.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/97/5266dbdcf791ce220f862add1e82dc5e966e41.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=975266dbdcf791ce220f862add1e82dc5e966e41 -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 && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/gemma/DEBIAN/md5sums chown 0:0 -- debian/gemma/DEBIAN/md5sums cd debian/.debhelper/gemma/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums 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 pkgstripfiles: Running PNG optimization (using 4 cpus) for package gemma ... dpkg-deb: building package 'gemma-dbgsym' in 'debian/.debhelper/scratch-space/build-gemma/gemma-dbgsym_0.98.1+dfsg-1_arm64.deb'. pkgstripfiles: No PNG files. dpkg-deb: building package 'gemma' in '../gemma_0.98.1+dfsg-1_arm64.deb'. Renaming gemma-dbgsym_0.98.1+dfsg-1_arm64.deb to gemma-dbgsym_0.98.1+dfsg-1_arm64.ddeb mv debian/.debhelper/scratch-space/build-gemma/gemma-dbgsym_0.98.1\+dfsg-1_arm64.deb ../gemma-dbgsym_0.98.1\+dfsg-1_arm64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../gemma_0.98.1+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20190130-0907 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ gemma_0.98.1+dfsg-1_arm64.changes: ---------------------------------- Format: 1.8 Date: Tue, 18 Dec 2018 16:16:05 +0100 Source: gemma Binary: gemma gemma-doc Architecture: arm64 Version: 0.98.1+dfsg-1 Distribution: disco-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: gemma - Genome-wide Efficient Mixed Model Association gemma-doc - Example folder for GEMMA Changes: gemma (0.98.1+dfsg-1) unstable; urgency=medium . * Team upload. * Simplify watch file Checksums-Sha1: 71c1c44ce3384a8fe3b8d2838878f46ea7bdae08 7829828 gemma-dbgsym_0.98.1+dfsg-1_arm64.ddeb 42f0d0f0660f10685b6c0bcf087ab649f408f92e 5328 gemma_0.98.1+dfsg-1_arm64.buildinfo dc8d6424952532d955e35e8306f6750e3e78729b 345180 gemma_0.98.1+dfsg-1_arm64.deb Checksums-Sha256: 78b1ec613959c4590311c2e1d6a6f6cc854b626b60d6aebb1be8ebb575781612 7829828 gemma-dbgsym_0.98.1+dfsg-1_arm64.ddeb 1814b7b8e71ed3db189cd36b8cb990a51ca08feab1cbfc25ec6faf5d4d8b5b0b 5328 gemma_0.98.1+dfsg-1_arm64.buildinfo d458337e49ef9732454bcd6580e348ee384d3c62516cdddf8aa929c42400fea3 345180 gemma_0.98.1+dfsg-1_arm64.deb Files: b6e166cda2e2a9bb544e9dabdaf53846 7829828 debug optional gemma-dbgsym_0.98.1+dfsg-1_arm64.ddeb a5aad5962db4fc22bef7e606d14fba59 5328 science optional gemma_0.98.1+dfsg-1_arm64.buildinfo 3a0987d162b030c01a6fd26b86a37d1c 345180 science optional gemma_0.98.1+dfsg-1_arm64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ gemma_0.98.1+dfsg-1_arm64.deb ----------------------------- new debian package, version 2.0. size 345180 bytes: control archive=1400 bytes. 2019 bytes, 35 lines control 327 bytes, 5 lines md5sums Package: gemma Version: 0.98.1+dfsg-1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 956 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 2018-12-18 15:16 ./ drwxr-xr-x root/root 0 2018-12-18 15:16 ./usr/ drwxr-xr-x root/root 0 2018-12-18 15:16 ./usr/bin/ -rwxr-xr-x root/root 957560 2018-12-18 15:16 ./usr/bin/gemma drwxr-xr-x root/root 0 2018-12-18 15:16 ./usr/share/ drwxr-xr-x root/root 0 2018-12-18 15:16 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-12-18 15:16 ./usr/share/doc/gemma/ -rw-r--r-- root/root 4692 2018-12-11 05:34 ./usr/share/doc/gemma/README.md.gz -rw-r--r-- root/root 3255 2018-12-11 05:34 ./usr/share/doc/gemma/RELEASE-NOTES.md.gz -rw-r--r-- root/root 755 2018-12-18 15:16 ./usr/share/doc/gemma/changelog.Debian.gz -rw-r--r-- root/root 2231 2018-12-18 15:16 ./usr/share/doc/gemma/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build-Space: 488228 Build-Time: 965 Distribution: disco-proposed Host Architecture: arm64 Install-Time: 20 Job: gemma_0.98.1+dfsg-1.dsc Machine Architecture: arm64 Package: gemma Package-Time: 993 Source-Version: 0.98.1+dfsg-1 Space: 488228 Status: successful Version: 0.98.1+dfsg-1 -------------------------------------------------------------------------------- Finished at 20190130-0907 Build needed 00:16:33, 488228k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=disco --arch=arm64 PACKAGEBUILD-15793601 Scanning for processes to kill in build PACKAGEBUILD-15793601